Abstract
These data are presented in support of a plastid phylogenomic analysis of the recent radiation of the Hawaiian endemic mints (Lamiaceae), and their close relatives in the genus Stachys, “The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)” [1]. Here we describe the chloroplast genome sequences for 12 mint taxa. Data presented include summaries of gene content and length for these taxa, structural comparison of the mint chloroplast genomes with published sequences from other species in the order Lamiales, and comparisons of variability among three Hawaiian taxa vs. three outgroup taxa. Finally, we provide a list of 108 primer pairs targeting the most variable regions within this group and designed specifically for amplification of DNA extracted from degraded herbarium material.
Keywords: Hawaii, Lamiaceae, Plastid genomes, Genome structure
Specifications Table
| Subject area | Biology, genetics, genomics |
| More specific subject area | Molecular phylogenetics and evolution |
| Type of data | Tables and figures |
| How data was acquired | High-throughput sequencing of contemporary and herbarium samples was conducted on the Illumina HiSeq 2500 and MiSeq platforms, followed by both de novo and reference-guided assemblies, mapping, and functional annotation |
| Data format | Raw, and analyzed |
| Experimental factors | De novo assemblies were created using SOAPdenovo and reference-guided assemblies were created using YASRA. Sequences were functionally annotated using DOGMA. SNPs were called and filtered using SAMtools and BCFtools |
| Experimental features | Data include chloroplast genome gene content, structure, and comparisons of variable loci in a suite of recently diverged species and outgroups |
| Data source location | Hawaii, North America, South America, Europe, Africa, and Asia |
| Data accessibility | Data are published with this article |
Value of the data
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•
These data provide a summary of the characteristics and structure of the chloroplast genomes of several taxa within Lamiaceae, which can be used to increase our understanding of molecular evolution of the chloroplast genome, as well as the evolution of its structure and function.
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A comparison of variable regions in mints can be used to identify rapidly evolving regions in other taxa.
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Primer sequences described here can be used to target highly variable regions in closely related taxa.
1. Data
Raw, demultiplexed sequence reads have been deposited in the NCBI sequence read archive (SRP070171) and full chloroplast genomes for 12 mint taxa have been deposited in GenBank (KU724130-KU724141). Data presented in the text include tables and figures giving information on gene content and variability in these 12 species, as well as comparison of genome structure with other members of the order Lamiales.
2. Experimental design, materials and methods
2.1. Samples, library construction, and shotgun sequencing
We selected 12 Hawaiian mint taxa for shotgun sequencing (five contemporary and seven from herbarium collections ranging up to ~100 years old), of which two extinct species were represented by two accessions each (see Tables 1 and 2 in [1]). We also sequenced four Stachys species, representing both close and more distantly related relatives.
DNA extraction, library construction and shotgun sequencing followed the methods described in [1]. Briefly, approximately 100 mg dried leaf tissue was homogenized using the TissueLyser system (Qiagen), and DNA was extracted using the DNeasy plant mini kit (Qiagen). DNA isolated from herbarium samples was processed separately from contemporary samples using stringent protocols and controls to prevent and detect any potential contamination. For contemporary samples, DNA extracts were sheared to 200–600 bp via sonication in a Covaris S220; DNA from herbarium samples is naturally degraded and therefore was not sheared further. Genomic shotgun sequencing libraries were constructed following the standard Illumina Tru-seq protocol for contemporary samples, or the NEBNext Library Prep Mastermix kit (New England Biolabs) for herbarium samples. Libraries were quantified using the PicoGreen High Sensitivity assay and then pooled and sequenced on the Illumina HiSeq and MiSeq platforms. Adapter sequences were trimmed from the reads using the AdapterRemoval software [2]. Assessment of DNA damage in old herbarium specimens was conducted using mapDamage 2.0 [3]. The presence of misincorporations characteristic of damaged DNA molecules typically found in old and degraded samples suggests that the data from herbarium samples are authentic, however, the overall levels of damage were low and within the range expected based on the age of the specimens (see Supplementary Figs. 2 and 3 in [1]).
2.2. Assembly of the Hawaiian mint reference chloroplast genome
Because no chloroplast genome sequence from a closely related taxon was available at the time this study was conducted, we implemented a combined reference-guided and de novo assembly approach [4] to determine the first complete chloroplast genome sequence for a Hawaiian mint. We assembled the sequence for Stenogyne haliakalae, an extinct species, as it had the largest number of reads. Briefly, the approach involved conducting both reference-guided assembly in YASRA 2.32 [5] with olive (Olea europaea, NC_013707; [6]) as the reference, as well as de novo assembly in SOAPdenovo v1.05 [7]. Assembly methods are described in more detail in [1]. The resulting contigs from both approaches were split into overlapping sequences, and then used as input for a further reference guided-assembly step in YASRA. Gaps between the final contigs were closed using PCR (see [1] for PCR reaction conditions and Supplementary Table 1 of this paper for primer information) and Sanger sequencing in both directions from high-quality DNA extracted from a contemporary sample of Stengyne bifida. This ensured that amplification could be carried out over potentially large gaps, which would not be possible with degraded DNA from the extinct Stenogyne haliakalae. Contigs and Sanger sequences were aligned in Sequencher 4.7 (Gene Codes) to create a pseudo-reference sequence [4]. Reads from Stenogyne haliakalae were then mapped to the pseudo-reference using BWA v. 0.6.2 [8]. The reference sequence was further refined through Sanger sequencing of areas with low coverage or poor mapping quality (e.g., the border between the inverted repeat and single copy region). Reads were mapped to the final sequence, PCR duplicates were flagged and removed with the MarkDuplicates tool of the Picard command line toolset (http://picard.sourceforge.net/index.shtml), and a consensus sequence was called using SAMtools [9].
2.3. Assembly of additional mint chloroplast genomes
Complete or nearly complete chloroplast genomes were assembled using similar methods for 11 additional taxa: seven from the endemic Hawaiian mints (two of which were from herbarium samples) and four Stachys outgroups (see Tables 1 and 2 in [1]). Since the Hawaiian mints have diverged recently, we used the new chloroplast genome sequence from Stenogyne haliakalae as the reference during reference-guided assembly for the remaining Hawaiian taxa. The resulting contigs were aligned to create an interim sequence, and then the reads were mapped to this using BWA and a final consensus sequence called using SAMtools.
Chloroplast genome sequences for the Stachys outgroup taxa were assembled in a similar manner. We first assembled the chloroplast genome sequence for Stachys chamissonis, as this species is most closely related to the Hawaiian lineage. We conducted independent YASRA runs using Olea europaea as the reference, in addition to newly available sequences from Stenogyne haliakalae, Sesamum indicum (NC_016433) [10], Origanum vulgare (JX880022) [11], and Salvia miltiorrhiza (NC_020431) [12]. The contigs from all five runs were aligned to create an interim sequence. The reads were then mapped to the interim sequence using BWA and a consensus called using SAMtools. Once the Stachys chamissonis sequence was assembled we used this as the reference in YASRA for reference guided assembly of both Stachys coccinea and Stachys sylvatica. For Stachys byzantina, the most distantly related outgroup, we performed the initial reference-guided assembly using the sequence from Stachys chamissonis, as well as Olea europaea and Sesamum indicum. The rest of the assembly proceeded as described for the other Stachys species.
2.4. Gene content and structure of mint chloroplast genomes
The Stenogyne haliakalae reference sequence and sequences from additional species were annotated using a combination of DOGMA [13], tRNAscan-SE [14], and additional manual BLAST searches. The borders of the inverted repeats were identified with the program Inverted Repeats Finder [15].
Overall the chloroplast genome sequences assembled here are very similar to other Lamiales. Table 1 shows the gene content of the Stenogyne haliakalae chloroplast genome, which mirrors the gene content of the chloroplast genomes for the 11 additional mint taxa, including the Stachys outgroups. Table 2 lists the genes that contain introns (and the number of introns present) in the mint taxa investigated here. Table 3 gives the lengths of the full chloroplast genome for each sequence assembled, as well as the lengths of the inverted repeats and single copy regions.
Table 1.
Gene content of the chloroplast genome of Stenogyne haliakalae and 11 additional mint species.
| Gene Products | Genes |
|---|---|
| Photosystem I | psaA, psaB, psaC, psaI, psaJ, ycf3 [20], ycf4 [20] |
| Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ/lhbA |
| Cytochrome b6/f | petA, petB, petD, petG, petL, petN |
| ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI |
| Rubisco | rbcL |
| NADH oxidoreductase | ndhA, ndhBa, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK |
| RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 |
| Large subunit ribosomal proteins | rpl2a, rpl14, rpl16, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl36 |
| Small subunit ribosomal proteins | rps2, rps3, rps4, rps7a, rps8, rps11, rps12b, rps14, rps15, rps16, rps18, rps19 |
| Other functions | accD, ccsA, cemA, clpP, matK, infA |
| Unknown functions | ycf1b, ycf2a, ycf15a |
| Ribosomal RNAs | rrn23a, rrn16a, rrn5a, rrn4.5a |
| Transfer RNAs | trnA(UGC)a, trnC(GCA), trnD(GUC), trnE(UUC), trnF(GAA), trnG(GCC), trnG(UCC), trnH(GUG), trnI(CAU)a, trnI(GAU)*, trnK(UUU), trnL(UAA), trnL(UAG), trnL(CAA)a, trnfM(CAU), trnM(CAU), trnN(GUU)a, trnP(UGG), trnQ(UUG), trnR(ACG)a, trnR(UCU), trnS(GCU), trnS(GGA), trnS(UGA), trnT(GGU), trnT(UGU), trnV(UAC), trnV(GAC)a, trnW(CCA), trnY(GUA) |
Gene fully located within the inverted repeats.
Gene partially located within the inverted repeats.
Table 2.
Genes containing introns in the chloroplast genomes of Stenogyne haliakalae and 11 additional mint species. Numbers represent the lengths (bp) of exons and introns in S. haliakalae.
| Gene | Location | # Introns | Exon I | Intron I | Exon II | Intron II | Exon III |
|---|---|---|---|---|---|---|---|
| atpF | LSC | 1 | 143 | 656 | 410 | ||
| clpP | LSC | 2 | 70 | 658 | 291 | 616 | 227 |
| ndhA | SSC | 1 | 552 | 1020 | 538 | ||
| ndhB | IR | 1 | 755 | 680 | 776 | ||
| petB | LSC | 1 | 5 | 718 | 650 | ||
| petD | LSC | 1 | 7 | 728 | 474 | ||
| rpl16 | LSC | 1 | 8 | 907 | 392 | ||
| rpl2 | IR | 1 | 390 | 658 | 433 | ||
| rpoC1 | LSC | 1 | 434 | 736 | 1634 | ||
| rps12 | LSC/IRa | 2 | 113 | a | 231 | 537 | 25 |
| rps16 | LSC | 1 | 39 | 875 | 226 | ||
| trnA-UGC | IR | 1 | 37 | 807 | 34 | ||
| trnG-UCC | LSC | 1 | 22 | 690 | 47 | ||
| trnI-GAU | IR | 1 | 34 | 938 | 36 | ||
| trnK-UUU | LSC | 1 | 36 | 2509 | 34 | ||
| trnL-UAA | LSC | 1 | 36 | 488 | 49 | ||
| trnV-UAC | LSC | 1 | 37 | 579 | 36 | ||
| ycf3 | LSC | 2 | 123 | 713 | 229 | 725 | 152 |
Trans-spliced
Table 3.
Lengths (bp) of the long single copy region (LSC), short single copy region (SSC), and inverted repeats regions (IR) for the chloroplast genomes of Stenogyne haliakalae and 11 additional mint species.
| Species | LSC | IR | SSC | Total |
|---|---|---|---|---|
| Haplostachys haplostachya | 81,755 | 25,441 | 17,495 | 150,132 |
| Haplostachys linearifolia | 81,752 | 25,441 | 17,495 | 150,129 |
| Phyllostegia velutina | 81,765 | 25,440 | 17,496 | 150,141 |
| Phyllostegia waimeae | 81,744 | 25,448 | 17,497 | 150,137 |
| Stachys byzantina | 81,245 | 25,480 | 17,517 | 149,722 |
| Stachys chamissonis | 81,774 | 25,464 | 17,552 | 150,254 |
| Stachys coccinea | 82,171 | 25,470 | 17,563 | 150,674 |
| Stachys sylvatica | 81,807 | 25,414 | 17,560 | 150,195 |
| Stenogyne bifida | 81,752 | 25,441 | 17,495 | 150,129 |
| Stenogyne haliakalae | 81,364 | 25,436 | 17,499 | 149,736 |
| Stenogyne kanehoana | 81,739 | 25,441 | 17,495 | 150,116 |
| Stenogyne sessilis | 81,743 | 25,441 | 17,495 | 150,120 |
To compare the genome structure of the Hawaiian and Stachys taxa to other taxa in the order Lamiales, we conducted analyses in Mauve 2.3.1 [16] (Fig. 1). In the analysis we included Stenogyne haliakalae, Stachys byzantina, Ajuga reptans (NC_023102), Andrographis paniculata (NC_022451), Boea hygrometrica (NC_016468), Jasminum nudiflorum (NC_008407), Lindenbergia philippensis (NC_022859), Olea europaea (NC_013707), Origanum vulgare (JX880022), Pinguicula ehlersiae (NC_023463), Salvia miltiorrhiza (NC_020431), Schwalbea americana (NC_023115), Sesamum indicum (NC_016433), Tectona grandis (NC_020098), and Utricularia gibba (NC_021449). The chloroplast genome sequences of some taxa in this analysis demonstrated rearrangements and inversions. Therefore, one of the inverted repeats was trimmed off at the coordinates suggested by Inverted Repeats Finder so that homology could be determined with the remaining region. Seed weight was set to 19, the gap opening penalty was set to −200, and the gap extension penalty to −30.
Fig. 1.
Comparison of structure and similarity among 15 complete chloroplast genomes from the order Lamiales.Cistanche deserticola (102,657 bp) and Epifagus virginiana (70,028 bp), both members of the Orobanchaceae, are not considered here because they are parasitic and lack chlorophyll, thus demonstrating largely reduced chloroplast genomes. Blocks with the same color represent homologous regions free of internal structural changes for that subset of taxa, and those above the centerline for each taxon are in the same orientation as in Stenogyne haliakalae, whereas those below the line are in the reverse direction. Within each block a similarity profile for the region is plotted. Areas outside of blocks are presumed to represent lineage-specific regions of the chloroplast genome. One copy of the inverted repeat has been trimmed so that homology of the remaining repeat (area shaded in light gray) can be shown.
To compare the genome structure of all of the Hawaiian and Stachys mints to each other, we conducted a separate analysis in Mauve (Fig. 2). The sequences were assumed to be collinear. The seed weight was set to 7, the gap opening penalty was set to −200, and the gap extension penalty to −30.
Fig. 2.
Conservation among 11 complete mint chloroplast genomes. The sequence for Haplostachys linearifolia was excluded due to missing data. A physical map is given at the top to show gene content and organization (see Fig. 2 in [1] for gene names and products). In the lower panels, regions of the genome are represented by bars, and those that are conserved among all 11 species are colored mauve, whereas those that are conserved among subsets of the taxa have different colors. The height of the bar shows the degree of similarity.
2.5. Variability in the chloroplast genome sequences of Hawaiian mints and Stachys outgroups
We investigated variability among the three highest quality chloroplast genome sequences of the Hawaiian mints (Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya), and the three highest quality sequences from the Stachys outgroups (Stachys chamissonis, Stachys coccinea, and Stachys sylvatica). These species represent all of the main lineages within our samples, and were sequenced at >10× depth. We used BWA to map the reads for each of these species onto the Stenogyne haliakalae reference genome and used SAMtools and BCFtools to call SNPs with a SNP quality score >30. Annotations of the S. haliakalae reference genome were transferred to the locations of the SNPs. We compared the levels of chloroplast genome diversity among the six genomes by identifying unique, variable positions, which we refer to as potentially informative characters (PICs) [17], [18]. We did not include indels and inversions in this definition, which have been included in other analyses of chloroplast genome variability.
To analyze diversity among the chloroplast genomes, we compared the number of PICs present in 1000 bp non-overlapping sliding windows across the entire chloroplast genome sequences (Table 4, see also Fig. 5 in [1]). We also compared the number of PICs per locus for coding (Table 5, Fig. 3a), intron (Table 6, Fig. 3b), and intergenic spacer and pseudogene regions (Table 7, Fig. 3c). Because this approach does not take into account the length of the locus, very long loci appear to have more PICs than shorter loci. Therefore, we also divided the number of PICs by the total length of the region to give the percent PICs per locus (Table 5, Table 6, Table 7, Fig. 4). However, very short regions may still appear to have a high percentage of variable sites, when in fact only a small number of the sites were variable. To minimize this, we have excluded regions less than 100 bp in length, and for clarity we have also excluded regions that were conserved among all six taxa.
Table 4.
Sliding window analysis of variability of complete chloroplast genome sequences of three Hawaiian and three Stachys taxa (Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica). PICs – Potentially informative characters.
| Begin | End | # PICsStachys | # PICs Hawaiian |
|---|---|---|---|
| 1 | 999 | 8 | 1 |
| 1000 | 1999 | 7 | 2 |
| 2000 | 2999 | 6 | 4 |
| 3000 | 3999 | 11 | 1 |
| 4000 | 4999 | 7 | 0 |
| 5000 | 5999 | 5 | 1 |
| 6000 | 6999 | 10 | 1 |
| 7000 | 7999 | 8 | 0 |
| 8000 | 8999 | 6 | 2 |
| 9000 | 9999 | 9 | 0 |
| 10,000 | 10,999 | 4 | 1 |
| 11,000 | 11,999 | 3 | 0 |
| 12,000 | 12,999 | 4 | 0 |
| 13,000 | 13,999 | 9 | 4 |
| 14,000 | 14,999 | 4 | 2 |
| 15,000 | 15,999 | 1 | 0 |
| 16,000 | 16,999 | 3 | 0 |
| 17,000 | 17,999 | 6 | 0 |
| 18,000 | 18,999 | 5 | 3 |
| 19,000 | 19,999 | 2 | 0 |
| 20,000 | 20,999 | 3 | 0 |
| 21,000 | 21,999 | 0 | 0 |
| 22,000 | 22,999 | 5 | 1 |
| 23,000 | 23,999 | 1 | 0 |
| 24,000 | 24,999 | 0 | 0 |
| 25,000 | 25,999 | 1 | 0 |
| 26,000 | 26,999 | 4 | 1 |
| 27,000 | 27,999 | 5 | 3 |
| 28,000 | 28,999 | 9 | 2 |
| 29,000 | 29,999 | 4 | 1 |
| 30,000 | 30,999 | 11 | 1 |
| 31,000 | 31,999 | 5 | 1 |
| 32,000 | 32,999 | 3 | 0 |
| 33,000 | 33,999 | 3 | 1 |
| 34,000 | 34,999 | 8 | 1 |
| 35,000 | 35,999 | 1 | 0 |
| 36,000 | 36,999 | 1 | 0 |
| 37,000 | 37,999 | 5 | 0 |
| 38,000 | 38,999 | 0 | 0 |
| 39,000 | 39,999 | 1 | 0 |
| 40,000 | 40,999 | 5 | 0 |
| 41,000 | 41,999 | 3 | 1 |
| 42,000 | 42,999 | 1 | 0 |
| 43,000 | 43,999 | 5 | 2 |
| 44,000 | 44,999 | 6 | 1 |
| 45,000 | 45,999 | 10 | 0 |
| 46,000 | 46,999 | 3 | 1 |
| 47,000 | 47,999 | 7 | 0 |
| 48,000 | 48,999 | 0 | 0 |
| 49,000 | 49,999 | 6 | 1 |
| 50,000 | 50,999 | 4 | 0 |
| 51,000 | 51,999 | 2 | 0 |
| 52,000 | 52,999 | 3 | 1 |
| 53,000 | 53,999 | 5 | 3 |
| 54,000 | 54,999 | 8 | 3 |
| 55,000 | 55,999 | 8 | 2 |
| 56,000 | 56,999 | 2 | 0 |
| 57,000 | 57,999 | 6 | 1 |
| 58,000 | 58,999 | 9 | 1 |
| 59,000 | 59,999 | 4 | 2 |
| 60,000 | 60,999 | 3 | 3 |
| 61,000 | 61,999 | 7 | 1 |
| 62,000 | 62,999 | 2 | 0 |
| 63,000 | 63,999 | 6 | 1 |
| 64,000 | 64,999 | 5 | 1 |
| 65,000 | 65,999 | 6 | 1 |
| 66,000 | 66,999 | 8 | 0 |
| 67,000 | 67,999 | 12 | 0 |
| 68,000 | 68,999 | 6 | 0 |
| 69,000 | 69,999 | 0 | 0 |
| 70,000 | 70,999 | 7 | 0 |
| 71,000 | 71,999 | 5 | 3 |
| 72,000 | 72,999 | 3 | 0 |
| 73,000 | 73,999 | 3 | 1 |
| 74,000 | 74,999 | 4 | 2 |
| 75,000 | 75,999 | 2 | 1 |
| 76,000 | 76,999 | 5 | 0 |
| 77,000 | 77,999 | 5 | 0 |
| 78,000 | 78,999 | 7 | 0 |
| 79,000 | 79,999 | 7 | 1 |
| 80,000 | 80,999 | 4 | 1 |
| 81,000 | 81,999 | 10 | 0 |
| 82,000 | 82,999 | 2 | 2 |
| 83,000 | 83,999 | 0 | 1 |
| 84,000 | 84,999 | 1 | 0 |
| 85,000 | 85,999 | 1 | 0 |
| 86,000 | 86,999 | 2 | 0 |
| 87,000 | 87,999 | 0 | 0 |
| 88,000 | 88,999 | 1 | 1 |
| 89,000 | 89,999 | 0 | 0 |
| 90,000 | 90,999 | 1 | 0 |
| 91,000 | 91,999 | 0 | 0 |
| 92,000 | 92,999 | 1 | 0 |
| 93,000 | 93,999 | 0 | 0 |
| 94,000 | 94,999 | 2 | 1 |
| 95,000 | 95,999 | 1 | 0 |
| 96,000 | 96,999 | 2 | 0 |
| 97,000 | 97,999 | 0 | 0 |
| 98,000 | 98,999 | 0 | 0 |
| 99,000 | 99,999 | 1 | 0 |
| 100,000 | 100,999 | 1 | 0 |
| 101,000 | 101,999 | 1 | 0 |
| 102,000 | 102,999 | 1 | 0 |
| 103,000 | 103,999 | 0 | 0 |
| 104,000 | 104,999 | 5 | 2 |
| 105,000 | 105,999 | 1 | 0 |
| 106,000 | 106,999 | 4 | 0 |
| 107,000 | 107,999 | 9 | 0 |
| 108,000 | 108,999 | 4 | 0 |
| 109,000 | 109,999 | 16 | 3 |
| 110,000 | 110,999 | 6 | 2 |
| 111,000 | 111,999 | 10 | 1 |
| 112,000 | 112,999 | 7 | 0 |
| 113,000 | 113,999 | 8 | 3 |
| 114,000 | 114,999 | 4 | 0 |
| 115,000 | 115,999 | 5 | 0 |
| 116,000 | 116,999 | 6 | 4 |
| 117,000 | 117,999 | 9 | 4 |
| 118,000 | 118,999 | 3 | 0 |
| 119,000 | 119,999 | 5 | 0 |
| 120,000 | 120,999 | 11 | 2 |
| 121,000 | 121,999 | 10 | 1 |
| 122,000 | 122,999 | 7 | 5 |
| 123,000 | 123,999 | 11 | 2 |
| 124,000 | 124,999 | 4 | 1 |
| Min | 0 | 0 | |
| Max | 16 | 5 | |
| Total | 565 | 104 | |
| Mean | 4.52 | 0.83 | |
| Median | 4.00 | 0.00 |
Table 5.
Comparison of variability of coding genes by exon in complete chloroplast genome sequences of three Hawaiian and three Stachys taxa (Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica). Note: Exon numbers are defined by position in overall chloroplast genome sequence (not direction of gene) and exons that are completely conserved among these taxa and/or shorter than 100 bp have been excluded. PICs – Potentially informative characters.
| Region | Length | #PICs per locusStachys | #PICs per locus Hawaiian | % PICs per locusStachys | % PICs per locus Hawaiian |
|---|---|---|---|---|---|
| psbA | 1056 | 0 | 2 | 0.00 | 0.19 |
| matK | 1530 | 14 | 5 | 0.92 | 0.33 |
| psbK | 186 | 1 | 0 | 0.54 | 0.00 |
| atpA | 1524 | 5 | 1 | 0.33 | 0.07 |
| atpF Exon1 | 411 | 1 | 0 | 0.24 | 0.00 |
| atpI | 744 | 1 | 0 | 0.13 | 0.00 |
| rps2 | 711 | 1 | 0 | 0.14 | 0.00 |
| rpoC2 | 4083 | 16 | 3 | 0.39 | 0.07 |
| rpoC1 Exon1 | 1635 | 1 | 0 | 0.06 | 0.00 |
| rpoC1 Exon2 | 435 | 1 | 0 | 0.23 | 0.00 |
| rpoB | 3213 | 4 | 0 | 0.12 | 0.00 |
| psbD | 1062 | 4 | 0 | 0.38 | 0.00 |
| psbC | 1422 | 3 | 1 | 0.21 | 0.07 |
| psaB | 2205 | 6 | 0 | 0.27 | 0.00 |
| psaA | 2253 | 2 | 0 | 0.09 | 0.00 |
| rps4 | 606 | 1 | 0 | 0.17 | 0.00 |
| ndhJ | 477 | 3 | 0 | 0.63 | 0.00 |
| ndhK | 678 | 3 | 0 | 0.44 | 0.00 |
| atpE | 402 | 2 | 0 | 0.50 | 0.00 |
| atpB | 1497 | 4 | 0 | 0.27 | 0.00 |
| rbcL | 1446 | 12 | 6 | 0.83 | 0.41 |
| accD | 1467 | 3 | 0 | 0.20 | 0.00 |
| ycf4 | 555 | 2 | 0 | 0.36 | 0.00 |
| cemA | 690 | 2 | 1 | 0.29 | 0.14 |
| petA | 963 | 2 | 1 | 0.21 | 0.10 |
| rpl33 | 201 | 1 | 0 | 0.50 | 0.00 |
| rpl20 | 387 | 2 | 0 | 0.52 | 0.00 |
| psbB | 1527 | 9 | 0 | 0.59 | 0.00 |
| petB Exon2 | 651 | 2 | 1 | 0.31 | 0.15 |
| rpoA | 1014 | 3 | 1 | 0.30 | 0.10 |
| rpl36 | 114 | 2 | 0 | 1.75 | 0.00 |
| rps8 | 414 | 1 | 0 | 0.24 | 0.00 |
| rpl14 | 369 | 2 | 0 | 0.54 | 0.00 |
| rpl16 Exon1 | 393 | 3 | 0 | 0.76 | 0.00 |
| rps3 | 663 | 3 | 0 | 0.45 | 0.00 |
| rpl22 | 465 | 1 | 1 | 0.22 | 0.22 |
| rps19 | 279 | 6 | 0 | 2.15 | 0.00 |
| rpl2 Exon1 | 434 | 1 | 0 | 0.23 | 0.00 |
| ycf2 | 6849 | 5 | 2 | 0.07 | 0.03 |
| ndhB Exon1 | 756 | 1 | 0 | 0.13 | 0.00 |
| rps7 | 468 | 2 | 1 | 0.43 | 0.21 |
| rrn23 | 2811 | 1 | 0 | 0.04 | 0.00 |
| ndhF | 2229 | 16 | 0 | 0.72 | 0.00 |
| rpl32 | 177 | 2 | 0 | 1.13 | 0.00 |
| ccsA | 970 | 3 | 2 | 0.31 | 0.21 |
| ndhD | 1521 | 11 | 1 | 0.72 | 0.07 |
| psaC | 244 | 1 | 0 | 0.41 | 0.00 |
| ndhE | 306 | 1 | 2 | 0.33 | 0.65 |
| ndhG | 531 | 1 | 0 | 0.19 | 0.00 |
| ndhI | 507 | 2 | 0 | 0.39 | 0.00 |
| ndhA Exon1 | 539 | 3 | 0 | 0.56 | 0.00 |
| ndhA Exon2 | 553 | 3 | 1 | 0.54 | 0.18 |
| ycf1 SSC | 4487 | 43 | 11 | 0.96 | 0.25 |
| Min | 114 | 0 | 0 | 0.00 | 0.00 |
| Max | 6849 | 43 | 11 | 2.15 | 0.65 |
| Total | 61110 | 225 | 43 | 23.43 | 3.45 |
| Mean | 1153 | 4.25 | 0.81 | 0.44 | 0.07 |
| Median | 678 | 2.00 | 0.00 | 0.33 | 0.00 |
Fig. 3.
Comparison of the number of potentially informative characters (PICs) per locus in (a) protein coding regions, (b) introns, and (c) intergenic spacers and pseudogenes for chloroplast genomes of three Hawaiian and three Stachys taxa: Stenogyne haliakalae, Stenogyne bifida, Haplostachys Haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica. Regions that were completely conserved among these species and/or that are shorter than 100 bp are not shown. Pink=three Hawaiian taxa; Black=three Stachys taxa. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Table 6.
Comparison of variability of introns in complete chloroplast genome sequences of three Hawaiian and three Stachys taxa (Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica). Note: Exon and intron numbers are defined by position in the overall chloroplast genome sequence (not direction of gene). The trnK-UUU intron contains the gene matK. Here trnK-UUU-1 refers to the region between exon 1 and matK, and trnK-UUU-2 refers to the region between matK and exon2. PICs – Potentially informative characters.
| Region | Length | #PICs per locusStachys | #PICs per locus Hawaiian | % PICs per locusStachys | % PICs per locus Hawaiian |
|---|---|---|---|---|---|
| trnK-UUU − 1 | 264 | 5 | 0 | 1.89 | 0.00 |
| trnk-UUU − 2 | 714 | 5 | 0 | 0.70 | 0.00 |
| rps16 | 874 | 5 | 1 | 0.57 | 0.11 |
| trnG-UCC | 689 | 7 | 0 | 1.02 | 0.00 |
| atpF | 655 | 3 | 0 | 0.46 | 0.00 |
| rpoC1 | 762 | 4 | 1 | 0.52 | 0.13 |
| ycf3-1 | 724 | 0 | 1 | 0.00 | 0.14 |
| ycf3-2 | 712 | 2 | 0 | 0.28 | 0.00 |
| trnL-UAA | 487 | 4 | 0 | 0.82 | 0.00 |
| trnV-UAC | 478 | 1 | 1 | 0.21 | 0.21 |
| clpP − 1 | 615 | 6 | 0 | 0.98 | 0.00 |
| clpP − 2 | 657 | 4 | 0 | 0.61 | 0.00 |
| petB | 717 | 2 | 0 | 0.28 | 0.00 |
| petD | 727 | 4 | 2 | 0.55 | 0.28 |
| rpl16 | 906 | 6 | 0 | 0.66 | 0.00 |
| rpl2 | 657 | 2 | 2 | 0.30 | 0.30 |
| trnI-GAU | 937 | 1 | 0 | 0.11 | 0.00 |
| ndhA | 1019 | 10 | 7 | 0.98 | 0.69 |
| Min | 264 | 0 | 0 | 0.00 | 0.00 |
| Max | 1019 | 10 | 7 | 1.89 | 0.69 |
| Sum | 12594 | 71 | 15 | 10.95 | 1.86 |
| Mean | 699.7 | 3.94 | 0.83 | 0.61 | 0.10 |
| Median | 713 | 4.00 | 0.00 | 0.56 | 0.00 |
Table 7.
Comparison of variability of intergenic spacers and pseudogenes in complete chloroplast genome sequences of three Hawaiian and three Stachys taxa (Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica). Note: Regions that are completely conserved among these taxa and/or shorter than 100 bp have been excluded. PICs – potentially informative characters.
| Region | Length | #PICs per locusStachys | #PICs per locus Hawaiian | % PICs per locusStachys | % PICs per locus Hawaiian |
|---|---|---|---|---|---|
| trnH-GUG-psbA | 323 | 8 | 1 | 2.48 | 0.31 |
| psbA-trnK-UUU | 244 | 2 | 0 | 0.82 | 0.00 |
| trnK-UUU-rps16 | 643 | 5 | 0 | 0.78 | 0.00 |
| rps16-trnQ-UUG | 828 | 10 | 1 | 1.21 | 0.12 |
| psbK-psbI | 374 | 7 | 0 | 1.87 | 0.00 |
| psbI-trnS-GCU | 121 | 1 | 1 | 0.83 | 0.83 |
| trnS-GCU-trnG-UCC | 694 | 5 | 1 | 0.72 | 0.14 |
| trnG-UCC-trnR-UCU | 160 | 2 | 0 | 1.25 | 0.00 |
| atpF-atpH | 365 | 5 | 1 | 1.37 | 0.27 |
| atpH-atpI | 975 | 8 | 5 | 0.82 | 0.51 |
| rps2-rpoC2 | 337 | 2 | 0 | 0.59 | 0.00 |
| rpoC2-rpoC1 | 154 | 1 | 0 | 0.65 | 0.00 |
| rpoB-trnC-GCA | 1098 | 6 | 4 | 0.55 | 0.36 |
| trnC-GCA-petN | 436 | 4 | 0 | 0.92 | 0.00 |
| petN-psbM | 509 | 5 | 2 | 0.98 | 0.39 |
| psbM-trnD-GUC | 518 | 3 | 0 | 0.58 | 0.00 |
| trnE-UUC-trnT-GGU | 570 | 7 | 1 | 1.23 | 0.18 |
| trnT-GGU-psbD | 1075 | 8 | 1 | 0.74 | 0.09 |
| psbC-trnS-UGA | 232 | 3 | 1 | 1.29 | 0.43 |
| trnS-UGA-psbZ | 328 | 3 | 0 | 0.91 | 0.00 |
| psbZ-trnG-GCC | 224 | 2 | 0 | 0.89 | 0.00 |
| trnG-GCC-trnfM-CAU | 149 | 1 | 0 | 0.67 | 0.00 |
| psaA-ycf3 | 730 | 7 | 0 | 0.96 | 0.00 |
| ycf3-trnS-GGA | 316 | 2 | 2 | 0.63 | 0.63 |
| trnS-GGA-rps4 | 162 | 1 | 0 | 0.62 | 0.00 |
| rps4-trnT-UGU | 385 | 3 | 1 | 0.78 | 0.26 |
| trnT-UGU-trnL-UAA | 690 | 9 | 0 | 1.30 | 0.00 |
| trnL-UAA-trnF-GAA | 295 | 3 | 0 | 1.02 | 0.00 |
| trnF-GAA-ndhJ | 658 | 0 | 1 | 0.00 | 0.15 |
| ndhC-trnV-UAC | 944 | 5 | 0 | 0.53 | 0.00 |
| trnV-UAC-trnM-CAU | 188 | 1 | 0 | 0.53 | 0.00 |
| trnM-CAU-atpE | 213 | 2 | 0 | 0.94 | 0.00 |
| atpB-rbcL | 801 | 1 | 1 | 0.12 | 0.12 |
| rbcL-accD | 707 | 7 | 2 | 0.99 | 0.28 |
| accD-psaI | 397 | 1 | 1 | 0.25 | 0.25 |
| psaI-ycf4 | 434 | 7 | 0 | 1.61 | 0.00 |
| ycf4-cemA | 306 | 5 | 1 | 1.63 | 0.33 |
| cemA-petA | 217 | 1 | 1 | 0.46 | 0.46 |
| petA-psbJ | 1059 | 9 | 3 | 0.85 | 0.28 |
| psbE-petL | 915 | 6 | 1 | 0.66 | 0.11 |
| petL-petG | 174 | 2 | 0 | 1.15 | 0.00 |
| petG-trnW-CCA | 125 | 1 | 0 | 0.80 | 0.00 |
| trnP-UGG-psaJ | 270 | 2 | 1 | 0.74 | 0.37 |
| psaJ-rpl33 | 478 | 5 | 0 | 1.05 | 0.00 |
| rpl33-rps18 | 146 | 0 | 1 | 0.00 | 0.68 |
| rps18-rpl20 | 216 | 5 | 0 | 2.31 | 0.00 |
| rpl20-rps12 | 739 | 10 | 0 | 1.35 | 0.00 |
| psbB-psbT | 184 | 1 | 1 | 0.54 | 0.54 |
| psbH-petB | 124 | 1 | 0 | 0.81 | 0.00 |
| petB-petD | 194 | 1 | 0 | 0.52 | 0.00 |
| infA-rps8 | 123 | 1 | 0 | 0.81 | 0.00 |
| rps8-rpl14 | 173 | 3 | 0 | 1.73 | 0.00 |
| rpl14-rpl16 | 126 | 1 | 0 | 0.79 | 0.00 |
| rpl16-rps3 | 141 | 1 | 1 | 0.71 | 0.71 |
| rps12-3׳end-trnV-GAC | 1448 | 3 | 0 | 0.21 | 0.00 |
| trnA-UGC-rrn23 | 199 | 1 | 0 | 0.50 | 0.00 |
| rrn4.5-rrn5 | 224 | 2 | 1 | 0.89 | 0.45 |
| rrn5-trnR-ACG | 234 | 2 | 1 | 0.85 | 0.43 |
| trnR-ACG-trnN-GUU | 569 | 2 | 0 | 0.35 | 0.00 |
| ycf1Truncated | 1059 | 1 | 0 | 0.09 | 0.00 |
| ndhF-rpl32 | 435 | 5 | 2 | 1.15 | 0.46 |
| rpl32-trnL-UAG | 737 | 13 | 2 | 1.76 | 0.27 |
| ccsA-ndhD | 180 | 4 | 0 | 2.22 | 0.00 |
| ndhD-psaC | 105 | 1 | 0 | 0.95 | 0.00 |
| psaC-ndhE | 251 | 5 | 0 | 1.99 | 0.00 |
| ndhG-ndhI | 375 | 6 | 0 | 1.60 | 0.00 |
| rps15-ycf1 SSC | 389 | 3 | 0 | 0.77 | 0.00 |
| Min | 105 | 0 | 0 | 0.00 | 0.00 |
| Max | 1448 | 13 | 5 | 2.48 | 0.83 |
| Sum | 29192 | 250 | 43 | 62.72 | 10.44 |
| Mean | 435.7 | 3.73 | 0.64 | 0.94 | 0.16 |
| Median | 328.0 | 3.00 | 0.00 | 0.82 | 0.00 |
Fig. 4.
Comparison of the % PICs (potentially informative characters) per locus in (a) protein coding regions, (b) introns, and (c) intergenic spacers and pseudogenes for chloroplast genomes of three Hawaiian and three Stachys taxa: Stenogyne haliakalae, Stenogyne bifida, Haplostachys haplostachya, Stachys chamissonis, Stachys coccinea, and Stachys sylvatica. Regions that were completely conserved among these species or that are shorter than 100 bp are not shown. Pink=three Hawaiian taxa; Black=three Stachys taxa. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
To identify the most variable regions of the mint chloroplast genome for targeted re-sequencing and high resolution phylogenetic analyzes, reads from all 15 taxa subjected to shotgun sequencing (including the partial genomes from all of the historical samples, except Phyllostegia variabilis) were mapped to the Stenogyne haliakalae reference sequence using BWA. SNPs were called with SAMtools and BCFtools, filtering out those with SNP quality <30. We selected a total of 108 variable loci (see Fig. 2 in [1] for a diagram of locations) identified from single copy regions, including (1) all the regions that had a variant position among the Hawaiian mints (except where every individual had an alternative allele as compared to the reference sequence) and (2) additional regions that had variant positions among at least two of the Stachys species. 100 bp of flanking sequence on either side of the SNPs was retrieved from the reference genome, and PCR primers were designed using BatchPrimer3 [19], with further manual examination for quality control (e.g. to ensure that primer sequences did not fall into a gap for one of the other taxa). Sequences complementary to the Illumina sequencing adapters were appended to the end of each primer (Table 8) so that sequencing libraries could be prepared directly from the cleaned multiplex PCR products. Overall, these regions represent roughly 20,000 bp of sequence from the chloroplast genome and contain additional variable sites beyond the initial targeted SNP.
Table 8.
Tailed primers used for multiplex amplification and targeted re-sequencing in mints. Sequences complimentary to the Illumina sequencing adapters were appended to the end of each primer (Forward: 5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-[locus specific sequence] and Reverse: 5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-[locus specific sequence]). The loci within each region are also indicated. When the names of two genes are given with an underscore between them, the intergenic spacer between these genes is included in the amplified region.
| Primer | Sequence 5’ – 3’ | Tm | Loci in region (excluding priming sites) |
|---|---|---|---|
| Mint204F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGC CCC TCT ACT ATA ATG AAT GA | 69.3 | trnH-GUG_psbA |
| Mint204R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAC AGG ATC CAG AAA AAG AAA GA | 68.1 | |
| Mint771F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCA TGA GCG GCT ACG ATA TT | 70.3 | psbA |
| Mint771R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCA GGC TGA GCA CAA CAT TCT | 70.2 | |
| Mint867F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGA ACC ATG CAT AGC ACT GA | 70.4 | psbA |
| Mint867R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTA CCC AAT CGG TCA AGG AAG | 69.1 | |
| Mint1170F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAC TCA CGA CCC ATG TAA CAA | 70.1 | psbA |
| Mint1170R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG AGC CTG TTT CTG GAT CTC T | 69.5 | |
| Mint1939F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCA AAA CAA AAG TTG AAT ACT CAG TTG | 67.6 | trnK-UUU Intron1, matK |
| Mint1939R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GAT TTG GTA TTT GGA TAT GA | 68.3 | |
| Mint3998F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GCT TCC CGT ATC AGG CAC T | 71.2 | trnk-UUU Intron2 |
| Mint3998R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC GAA TTC TTG GAA CGG AAC | 68.6 | |
| Mint4546F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAG AAT TGT CAA AAT GTA TAG AGC A | 68.2 | trnK-UUU Exon2_rps16 Exon1 |
| Mint4546R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCA TCG TGA TAA GCG ATC TGG | 69.2 | |
| Mint4714F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAC CCA GAT CGC TTA TCA CG | 70.1 | trnK-UUU Exon2_rps16 Exon1 |
| Mint4714R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG TCA ATC CAA GAC AAT TTT GAA | 67.8 | |
| Mint5533F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCC GAT CCA GTT ATT GAG ACG | 69.0 | rps16 Intron |
| Mint5533R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GGA ATC GAC TGT CCA TAG | 69.7 | |
| Mint5985F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GCC CCC GAG AAA TGA ATT A | 69.9 | rps16 Intron |
| Mint5985R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTA GAA AGC AAC GTG CGA CTT | 69.3 | |
| Mint6787F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTC CAA TTT TGC ATT CGA GTC | 68.5 | rps16 Exon2_trnQ-UUG |
| Mint6787R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA AAG GGT GAG TGG GTA GGA | 69.7 | |
| Mint7334F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCA AAA ACG CAA CCA AAA TG | 68.4 | trnQ-UUG_psbK, psbK |
| Mint7334R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GCA TAA CAT CCA CGA TTG | 68.8 | |
| Mint8052F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGT TTC CTT GGG TTT GGT TA | 69.9 | psbI-trnS-GCU, trnS-GCU |
| Mint8052R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG AGA GAT GGC TGA GTG GAC | 70.3 | |
| Mint8691F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCG AAC TCA AAA ATA AAC TGT CG | 68.7 | trnS-GCU_trnG-UCC Exon1 |
| Mint8691R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCA AAA CGA GAA CGT TGC ACT | 69.7 | |
| Mint8791F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG ATG AAG CCT CTT TCC CGA A | 69.8 | trnS-GCU_trnG-UCC Exon1, trnG-UCC Exon1 |
| Mint8791R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GTT ACT AGA ACG AAT CAC ACT TT | 68.9 | |
| Mint10381F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGC GCC AAT TCC AAT TTT A | 69.0 | atpA |
| Mint10381R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC AAT CGG GAG ATG TTT CG | 68.7 | |
| Mint10531F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAT TAA TGG CGG GTC TGA TT | 69.9 | atpA |
| Mint10531R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCT TTT GGA AAG AGC CGC TAA | 69.6 | |
| Mint11293F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTG AGC AAT TCT TCC TGT TGC | 69.9 | atpA |
| Mint11293R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG CGA TGG TAT TGC TCG TAT | 69.8 | |
| Mint13441F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAG CAG CAA TAA CGG AAG C | 70.3 | atpH, atpH_atpI |
| Mint13441R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG AAG TCG TTC TGA TGA TTC AA | 68.8 | |
| Mint13731F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AGC CAC GAC GAT ATG AAA GG | 69.4 | atpH_atpI |
| Mint13731R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA AGT GGA TTG GTT GTC GAA | 68.7 | |
| Mint14054F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAT TGA TCT AAG TTC ATG CAA TTT TT | 67.8 | atpH_atpI |
| Mint14054R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GTC CAC TTA ATA TCC TAC CTT TCC | 67.9 | |
| Mint16824F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGA AAT CAA GAC CTT TGA TGT TAT T | 67.7 | rpoC2 |
| Mint16824R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA GGG TTG GAA CGA ACG TAT | 69.8 | |
| Mint17255F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCG GAG TGG CCA AAT AAG T | 70.8 | rpoC2 |
| Mint17255R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GGT ATT TTC TCC ATC CCA AT | 68.3 | |
| Mint17928F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGG ATT TCA GCA AGT CGA TTC | 68.9 | rpoC2 |
| Mint17928R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC TTT ATG GAA ATG GGA AAC C | 68.8 | |
| Mint20423F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG ATG CCA TTC CGA AGT GAT CT | 69.6 | rpoC2, rpoC2_rpoC1 Exon1 |
| Mint20423R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG CGA ATC AAG ATC GAG AAC | 69.3 | |
| Mint20572F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGA TTT GAC AAT GGG TTT GA | 69.4 | rpoC2_rpoC1 Exon1, rpoC1 Exon1 |
| Mint20572R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA GCC ATA CAG GGG TTT TCC | 69.4 | |
| Mint21910F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAG CTC ATT AAT TTA CCC CCA TC | 69.0 | rpoC1 Exon1 |
| Mint21910R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG GAA TGA ATG GGA AGA TCA | 69.2 | |
| Mint22486F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCA AGT TAC CAG TGA AGA CTA AGC A | 69.0 | rpoC1 Intron |
| Mint22486R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA TTC ATC ATT CGA AGG GAA GT | 68.8 | |
| Mint23294F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAA TTC GAC TCC GCA TTG TT | 69.2 | rpoC1 Exon2 |
| Mint23294R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC CCA ATG GAG AGA TAG TCG | 69.7 | |
| Mint23536F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAT CCA ATT CGG AGC TGT TG | 69.1 | rpoB |
| Mint23536R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GTC AAG TCA TAA AGT CAA ATA AA | 67.2 | |
| Mint24088F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGC GCT ATT CGA TAA TGT CTG | 69.3 | rpoB |
| Mint24088R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG AAG ACA CGG AWA CAA AGG | 69.3 | |
| Mint24204F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAA CAG GTC TTC CAT CTT GC | 69.9 | rpoB |
| Mint24204R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC GGG TTA TTG ATG TGA GGT | 70.0 | |
| Mint27582F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTG ATT GGT TCA GTC TCA GTT TTT | 69.1 | rpoB_trnC-GCA |
| Mint27582R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC GAG AGA ATG TTT TTA GCA TTG | 68.4 | |
| Mint27884F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GCA AAT CCT TTT TCC CCA GT | 70.1 | trnC-GCA, trnC-GCA_petN |
| Mint27884R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA CGG GGC TTC ACA ATC TTT | 69.5 | |
| Mint28672F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAG AGA TTC GGA TGA TTG GAA A | 68.4 | petN_psbM |
| Mint28672R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG AGC GCA CTA TAA TCA GCA | 69.9 | |
| Mint28881F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GCT GAT TAT AGT GCG CTC GTT | 70.0 | petN_psbM, psbM |
| Mint28881R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC CTA CCG CCT TTC TGC TTA | 69.7 | |
| Mint30267F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGG GAG GAG TAG AAT CTC TTC A | 69.9 | trnE-UUC_trnT-GGU |
| Mint30267R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GTT TCA AGA CCA GCC CTA | 69.3 | |
| Mint31916F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGG GTT GGT TCA CAG GTA CA | 71.0 | psbD |
| Mint31916R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC ACC TAA TTG ACA CCA ACG | 69.5 | |
| Mint32003F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGT CCT GAA GCA CAA GGA GA | 70.9 | psbD |
| Mint32003R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC AAT TGG ACC AGA GAA TGC | 69.6 | |
| Mint32348F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTC ATA ATT GGA CGC TGA ACC | 68.9 | psbD |
| Mint32348R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC GGT CAC CAT GGA ATA AGT | 70.0 | |
| Mint33303F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGG AGG GGG AGA TGT AAG AA | 70.6 | psbC |
| Mint33303R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA TAT GCC AGA TTC CAC CAA G | 69.1 | |
| Mint34416F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGG ATT CGA ACC CTC GAT A | 70.1 | trnS-UGA, trnS-UGA_psbZ |
| Mint34416R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAC CGG TCG GTA GAT TCA CAC | 69.6 | |
| Mint35190F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAT GCG GAT ATG GTC GAA TG | 68.9 | trnG-GCC, trnG-GCC_trnfM_CAU |
| Mint35190R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG TTT GGC TCT TAC CCC TTT | 70.1 | |
| Mint35459F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AGG ATT TGA ACC CGT GAC CT | 70.2 | trnfM-CAU, trnfM-CAU_rps14 |
| Mint35459R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAC GGT CGA CGA TCA TAA AGG | 68.9 | |
| Mint36179F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCA ATC TTG CTT GCA CAA TG | 69.7 | psaB |
| Mint36179R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCT GGG CGT GGA TGT TCT TAT | 70.0 | |
| Mint36649F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GTC CCA TGC CGA AAT ATC AC | 69.7 | psaB |
| Mint36649R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC CTG GAG ACT TTT TGG TTC | 69.5 | |
| Mint36907F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAT TGA GCA AAT ATG GGT TCG | 69.2 | psaB |
| Mint36907R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA GAT TAC AAC CCG GAG CAA | 69.9 | |
| Mint38366F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGC CAT AAT GCC TTT CAA ATC | 68.6 | psaB-psaA, psaA |
| Mint38366R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAT CCA TCG TTT GGG CTC AT | 69.5 | |
| Mint41292F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TAT TCG AAA CGC CTC GTG AT | 69.5 | ycf3 Exon1, ycf Intron1 |
| Mint41292R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GTT CTA AGG GAA GGG ATT | 69.9 | |
| Mint43421F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTG GAG CCT CGA AAG AAA GA | 69.5 | ycf3 Exon3_trnS-GGA |
| Mint43421R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAC TCG GCC ATC TCT CCT ACA | 70.0 | |
| Mint47802F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAT GGC GTT TGA TAG AGG AAT C | 69.1 | ndhK |
| Mint47802R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GTC CAC CTA AAC CGG AAG | 69.3 | |
| Mint50255F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTG GTA CCT AAA CGG GCA CT | 70.3 | trnV-UAC Intron, trnV-UAC Exon2 |
| Mint50255R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC AGT TGG TAG AGC ACC TCG T | 70.0 | |
| Mint51642F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTC GGA TAA TTC GTC CAA CC | 68.9 | atpB |
| Mint51642R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG CCA AAG GGA TCT ATC CAG | 69.2 | |
| Mint51809F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AGG ATC GGT CAA ATC GTC TG | 69.3 | atpB |
| Mint51809R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC GAC AAT ATC TTC CGT TTC G | 68.2 | |
| Mint52064F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGA AAT ATT CCG CCA TCG TT | 69.8 | atpB |
| Mint52064R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTA TCC GTA TTT GGC GGA GTG | 69.1 | |
| Mint53793F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAC AAC TGT GTG GAC CGA TG | 70.3 | rbcL |
| Mint53793R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAG CAC GTA GGG CTT TGA ATC | 69.3 | |
| Mint53955F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAA GCC CTA CGT GCT CTA CG | 70.0 | rbcL |
| Mint53955R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAG CAG ATA ACC CCA ATT TCG | 68.7 | |
| Mint54300F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT ATG CGT TGG AGA GAT CG | 68.8 | rbcL |
| Mint54300R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAT TGG CAG TGA ATC CTC CTG | 69.3 | |
| Mint54974F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAC GTG ATC TTG CTG CTG AG | 70.3 | rbcL, rbcL_accD |
| Mint54974R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA TTG GGC CGA GTT TAA TTG | 68.9 | |
| Mint55144F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAA TTA AAC TCG GCC CAA TC | 69.4 | rbcL_accD |
| Mint55144R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GTG GAT CCA AGA CAC CAA | 69.4 | |
| Mint55263F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGA AGA CTC CCA TTT TTC TCA | 69.5 | rbcL_accD |
| Mint55263R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGT CTA TTC CAA CAC GGA ACG A | 69.5 | |
| Mint56316F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGC CCA CTG TAA GTG ATA GC | 70.3 | accD |
| Mint56316R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC ATT GAA CCC ACA ACT GCT | 70.4 | |
| Mint57465F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT TTG AGT TCT ACA TTC CTT GGA C | 68.2 | accD_psaI |
| Mint57465R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GGT ACC TCG ATT TAC TAT TTG T | 68.2 | |
| Mint58710F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGA TGA GAA TTT GAC TCC ACG A | 69.0 | ycf4, ycf4_cemA |
| Mint58710R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG TGA TGA TCA AAA AGT CGA TTG | 67.7 | |
| Mint59661F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCC GTC ACT TGT AGT TAT TTA TCA TTC | 67.6 | cemA, cemA_petA |
| Mint59661R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT CCC TGT CCA AGA TTC TGC | 69.3 | |
| Mint60529F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AGA TTT ATC CCG ACG GAA GC | 69.4 | petA |
| Mint60529R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GAT GGA TTC ACC CTC TGA | 69.1 | |
| Mint60945F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGG ATT TAT GGA CAT CAG GTT | 69.5 | petA_psbJ |
| Mint60945R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GTC AAG TCA TAA AGT CAA ATA AA | 67.2 | |
| Mint61133F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAC TTG ACC ACC CCC TTC TT | 71.0 | petA_psbJ |
| Mint61133R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAT TCT TTG TCC CAC GCA TTC | 68.8 | |
| Mint62265F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCC CCA GTA GAG ACT GGT ACG | 71.0 | psbL, psbL_psbF, psbF |
| Mint62265R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAG TAC GCT GGT TGG CTG TTC | 70.0 | |
| Mint64488F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAA ACA AAC GCG CTA CCA AG | 69.4 | trnP-UGG, trnP-UGG_psaJ |
| Mint64488R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC AAT TGA AAT GTA AAA CGC TCT | 68.6 | |
| Mint65276F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT ACT ATG GCT TTG CTT TGA TTT | 68.0 | psaJ_rpl33, rpl33 |
| Mint65276R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT CCA AAA TCA CCG TTA CCC | 68.8 | |
| Mint65764F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGG GGG ATC GAA TTG ATT AT | 69.6 | rps18 |
| Mint65764R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG TCG ACT CGA TTC TTT CAA AT | 68.8 | |
| Mint68295F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCT CTC GAT ACA TAA TCG AAT CTT TT | 67.5 | clpP Intron1, clpP Exon2 |
| Mint68295R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GTT GGA GGA GAA ATT ACC A | 69.0 | |
| Mint68800F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT TTT GGT GCA TAC GGT TC | 70.1 | clpP Intron2 |
| Mint68800R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC ATC GTG ATT TGG ATT GAA | 68.9 | |
| Mint71208F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG ATC GTG CGA CTT TGA AAT CC | 69.1 | psbB |
| Mint71208R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC CAA GTT TTT GGA ATG CTC | 69.2 | |
| Mint71701F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGA GAA CCA CCT AAA GTT CCA | 70.0 | psbT, psbT_psbN, psbN |
| Mint71701R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC GGG TAC GCC TTA TAT ACC | 69.6 | |
| Mint72221F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAC TCC TTT GAT GGG TGT CG | 70.2 | psbH, psbH_petB Exon1 |
| Mint72221R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG CCG CAA ATT TGA GTT CTA | 69.5 | |
| Mint73489F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTG ACT TGG GTT ACG GGT GT | 70.3 | petB Exon2 |
| Mint73489R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG AGT CAA GGT GGA TTG TCC | 70.0 | |
| Mint74004F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTA TGG GAG TGT GCG ACT TG | 69.6 | petD Intron |
| Mint74004R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GAG CCT ACT CAT GTA CAA C | 69.5 | |
| Mint74125F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAG AAG ATG GGC TGG TTC AC | 70.6 | petD Intron |
| Mint74125R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA TGC AGA GGA AAT GAA TGC | 68.3 | |
| Mint75956F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGA CAT AAG GCG GTA AGA TGA | 69.9 | rpoA |
| Mint75956R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG AGA ATG TCC CGC ATG AAT | 69.4 | |
| Mint76974F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCT GCG GAT TAG TCG ACA TTT | 69.3 | rpl36 |
| Mint76974R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC GAA ACA AGG ATT CGA AAG | 68.9 | |
| Mint79374F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG ATT GCT TTC CGG TTC ATT TC | 68.6 | rpl16 Intron |
| Mint79374R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCA AGA GCT TCG AGC CAA TAA | 69.4 | |
| Mint79823F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAT ATG AAG CGA TGG GTT GG | 69.0 | rpl16 Intron, rpl16 Exon2, rpl16 Exon2_rps3 |
| Mint79823R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GCC AAT CAA ACA AAT TCC | 68.6 | |
| Mint80282F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGC CTG TTC AGT CAA TTC AA | 69.2 | rps3 |
| Mint80282R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG CGA GGA ATC GAA GAA TTA | 69.1 | |
| Mint80833F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TAG CCC GGG GTT TTA ATT TC | 69.2 | rpl22 |
| Mint80833R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCC GTT CCT ACG AGG AAA CAC | 69.9 | |
| Mint106808F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGG ACC CGT TTC TGA AGA GT | 70.1 | ycf1Truncated, ycf1Truncated_ndhF, ndhF |
| Mint106808R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT TTT GGA GAA GGG ATC AAA | 68.1 | |
| Mint107075F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCC ATC GTT TTC TTT TTG GA | 69.4 | ndhF |
| Mint107075R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG ATT CGG CAA GTT GGT ATG | 69.4 | |
| Mint107435F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCG TAT TGG CGG ATT CAT AA | 68.8 | ndhF |
| Mint107435R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG GGT AAA GGG TAT TCC AAA A | 69.1 | |
| Mint107714F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGA ATG TTT AAA TGC CCC TCA | 69.0 | ndhF |
| Mint107714R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAG GTA CAC TTT CGC TTT GTG G | 69.1 | |
| Mint108575F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CGC TTT TTG ACA AGC ATT TG | 69.1 | ndhF |
| Mint108575R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GCT CAC GAT CAA GGA TAC | 69.1 | |
| Mint109649F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GTA TCG GGC AGC GTT AAA AG | 69.7 | rpl32, rpl32_trnL-UAG |
| Mint109649R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAT TCC CCG TTG AAG GAA ATG | 68.8 | |
| Mint110066F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TCT CGC TAT CAA TCC ACA CAA | 69.2 | rpl32_trnL-UAG |
| Mint110066R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTA GAA CCC TCC CTC CCC AAA | 70.4 | |
| Mint110450F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGT AGA CAC GCT GCT CTT AGG | 70.4 | trnL-UAG, trnL-UAG_ccsA, ccsA |
| Mint110450R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTC GAA ACG ATC GAA AAA GAA | 67.9 | |
| Mint111053F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTA TGC GGC CCT TTT ATG TG | 70.0 | ccsA |
| Mint111053R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT GGA ATT CAC CAA CGA AAA | 68.3 | |
| Mint113090F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GGA TCA TCC GAT TGA AAA TGA | 68.8 | ndhD |
| Mint113090R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAC GAA CCA TTT TCC TTG CTT | 68.9 | |
| Mint113960F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTC AGC GGC TGC AAT AGT TA | 69.7 | ndhE |
| Mint113960R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG CCT ATT TAT TTT CCA TTG GT | 67.9 | |
| Mint116500F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCG TTA CCG TCG CTA TTA CAG | 69.9 | ndhA Intron |
| Mint116500R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC AGA CAG AAT TCC ATT GGT C | 69.2 | |
| Mint116861F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTG CAA TTC TCG TTT TTG GA | 68.7 | ndhA Intron |
| Mint116861R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA ATT GGG GCT TTA AGT TGG T | 69.4 | |
| Mint116914F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGG TGG ATA GGA ACA TAC TCT GG | 69.3 | ndhA Intron |
| Mint116914R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GAT GGT TAG GAA GAC CAA A | 69.0 | |
| Mint117269F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAG CAA AAT TTT AAG CCG TTT T | 68.9 | ndhA Intron |
| Mint117269R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG TGT GAT TCG GTG AGA CAT | 69.9 | |
| Mint117433F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TGT CTC ACC GAA TCA CAC GTA | 69.7 | ndhA Exon2 |
| Mint117433R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG CCG ATC TTA GTA TTG GTG T | 69.6 | |
| Mint119376F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT TGA CAA ATA GGC CAG CA | 69.3 | rps15 |
| Mint119376R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG CAT CGA TTT CGG TTA TTT C | 68.0 | |
| Mint122192F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CAT TTC TTG GTT TTC GAA TTT TT | 67.9 | ycf1 single copy |
| Mint122192R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGC ATC TCC GAG TTG GAC AAA | 70.0 | |
| Mint122492F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG AAA AAC ACT TTT GAG AAC CCA TTT | 68.2 | ycf1 single copy |
| Mint122492R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAA CCG AAC TCC CCT TTT GTT | 69.4 | |
| Mint122638F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT TTC GGG GTG AAC AAA AG | 68.8 | ycf1 single copy |
| Mint122638R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTG GTT GAC GGA TGG TAT TCA | 69.1 | |
| Mint123159F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTT GAA ATG CTT CCC CCT TA | 69.2 | ycf1 single copy |
| Mint123159R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GCG GCA CGG TAT AAT CAA AGG | 69.4 | |
| Mint124145F | TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TTC GAT TAT AGG CGG GGA TA | 69.1 | ycf1 single copy |
| Mint124145R | GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GAT CGC TGG AAT CGA CCA TTT | 69.3 |
Acknowledgments
We thank the Bernice P. Bishop Museum, The National Tropical Botanic Garden, and the Volcano Rare Plant Facility for access to samples. Webb Miller provided helpful advice on data analysis. We also thank the Center for Computational Resources at the University of Buffalo for access to computational resources. This work was supported by the College of Arts and Sciences, University at Buffalo.
Footnotes
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2016.03.037.
Contributor Information
Andreanna J. Welch, Email: andreanna05@gmail.com.
Charlotte Lindqvist, Email: cl243@buffalo.edu.
Appendix A. Supplementary material
Supplementary material
Supplementary material
References
- 1.Welch A.J., Collins K., Ratan A., Drautz-Moses D.I., Schuster S.C., Lindqvist C. The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae) Mol. Phylogen. Evol. 2016;99:16–33. doi: 10.1016/j.ympev.2016.02.024. [DOI] [PubMed] [Google Scholar]
- 2.Lindgreen S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes. 2012;5:337. doi: 10.1186/1756-0500-5-337. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Jónsson H., Ginolhac A., Schubert M., Johnson P.L.F., Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013;13:1682–1684. doi: 10.1093/bioinformatics/btt193. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Cronn R., Liston A., Parks M., Gernandt D.S., Shen R., Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 2008;36:e122. doi: 10.1093/nar/gkn502. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Ratan A. University Park; PA: 2009. Pennsylvania State University. [Google Scholar]
- 6.Mariotti R., Cultrera N.G.M., Díez C.M., Baldoni L., Rubini A. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biol. 2010;10:211. doi: 10.1186/1471-2229-10-211. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z., Li Y., Li S., Shan G., Kristiansen K., Li S., Yang H., Wang J., Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265–272. doi: 10.1101/gr.097261.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. & 1000 Genome Project Data Processing Subgroup, The sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Yi D.-K., Kim K.-J. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One. 2012;7:e35872. doi: 10.1371/journal.pone.0035872. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Lukas B., Novak J. The complete chloroplast genome of Origanum vulgare L. (Lamiaceae) Gene. 2013;528:163–169. doi: 10.1016/j.gene.2013.07.026. [DOI] [PubMed] [Google Scholar]
- 12.Qian J., Song J., Gao H., Zhu Y., Xu J., Pang X., Yao H., Sun C., Li Xe, Li C., Liu J., Xu H., Chen S. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One. 2013;8:e57607. doi: 10.1371/journal.pone.0057607. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Wyman S.K., Jansen R.K., Boore J.L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004;20:3252–5255. doi: 10.1093/bioinformatics/bth352. [DOI] [PubMed] [Google Scholar]
- 14.Schattner P., Brooks A.N., Lowe T.M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33:W686–W689. doi: 10.1093/nar/gki366. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Warburton P.E., Giordano J., Cheung F., Gelfand Y., Benson G. Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res. 2004;14:1861–1869. doi: 10.1101/gr.2542904. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Darling A.E., Mau B., Perna N.T. progressiveMauve: multiple genome alignment with gene gain, loss, and rearrangement. PLoS One. 2010;5:e11147. doi: 10.1371/journal.pone.0011147. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Shaw J., Lickey E.B., Beck J.T., Farmer S.B., Liu W.B., Miller J., Siripun K.C., Winder C.T., Schilling E.E., Small R.L. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005;92:142–166. doi: 10.3732/ajb.92.1.142. [DOI] [PubMed] [Google Scholar]
- 18.Shaw J., Lickey E.B., Schilling E.E., Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 2007;94:275–288. doi: 10.3732/ajb.94.3.275. [DOI] [PubMed] [Google Scholar]
- 19.You F.M., Huo N., Gu Y.Q., Luo M.-C., Ma Y., Hane D., Lazo G.R., Dvorak J., Anderson O.D. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinf. 2008;9:253. doi: 10.1186/1471-2105-9-253. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.Boudreau E., Takahashi Y., Lemieux C., Turmel M., Rochais J.-D. The chloroplast ycf3 and ycf4 open reading frames of Chlamydomonas reinhardtii are required for the accumulation of the photosystem I complex. EMBO J. 1997;16:6095–6104. doi: 10.1093/emboj/16.20.6095. [DOI] [PMC free article] [PubMed] [Google Scholar]
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