The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

Abstract

Background

Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms.

Results

Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species.

Conclusions

We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.

Background

More than three thousand seed plant chloroplast genomes have been sequenced [1], but only 209 mitochondrial genomes (mitogenomes) are available for approximately 190 species of land plants (https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/, 09/12/2019) because plant mitogenomes are remarkably variable in both structure and sequence content [2]. Most (121) sequenced plant mitogenomes are from angiosperms. In contrast to the numerous sequenced angiosperm mitogenomes, however, mitogenomic sequences have been generated for only 6 gymnosperm species, i.e., Cycas taitungensis [3], Ginkgo biloba, Welwitschia mirabilis [4], Pinus taeda (direct submission, MF991879.1, http://www.ncbi.nlm.nih.gov/), Picea abies [5], and Picea sitchensis [6].

A comparison among the mitogenomes of Cycas, Ginkgo and Welwitschia showed that the Cycas and Ginkgo mitogenomes represent the ancestral mitogenome type in seed plants, which is small, has a low substitution rate, and possesses numerous genes, introns and RNA editing sites, whereas the Welwitschia mitogenome is relatively large, has a high substitution rate, and has lost many genes and introns [3, 4]. The mitogenome of three species of Pinaceae (Picea abies, ca. 4.90 MB; Picea sitchensis, 5.5 Mb; Pinus taeda, 1.19 Mb) is extremely expanded [5, 6] and larger than that of Cycas, Ginkgo and Welwitschia [3, 4]. Although all of these Pinaceae mitogenomes have gene and intron contents similar to those in the Cycas and Ginkgo mitogenomes [5–7], these mitogenomes from different gymnosperm lineages are different in many other aspects, such as genome structure, repeats, turnover rates, and foreign sequence ratios [4].

Based on the recent phylogenomic study of Ran et al. [8], gymnosperms represent five of the six main lineages of seed plants, namely, cycads, ginkgo, gnetophytes, Pinaceae and Conifer II (non-Pinaceae conifers or Cupressophyta) [9, 10]. These lineages diverged before the Jurassic and have diversified dramatically in morphological characters and molecular evolutionary rates [8, 11]. The six sequenced mitogenomes come from four lineages (cycads, ginkgo, gnetophytes and Pinaceae). Therefore, complete mitogenomes are available for all major seed plant lineages except Conifer II, an important lineage including six families (Araucariaceae, Cephalotaxaceae, Cupressaceae, Podocarpaceae, Sciadopityaceae, and Taxaceae). Conifer II includes approximately 380 species, which are widely distributed on all continents except Antarctica [12]. Previous morphological studies supported the sister relationship between Conifer II and Pinaceae. However, recent phylogenomic studies yielded a topology with Conifer II sister to Pinaceae + Gnetales [8]. Therefore, knowledge of mitogenomic features in Conifer II is essential for a comprehensive understanding of the evolution and diversification of gymnosperm mitogenomes.

In this study, we sequenced and analyzed the complete mitogenome of Taxus cuspidata, a species belonging to Taxaceae of Conifer II, and then compared it with published gymnosperm mitogenomes. By comparing mitogenomes from the five main lineages of gymnosperms, we aimed to reveal the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates in gymnosperm mitogenomes. This study will shed light on the evolution of plant mitogenomes.

Methods

Mitochondrial DNA isolation, total RNA extraction, sequencing and mitogenome assembly of Taxus cuspidata

Young leaves and seeds of Taxus cuspidata were collected from a female tree growing at the Institute of Botany, Chinese Academy of Sciences. Mitochondria were isolated from leaves by using density gradient centrifugation [13] and digested with DNase I (Promega, Madison, USA) to eliminate genomic DNA contamination. Total RNA was extracted from seeds after one day of germination using RNAplant Plus Reagent (Tiangen, Beijing, China) because almost all mitochondrial genes are highly expressed in germinating seeds [14] and then digested by DNase I.

To obtain a full-length mitogenome sequence and identify the comprehensive RNA editing sites, we used both short-read (Illumina) and long-read sequencing (Oxford Nanopore) technologies in this study. First, approximately two micrograms of mitochondrial DNA was sheared by using Megaruptor. A > 20-kb library was constructed by using the ONT Ligation Sequencing Kit 1D (SQK-LSK108) and sequenced using an Oxford Nanopore GridION X5 Sequencer following the manufacturer’s protocol. Second, approximately one microgram of mitochondrial DNA was sonicated to ~ 500 bp using the Covaris M220 system. The sonicated DNA was purified using a TIANgel Midi Purification Kit, and a sequencing library was constructed using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, England) according to the manufacturer’s instructions. In addition, approximately 5 μg of total RNA was used to construct the cDNA library (NEBNext Ultra Directional RNA Library Prep Kit for Illumina, Illumina, San Diego, CA). Libraries were sequenced using an Illumina HiSeq 2500 (Illumina) with paired-end reads of 150 bp for cDNA and 250 bp for DNA.

The short raw reads were checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed by Trimmomatic (ILLUMINACLIP:TruSeq-PE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:20) [15]. The long raw reads were base-called by using Albacore v2.1.7 (mean_qscore > 7) with barcode demultiplexing.

The mitogenomes of higher plants are markedly variable in both structure and sequence content [2, 16–21]. To improve assembly reliability, we used two strategies to assemble the Taxus mitogenome. In the first strategy, we followed the assembly process of Gui et al. [22] and Ye et al. [23]. First, the short clean reads were de novo assembled with SPAdes v 3.13.0 [24] using multiple k-mer values [21, 33, 55, 77]. Second, potential mitochondrial contigs were extracted by aligning against the mitochondrial protein-coding genes of Cycas taitungensis [3] with BLAST v 2.3.0 [28]. Then, the putative long mitochondrial reads were baited by mapping the short reads to the plant mitogenome database (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/) and the potential mitochondrial contigs using BLASR v5.1 [29]. Finally, the putative long mitochondrial reads were assembled by Canu v1.7.1 [30]. In the second strategy, all short clean reads were assembled de novo by using Canu directly [30].

Subsequently, we used bowtie2 to map the short clean reads to the draft contigs and improved the draft contigs with Pilon v1.22 [31, 32]. Then, MUMmer was used to check whether these contigs were circular [33]. Finally, the corrected contigs obtained from the above two assembly strategies were aligned with each other using MUMmer 3.0 and MAFFT v. 7 [33, 34], and the result showed that these two contigs were identical. Based on the above assembly steps, we obtained a master circle of the Taxus mitogenome.

Mitogenome annotation

Protein and rRNA genes of the Taxus mitogenome were annotated by tblastn using a local database of extracted gene sequences from Cycas taitungensis, Ginkgo biloba and Welwitschia mirabilis because Cycas and Ginkgo have all 41 protein-coding genes and three rRNA genes that are similar to those of the basal angiosperms [3, 4]. Then, we downloaded the mitogenome data of Cycas taitungensis, Ginkgo biloba, Pinus taeda and Welwitschia mirabilis from the National Center for Biotechnology Information (NCBI). We identified tRNA genes, introns, and open reading frames (ORFs) in all five mitogenomes (Cycas taitungensis, Ginkgo biloba, Pinus taeda, Taxus cuspidata, and Welwitschia mirabilis). tRNA genes were identified by tRNAscan-SE 2.0 [35], and group I and II introns were detected by the RNAweasel tool [25]. ORFs were predicted by ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) with the standard genetic code and a minimal length of 102 nt, and ORFs longer than 300 bp were annotated by Blast2GO with default parameters [36]. The circular mitogenome map was drawn with OGDRAW [37].

RNA editing site identification

RNA editing sites of the Taxus mitogenome were identified by RES-Scanner, a powerful software that provides comprehensive identification and annotation of RNA editing sites with the short clean reads of the genome and transcriptome as input files [38]. The editing efficiency of each site was estimated by calculating the proportion of cDNA reads that contained the edited nucleotide, and the minimum number of DNA and RNA reads required for determining RNA editing sites was set to ten and three (the default parameters in RES-Scanner), respectively. In addition, similar to Guo et al. [4], we predicted RNA editing sites in all five mitogenomes using PREP-Mt [39], with a cutoff value of 0.2, so that we could compare the evolutionary patterns of the mitochondrial RNA editing sites in gymnosperms.

Identification of genes that have been transferred to the nuclear genome in Taxus and Welwitschia

We used the depth of sequencing coverage and real-time PCR to detect whether some protein-coding genes have transferred to the nuclear genome in Taxus. The depth of sequencing coverage of each gene was calculated with Bowtie2 v 2.2.9 [32] and SAMtools v 1.6 [40], using the short clean reads of the genome as the input file. Absolute quantitative real-time PCR was used to quantify the copy number of all 41 protein-coding genes (excluding rpl10, for which no homologous sequence was found by blast or PCR) in Taxus, with the single-copy nuclear gene LEAFY as an experimental control. The digested genomic DNA was used as the input DNA. All primers are listed in Additional file 1: Table S1. PCRs were conducted using a SYBR® Premix Ex Taq™ Kit (TaKaRa), and melting analysis was routinely performed to check the identity of PCR products. The detailed experimental and analytical protocols were similar to those of Ran et al. [41]. For Welwitshcia, we searched mitochondrial homologs in the transcriptome [8] using all mitochondrial genes of Cycas and Pinus as queries.

Identification of repeats, tandem repeats, Bpu elements and foreign sequences

Repeats were detected by ROUSFinder.py, and tandem repeats were identified using Tandem Repeats Finder with default parameters [42]. Plastid-derived mtDNA (MTPTs) and Bpu-like elements were identified following the procedure of Guo et al. [4]. Briefly, MIPTs were identified by using blastn, and the sequences matching genes that occurred in the mitochondrial and plastid genomes simultaneously (i.e., atp1/atpA, rrn26/rrn23, and rrn18/rrn16) were excluded. Bpu-like elements were identified by blastn using the Cycas Bpu consensus sequence as a query. In addition, the nuclear-derived repetitive sequences were identified by using the RepeatMasker web server (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker).

Shared DNAs and gene cluster analyses

To determine mtDNA shared between species, each pair of mitogenomes was searched using blastn with a word size of 7 and an e-value cutoff of 1 × 10^− 6. Syntenic relationships were generated using Circos v. 0.69 [43]. To evaluate the conservation of gene order, we searched for gene clusters shared by gymnosperms by simple visual inspection.

Evolutionary rate heterogeneity test

All mitochondrial protein-coding genes were obtained from the five gymnosperms, three basal angiosperms [Amborella trichopoda (KF754799, KF754800, KF754801, KF754802, and KF754803), Liriodendron tulipifera (NC_021152), and Nymphaea colorata (NC_037468)], and two fern species [Ophioglossum californicum (NC_030900) and Psilotum nudum (KX171638 and KX171639)], and putative transferred genes were retrieved from the transcriptome data for Taxus cuspidata and Welwitschia mirabilis [8]. Sequence alignment, unreliable sequence alignment filtering, synonymous (d_S) and nonsynonymous (d_N) length calculations, and absolute nonsynonymous (R_N) and synonymous rate (R_S) calculations were similar to those in Ran et al. [8]. To mitigate the confounding effects of C-to-U RNA editing on substitution-rate calculations and phylogenetic reconstruction, the predicted editing sites were excluded in the sequence alignments. The phylogenetic topology and divergence times among gymnosperms were obtained from Ran et al. [8].

Results

Mitogenome size and gene and intron contents of Taxus cuspidata

The mitogenome of Taxus cuspidata was assembled as a single circular molecule (Fig. 1) with a size of 468,924 bp. The mitogenome contains 46 genes, including 32 for proteins, ten for tRNAs (three of them have two copies, respectively), and three for rRNAs. Among the 32 protein-coding genes, there are five and two encoding small and large subunit ribosomal proteins, respectively; nine, one, one, three, and five encoding mitochondrial respiratory chain complexes I, II, III, IV, and V, respectively; four involved in cytochrome C biogenesis; one for transport membrane protein, and one for maturase-related protein (Additional file 2: Table S2). No group I introns were detected in the Taxus mitogenome. In contrast, 15 group II introns were found in the cox2, nad1, nad2, nad4, nad5 and nad7 genes, of which four and eleven were cis- and trans-spliced, respectively (Fig. 1). Among the ten tRNA genes, nine were mitochondrially native, and one was derived from plastids. Among the three rRNA genes, rrn5 and rrn26 had one copy, and rrn18 had two copies. The lengths of the Taxus mitochondrial genes, exons, and introns ranged from 225 to 4104 bp, 22 to 1224 bp, and 804 to 2461 bp, respectively. Detailed information on the Taxus cuspidata mitochondrial genes, exons, and introns is provided in supplementary Additional file 2: Table S2.

Fig. 1.

Gene map of the complete mitogenome of Taxus cuspidata. Genes inside and outside the outer circle are transcribed in clockwise and counterclockwise directions, respectively. The inner circle represents GC content (%)

Variation in gene and intron contents in the gymnosperm mitogenomes

We compared the mitogenomes of Taxus, Pinus, Welwitschia, Cycas and Ginkgo, representing all five lineages of gymnosperms. The genome sizes of Pinus and Welwitschia are 1.19 Mb and 979 kb, respectively, which are larger than those of Taxus (429 kb), Cycas (414 kb) and Ginkgo (346 kb). Cycas, Ginkgo and Pinus have 41 mitochondrial protein-coding genes, whereas only 32 and 29 such genes were found in the Taxus and Welwitschia mitogenomes (Table 1). Eight genes were lost in both Taxus and Welwitschia, one was lost only in Taxus, and four were lost only in Welwitschia (Fig. 2). Similar to angiosperm mitogenomes, the gymnosperm mitogenomes contain three kinds of rRNA genes (rrn5, rrn16, and rrn26) (Table 2). In addition, the number of tRNA genes varies greatly among these gymnosperm mitogenomes. Cycas and Ginkgo contain 27 and 23 tRNA genes for 17 and 16 amino acids, respectively. However, in the mitogenomes of Pinus, Welwitschia and Taxus, only twelve, eight and ten tRNA genes transporting ten, eight and seven amino acids, respectively, were found (Table 2).

Table 1.

General features of five gymnosperm mitogenomes

	Cycas	Ginkgo	Pinus	Welwitschia	Taxus
Accession	AP009381	KM672373	MF991879.1	KT313400	MN593023
Size (bp)	414,903	346,544	1,191,054	978,846	468,924
GC%	46.9	50.4	47	53	50.39
Genes	71	67	59	40	46
tRNAs	27	23	12	8	10
rRNAs	3	3	6	3	4
Protein coding	41	41	41	29	32
ORF	3945 (414,858 bp)	3944 (323,967 bp)	10,587 (1,191,015 bp)	11,171 (978,799 bp)	3923 (468,857 bp)
Introns	26	25	26	10	15
Predicted edit sites	1206	1306	1179	225	1102
Repeats (kb)	80 (19.2%)	32 (9.3%)	170 (14.2%)	50 (5.0%)	62 (13.2%)
Tandem repeats (kb)	22 (5.3%)	3.6 (1.1%)	71 (6.0%)	24 (2.5%)	48 (10.2%)
Plastid-derived (kb)	19 (4.6%)	0.3 (0.1%)	5.6 (0.5%)	7.9 (0.8%)	0 (0%)
Nuclear-derived repetitive (kb)	3.4(0.8%)	1.9(0.6%)	5.3(0.5%)	2.5(0.3%)	3.5(0.8%)

Fig. 2.

Loss and pseudogenes of mitochondrial protein-coding genes in selected gymnosperms, angiosperms and fern species. Gray and white bars represent events of pseudogenization and gene loss, respectively. The topology is based on Ran et al. [8] and the Angiosperm Phylogeny Website (http://www.mobot.org/mobot/research/apweb/)

Table 2.

Mitochondrial RNA genes in Gymnosperms

Gene	Cycas	Ginkgo	Pinus	Welwitschia	Taxus
rrn5	1	1	3	1	1
rrn18	1	1	1	1	2
rrn26	1	1	2	1	1
trnC-GCA	1	1	0	0	0
trnD-GUC	1	1	1	1	2
trnE-UUC	1	1	1c	1	2
trnF-GAA	1	2	0	0	0
trnG-UCC	0	1c	0	0	0
trnG-GCC	1	0	0	0	0
trnH-GUG	0	0	1	0	0
trnH-GUG-cp	1	1	0	0	0
trnK-UUU	1	1c	1	0	0
trnL-CAA	1a	0	0	0	0
trnL-UAA	1b	2	0	0	0
trnL-UAG	1	1	0	0	0
trnfM-CAU	4	1	2	0	2
trnfM-CAU-cp	0	0	0	1	0
trnM-CAU-cp	2	1	0	0	0
trnN-GUU	1d	0	0	0	0
trnP-AGG	1	1	0	0	0
trnP-UGG	1c	1	2	0	0
trnQ-UUG	1c	1	1	1	0
trnR-ACG-cp	0	0	0	1	0
trnR-UCU	1c	1	0	0	0
trnR-UCG	0	0	0	0	1
trnS-GCU	1	1	0	0	0
trnS-GGA-cp	1b	0	0	0	0
trnS-UGA	1	1	0	0	0
trnW-CCA	1	2	1	0	0
trnW-CCA-cp	0	0	0	1	1
trnY-GUA	1	1	1	1	1
Total rRNA	3	3	6	3	4
Total tRNA	27	23	12	8	10

^apreviously un-annotated tRNA genes; ^b tRNA gene(s) containing intron(s); ^c Anticodon is inferred to be edited; ^d tRNA genes characterized as a “chlamydial” copy

Homologous transcripts of eight of the nine lost mitochondrial genes (excluding rpl10) were found in the transcriptome of Taxus cuspidata (GenBank accession numbers: MN886610-MN886617). Regardless of whether the universal primers [44] or specific primers we designed based on other sequences from gymnosperms were used, we failed to amplify the rpl10 gene in Taxus. The average sequencing coverage depth of the eight genes is much lower than that of other mitochondrial genes, and their copy numbers are similar to those for the single-copy nuclear gene LEAFY and much lower than those of other mitochondrial genes (Additional file 3: Figure S1). In addition, at least four genes (rps2, rps7, rps10 and rps11) have acquired one to two introns, showing different gene structures from their mitochondrial counterparts in Cycas, Ginkgo and Pinus (Additional file 4: Figure S2). Moreover, using all mitochondrial genes of Cycas and Pinus as queries, we found that eleven possible nuclear homologs (rps1, rps2, rps7, rps10, rps11, rps13, rps14, rps19, rpl2, rpl5, and sdh3) had been reported lost in the mitogenome of Welwitschia [4].

The mean GC content of the mitochondrial protein-coding genes of Taxus is much higher than that of the other four gymnosperms. In addition, the mean values of the GC, GC1, and GC2 contents of the mitochondrial protein-coding genes of Welwitschia are lower than those of the other four gymnosperms, but the GC3 content is similar to that of Cycas, Ginkgo, and Pinus and lower than that of Taxus (Additional file 5: Figure S3).

The detailed intron information for the five gymnosperm mitogenomes is shown in Fig. 3. Cycas has 26 introns, of which 21 are cis-spliced and five are trans-spliced. In comparison with Cycas, Ginkgo lost one intron (rps10i235). Simialr to Cycas, Pinus also have 26 introns, of which eight introns were converted from cis- to trans-spliced. In addition, the Taxus and Welwitschia mitogenomes contained only 15 (four cis- and eleven trans-spliced) and ten (three cis- and seven trans-spliced) introns, respectively, which are fewer than that of the Pinus mitogenome. Furthermore, the mean intron sizes are similar among these five mitogenomes (Additional file 6: Figure S4).

Fig. 3.

Comparison of mitochondrial introns among the studied plants. The arrowhead indicates the position of an intron insertion. Solid and hollow triangles represent cis- and trans-spliced introns, respectively. The asterisk indicates that the intron was acquired before the divergence of nonvascular and vascular plants

RNA editing site abundance and efficiency in the gymnosperm mitogenomes

By using RES-Scanner, we identified the exact number of RNA editing sites in the Taxus mitogenome. When the editing efficiency was set to 0.05, 974 C-to-U editing sites were detected. Most (791) of these editing sites were detected in protein-coding genes, of which 730 were in coding regions and 61 were in introns. In addition, two, one, and 180 editing sites were identified in rRNA, tRNA and intergenic regions, respectively (Additional file 7: Table S3 and Additional file 8: Table S4). Editing sites in the first and second codon positions have higher editing efficiencies than those in the third position, and nonsilent editing sites have higher editing efficiencies than silent sites (Fig. 4a and b).

Fig. 4.

Frequency of RNA editing sites in the Taxus mitogenome. a Number of RNA editing sites with different editing efficiencies at the first, second and third codon positions; introns, rRNA and intergenic regions. b Number of RNA editing sites with different editing efficiencies at nonsilent and silent sites. c Comparison of the numbers of predicted and observed nonsilent RNA editing sites

Because only nonsilent RNA editing sites in protein-coding genes could be predicted by using PREP-Mt, we compared the predicted editing sites with the empirically derived nonsilent editing sites. By using PREP-Mt with the cutoff score set to 0.2, 1102 C-to-U editing sites within the protein-coding genes of the Taxus mitogenome were predicted (Fig. 4c). However, only 474 were identical between the predicted and observed editing sites. Using the same cutoff score, we predicted the RNA editing sites in Cycas, Ginkgo, Pinus and Welwitschia. More than 1000 editing sites were found in Cycas, Ginkgo and Pinus, whereas only 225 editing sites were predicted in Welwitschia (Table 1). In Welwitschia, almost all genes have fewer editing sites than those in the other four mitogenomes. In Taxus, it is clear that genes with intron losses have fewer observed editing sites than their counterparts in Cycas, Ginkgo and Pinus (Fig. 5). In addition, we also used PREPACT 3.0 (Filter hits = 0.2) to predict the RNA editing sites [45], and the result showed that the numbers and positions of RNA editing sites predicted by PREP and PREPACT are similar (Additional file 9: Figure S5 and Additional file 10: Table S5).

Fig. 5.

Localization of editing sites in exons of genes with intron losses in Taxus and Welwitschia. The red arrow represents the intron position

Structural and gene cluster dynamics in the gymnosperm mitogenomes

A comparison of the syntenic blocks showed that the length of the DNA shared between Cycas and Ginkgo was up to 200 kb, approximately half the length of the mitogenomes of these two species. However, the lengths of the DNA shared among the other three species and between each of these three species and Cycas or Ginkgo were very short. For example, only approximately 50 kb were shared between Pinus and Cycas or between Pinus and Ginkgo, and only approximately 30 kb were shared between Welwitschia and the other four species and between Taxus and the other four species (Fig. 6).

Fig. 6.

Syntenic block comparative analysis in gymnosperms generated using Circos. a Syntenic block of Cycas with the four other gymnosperms. b Syntenic block of Ginkgo with the four other gymnosperms. c Syntenic block of Pinus with the four other gymnosperms. d Syntenic block of Welwitschia with the four other gymnosperms. e Syntenic block of Taxus with the four other gymnosperms. f Shared sequence length of each species with the four other gymnosperms

Among the 29 conserved gene clusters identified in angiosperms [46], only one gene cluster (nad3-rps12) was shared by the five gymnosperm mitogenomes. In addition, only three were shared by Cycas and Ginkgo, and two were shared by Cycas, Ginkgo and Pinus. Taxus-Ginkgo, Taxus-Welwitschia, Cycas-Ginkgo-Taxus, and Cycas-Ginkgo-Pinus-Taxus each shared one cluster (Additional file 11: Figure S6).

Repeats, tandem repeats, and foreign DNA sequences in the gymnosperm mitogenomes

The Cycas and Pinus mitogenomes contain more dispersed repeats than those of the other three species (Table 1). A wealth of intermediate repeat pairs and a large number of small repeat pairs were identified in these two mitogenomes, and large repeats were found in all species except Welwitschia (Fig. 7). In addition, most repeats had more than two copies in the Cycas and Pinus mitogenomes (Additional file 12: Figure S7). Furthermore, the Pinus and Taxus mitogenomes contained more tandem repeat sequences (71 kb and 48 kb) than those of Welwitschia, Cycas and Ginkgo (24 kb, 22 kb, and 3.6 kb) (Table 1).

Fig. 7.

Length and distribution of repeats in gymnosperm mitogenomes. The bar shows the length of repeats, and the map shows the distributions of repeats. Yellow and blue represent large (> 1000 bp) and medium-sized (100–1000 bp) repeats, respectively, and green indicates the length of overlapping regions between large and medium-sized repeats

Plastid-derived sequences (length > 100 bp) were detected in Cycas, Ginkgo, Pinus and Welwitschia but were not found in Taxus after excluding sequences matching genes that occurred in the mitochondrial and plastid genomes simultaneously (i.e., atp1/atpA, rrn26/rrn23, and rrn18/rrn16) (Table 1). In addition, we also identified nuclear-derived repetitive sequences in the five mitogenomes, and two kinds of repeats (copia and small RNA) with a total length of 3.4 kb were identified in the Cycas mitogenome. Four kinds of repeats were found in the mitogenomes of Ginkgo (CIN4, copia, gypsy, and small RNA), Welwitschia (copia, gypsy, DNA transposons and small RNA) and Taxus (copia, gypsy, DNA transposons and small RNA), with lengths of 1.9 kb, 2.5 kb, and 3.5 kb, respectively. In addition, the Pinus mitogenome contains five kinds of repeats (CIN4, copia, gypsy, DNA transposons and small RNA) (Table 1 and Additional file 13: Table S6).

Variation in nucleotide substitution rates among gymnosperm mitogenomes

The comparison of evolutionary rates of all mitochondrial protein-coding genes and eight putative transferred genes revealed that the synonymous substitution rate of the mitochondrial genes in Welwitschia and Taxus was higher. When genes were transferred to the nuclear genome, their synonymous and nonsynonymous substitution rates greatly increased. In addition, although eight putatively transferred genes in Taxus and Welwitschia were still found in the mitogenomes of Cycas, Ginkgo and Pinus, their synonymous and nonsynonymous substitution rates were higher than those of other mitochondrial genes (Additional file 14: Figure S8).

Discussion

Separate losses of multiple mitochondrial protein-coding genes in Taxus and Welwitschia

The transfer of functional mitochondrial genes to the nucleus is a frequent, ongoing process during plant evolution that has played a major role in cytonuclear interactions and mitogenome evolution [47–51]. The tempo of mitochondrial gene loss in plants is punctuated [47, 48, 52]. Only two genes were lost in the first approximately 300 myr of land plant evolution if maturase is not considered, and parallel gene losses documented in hornworts, lycophytes, and ferns also happened in more recent times [47, 52, 53]. In angiosperms, a large number of protein-coding genes have been lost in some lineages, although most of the oldest groups still exhibit near stasis in mitochondrial gene content [46, 47, 54, 55].

Previous studies showed that the Cycas, Ginkgo, Picea and Pinus mitogenomes contain 41 protein-coding genes [3–6, 56]. However, Welwitschia mirabilis lost eleven protein-coding genes [4], including ten ribosomal protein genes (rpl2, rpl5, rps1, rps2, rps7, rps10, rps11, rps13, rps14, and rps19), and the sdh3 gene. It seems that gene loss is an uncommon phenomenon in gymnosperm mitogenomes because gene loss has been detected in only one of the four lineages [5]. However, it is intriguing that nine protein-coding genes (rpl2, rpl10, rps1, rps2, rps7, rps10, rps11, rps14, and sdh3) have been lost from the newly sequenced Taxus cuspidata mitogenome. Except rpl10, these genes lost from the Taxus mitogenome were also absent from the Welwitschia mitogenome (Fig. 2). One may hypothesize that these genes were lost in the ancestor of Taxus and Welwitschia. However, mapping the lost genes onto the phylogeny of gymnosperms reveals that these genes could have been lost separately in the two species because Pinaceae contains all 41 protein-coding genes and Taxaceae is sister to Welwitschia + Pinaceae (Fig. 2). In addition, the genes lost from these two species are the most frequently lost genes in angiosperms [17, 47], implying that these genes could also be prone to loss in gymnosperms.

Whether genes missing from the mitogenome are completely lost or transferred to the nuclear genome is sometimes unknown. In theory, most or all lost mitochondrial genes are functionally transferred to the nucleus, such as rpl5 being transferred to the nucleus in Poaceae [26]. However, frequent gene losses have also been reported for some species. For example, rps7 is one of the most frequently lost ribosomal protein genes, and it rarely appears to be functionally transferred to the nucleus [18, 57]. In combination with the genomic and transcriptomic sequences, we found that all mitochondrial genes missing from Taxus and Welwitschia (except rpl10) have been functionally transferred to the nucleus. Additionally, we found that compared to the rates in their mitochondrial counterparts, both the synonymous and nonsynonymous substitution rates of the transferred genes increased considerably (Additional file 14: Figure S8). Furthermore, in Taxus, four of the transferred genes have acquired one or two introns (Additional file 4: Figure S2).

Separate losses of multiple mitochondrial tRNA genes in Pinaceae, Taxus and Welwitschia

Similar to angiosperms, all gymnosperms have three rRNA genes in their mitogenomes (Table 1). In contrast, the number of tRNAs differs greatly, with 27, 23, 12, 8 and 10 tRNAs in the Cycas, Ginkgo, Pinus, Welwitschia and Taxus mitogenomes, respectively (Table 2). After excluding plastid-derived tRNA genes due to their potential to be nonfunctional, only 23, 21, 12, 5, and 9 tRNA genes with 16, 15, 10, 5, and 6 amino acids remained, respectively, which seems to imply that tRNA genes have been lost in some lineages of gymnosperms. Considering that only four tRNA genes (trnD-GUC, trnM-CAU, trnI-CAU and trnY-GUA) are shared among all five gymnosperm mitogenomes and that Cycas, Ginkgo, and Pinus have some putative tRNA genes that other species do not have, we deduce that the mitogenome of the common ancestor of gymnosperms harbored many more tRNA genes than those of extant gymnosperms. Of course, we cannot rule out that some species have integrated some new tRNA genes by EGT (Table 2) [16].

Frequent losses and cis- to trans-splicing of introns in the mitogenomes of gymnosperms

Both the ancestral angiosperm and gymnosperm mitogenomes contain 26 group II introns [3, 46]. In gymnosperms, Cycas and Ginkgo, have 26 and 25 introns, respectively, whereas only ten introns are found in Welwitschia [3, 4]. In addition, Pinus taeda contains 26 introns, and only 15 introns have been identified in the Taxus mitogenome (Fig. 3). Therefore, similar to in angiosperm mitogenomes [58–60], intron losses are more frequent than intron gains in gymnosperm mitogenomes.

Both Taxus and Welwitschia lost ccmFci829, nad1i477, nad2i156, nad7i140/676, and rps3i74/257. We deduced that they lost these introns separately for the following reasons. First, the nad1i477 intron was found in Gnetum and Ephedra, the other two genera of gnetophytes, and rps3i74/257 were retained in Gnetum [41, 61]. Second, Pinus taeda, the sister group of Welwitschia, contains all of these introns (Fig. 3). When comparing the five gymnosperm mitogenomes, we found that an extremely large number of introns had converted from cis- to trans-spliced in Pinus, Taxus and Welwitschia (Fig. 3). This finding is consistent with evidence from other plant mitochondria, suggesting that the evolution of intron splicing patterns proceeds from cis- to trans-splicing [17, 62].

Previous studies suggested some possible mechanisms for intron loss, including genomic deletion, exonization, gene conversion, EGT, and retroprocessing [63]. Deletion can be ruled out because all introns in the Taxus and Welwitschia mitogenomes are precisely removed. Exonization is also impossible because the exon structures in all genes are intact and because no exonization has been detected in the plant mitogenome [64]. Gene conversion also seems impossible since no chimeric structures have been noted in any gene regions. EGT could be the reason for the losses of rpl2i846 and rps10i235 from the Taxus mitogenome because rpl2 and rps10 have been transferred to the nuclear genome. Considering the precision of the intron cut, the most likely mechanism of other intron losses from the Taxus mitogenome is retroprocessing [64, 65]. Retroprocessing, also known as a reverse transcriptase-mediated model, is the most frequently reported mechanism for the removal of introns [65–68]. Under this model, introns located at the 3′ ends of genes are more likely to be lost than those at the 5′ ends [63, 65, 69]. However, introns have been lost from the start or center of the genes nad1, nad2 and nad7 in Taxus, which is similar to the finding for cox1 in Calypogeia [63]. A mutational mechanism (e.g., internally primed reverse transcription) or selective pressure to maintain introns near the 5′ and 3′ ends of genes could explain this pattern of intron loss [70].

Usually, losses of introns are accompanied by the absence of editing sites in a gene [65]. However, based on transcriptome and genome high-throughput sequencing, the genes with instances of intron loss still have some RNA editing sites. Nevertheless, most genes with intron loss in Taxus and Welwitschia have fewer RNA editing sites than their counterparts in Pinus, Cycas and Ginkgo (Fig. 5). This discrepancy could be caused by a partially processed cDNA undergoing conversion with the native intron-bearing gene. As a result, although introns are removed, some RNA editing sites still remain [71]. Another possibility is that the full-length cDNA molecules have partially recombined with the native gene. The third possibility is that microconversion is responsible for the partial loss of edited sites [72]. The last possibility is that RNA editing resumed again after retroprocessing [73].

In our previous study, we reported the rapid evolution of the retroprocessed mitochondrial rps3 gene in Conifer II [41]. We did not find an RNA editing site in the rps3 gene of Conifer II. However, in this study, we found 23 RNA editing sites with an editing efficiency greater than 5% in the Taxus rps3 gene. This may have occurred because only a partial gene without an RNA editing site was chosen in the previous RT-PCR experiment or because of a difference in the number of edited sites between organs [74, 75], as needles were used in the previous study but seeds were used in this study.

Gene clusters could be less conserved in gymnosperms, and transposable elements and specific repeats are rare in the Taxus and Welwitschia mitogenomes

Richardson et al. [46] described the distribution of 29 colinear gene clusters among angiosperm mitogenomes, 14 of which were assumed to be ancestral in angiosperms. However, in gymnosperms, eight gene clusters were found, and only one (nad3-rps12) was conserved in all five gymnosperm mitogenomes (Additional file 11: Figure S6). In addition, considering that at least seven gene clusters occur in the sampled angiosperms [46], but only two occur in Welwitschia and four in Pinus (Additional file 11: Figure S6), mitochondrial gene clusters in gymnosperms could be less conserved than in angiosperms. Seven gene clusters are conserved in the Cycas and Ginkgo mitogenomes, supporting their close relationship. The loss of the cox3-sdh4 and rrn18-rrn5 clusters seems to support the sister relationship between Pinus and Welwitschia. In contrast, the existence of the atp8-cox3 cluster and the loss of rpl2-rps19 and trnP(TGG)-sdh3 seem to support the close relationship between Taxus and Welwitschia. However, Taxus and Welwitschia could have lost rpl2-rps19 separately because Taxus lost only rpl2 but Welwitschia lost a long cluster including rpl2, rps19, rps3 and rpl16 (Additional file 11: Figure S6) [41]. In addition, Pinus lost a long cluster including cox3, sdh4 and atp8, whereas Welwitschia lost only the cluster cox3-sdh4. Therefore, it is difficult to find evidence to resolve the phylogenetic relationships of Pinaceae, Gnetales and Conifer II based on mitochondrial gene clusters.

Approximately 500 and 100 variants of a 36-bp Bpu element were identified in Cycas and Ginkgo, respectively. This element is putatively mobile because it contains a 4-bp direct terminal repeat [3, 4]. However, only one and two reduced similar sequences were found in Welwitschia and Pinus, respectively, and no similar sequences were found in Taxus, supporting expansion of the Bpu element in only Cycas and Ginkgo [3, 4]. In addition, we did not find other transposable elements in the Pinus and Taxus mitogenomes. In fact, no expansion of other repeat families has been reported in plants, implying that the expansion of repeat families is rare in land plant mitogenomes.

The number of RNA editing sites is not correlated with the GC content of mitochondrial genes

We obtained a mitochondrial RNA editing site map of Taxus cuspidata by comparing the transcriptomic and genomic high-throughput sequencing data. The results showed that all editing sites are C-to-U conversions, which is similar to the findings for other seed plants [76]. RNA editing occurred not only in protein-coding genes (exons and introns) but also in rRNA, tRNA and intergenic regions. A total of 974 editing sites were identified when the editing efficiency was set to greater than 0.05. A total of 730 editing sites were found in exons, of which 582 were nonsilent, affecting 1.63% of coding sequences (Additional file 7: Table S3 and Additional file 8: Table S4). This supports the essential role of nonsilent editing sites in the proper functioning of mitochondrially encoded proteins [27, 77, 78].

A total of 1206 and 1306 editing sites were predicted in the 41 protein-coding genes shared by Cycas and Ginkgo, respectively, but only 225 predicted editing sites were found in Welwitschia (Additional file 15: Table S7). We predicted RNA editing sites by using the same online tool (PREP-Mt) with the same cutoff of 0.2 and found 1179 and 1102 editing sites in Pinus taeda and Taxus cuspidata, respectively (Table 1). The number of predicted editing sites was greater than the number from empirical data in Taxus, but the prediction and empirical data in Cycas and Ginkgo were similar in terms of the number of editing sites [4, 79, 80] (Additional file 16: Table S8). Therefore, multiple mitochondrial RNA editing sites have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms [46].

Due to the very large difference between the numbers of predicted and empirically measured RNA editing sites in Taxus (this study) and Welwitschia [81], we did not compare the variation in RNA editing sites among the five focal species in detail. Generally, the number of mitochondrial RNA editing sites is not correlated with mitogenome size or GC content but is significantly correlated with the GC content of genes [53, 82]. However, this correlation is not supported in this study. The Taxus and Welwitschia mitogenomes have fewer editing sites than those of Cycas, Ginkgo, and Pinus, but the GC contents of the Taxus and Welwitschia mitochondrial genes are the highest and lowest among these five species, respectively.

Size variation in gymnosperm mitogenomes is still a mystery

In land plants, mitogenome size varies greatly, from 66 kb in Viscum scurruloideum [83] to as large as 11 Mb in Silene conica [84]. Because there is no significant difference in the number of mitochondrial genes, the variation of noncoding DNA content are statistically associated with variation in mitogenome size. Variation in noncoding DNA content could be affected by different factors, such as the proliferation of retrotransposons, the generation of repetitive DNA by homologous recombination, and the incorporation of foreign sequences via intracellular transfer from the plastid or nuclear genome or horizontal transfer of mitochondrial DNA (e.g., [3, 4, 55, 85–87]). However, in different species, the increase in mitogenome size could be caused by different factors. For example, although foreign sequences were suggested to contribute to mitogenome size variation, the origins of foreign sequences differ among species. The mitogenome of Amborella trichopoda contains six genome equivalents of foreign mitochondrial DNA from algae, mosses, and other angiosperms, whereas DNA sequence transfer from the nucleus is a core mechanism for mtDNA size expansion in apple, maize and grape [86]. In some cases, mitogenome size variation is affected by multiple factors. For example, the mitogenome expansion of Cucurbita pepo was largely the result of the accumulation of unprecedented amounts of both chloroplast sequences (~ 113 kb) and short repeat sequences (~ 370 kb) [88]. In addition, changes in recombination, including gene conversion, may contribute to the variation in mitogenome size [84]. Furthermore, many mitogenomes contain multiple repeats, but there is no strict relationship between repeat content and genome size in angiosperm mtDNA [83, 87], although repeat was considered to be a main factor for some mitogenome expansion. For example, an accumulation of repeats in intergenic regions contributed to 371 kb or 38% of the Cucurbita mitogenome [88].

Both the Welwitschia mirabilis and Pinus taeda mitogenomes are larger than those of Cycas and Ginkgo (Table 1). The mitogenome size of Welwitschia mirabilis and Pinus taeda is 978,846 bp and 1,191,054 bp, respectively. That is, the size difference between their genomes is only approximately 200 kb. However, there is some disparity between their noncoding regions. In Pinus, 170 kb of repeats and 5.6 kb of chloroplast-derived sequences were identified, whereas 50 kb of repeats and 7.9 kb of chloroplast-derived sequences were found in Welwitschia. In addition, numerous tandem repeats (71 kb) were identified in Pinus, but only a few (24 kb) were found in Welwitschia. Considering that the difference in the mitogenome size of gymnosperms is larger than 500 bp, the number of repeats and the increase in the abundance of plastid-derived sequences were not the main reasons for the mitogenome expansion of Pinus and Welwitschia. Guo et al. [4] suggested that the substantial amount of unidentified DNA could contribute to the expansion of the Welwitschia mitogenome, and they deduced that these unidentified DNAs could be derived from the nuclear genome by intracellular transfer. As nuclear-derived repetitive sequences originated unambiguously and generally did not proliferate after transfer [89], we identified them in the mtDNA of Pinus and Welwitschia, and the results showed that only approximately 5.3 kb and 2.5 kb were found in these species (Table 1), which did not show significant differences from the other gymnosperms. Therefore, the origin of most unidentified noncoding regions in these two species is still unknown. Small repeats contributed to the recombination in mitogenomes [90]. However, although a large number of small repeats (150 kb) were found in the Pinus mitogenome, only 48 kb of small repeats were identified in the Welwitschia mitogenome. The newly sequenced mitogenome of Taxus cuspidata is slightly larger than that of Cycas and Ginkgo (Table 1). However, the mitogenome of Taxus has fewer protein-coding genes, tRNAs, introns and RNA editing sites, and higher mutation rates than that of Cycas and Ginkgo (Additional file 14: Figure S8 and Table 1). We speculate that the mechanisms of mitogenome expansion could differ in gymnosperms.

Some nonadaptive mechanisms have been developed to explain the origins of variation in mitogenome size and complexity, such as the mutational hazard hypothesis (MHH) [91], different DNA repair mechanisms in transcribed and nontranscribed regions [92], and break-induced replication [93]. However, the MHH was rejected because some Silene species have extremely large mitogenomes but also have high rates of mutation [55]. In this study, Welwitschia also has a large mitogenome but high rates of mutation (Additional file 14: Figure S8). In addition, the possibility of different mechanisms of repair for coding and noncoding DNA was also not supported because transcription-coupled repair (TCR) is not found in plants [92, 93]. The number of repeats is significantly different between Pinus and Welwitschia, both of which have a large mitogenome, implying that the frequency of recombination caused by repeats would also be different between their mitogenomes. Furthermore, the model of Christensen [92, 93] cannot explain the occurrence of RNA editing, HGT and intron accumulation in land plant mitogenomes [94]. Smith (2016) suggested that there could be a threshold mutation rate in mitogenomes, but it is difficult to determine this value. More research will help uncover the underlying mechanism of the size variation in plant mitogenomes.

Conclusions

In this project, we sequenced the complete mitogenome of Taxus cuspidata in Conifer II. By comparing the mitogenomes from the five gymnosperm lineages, we show that some protein-coding genes have been transferred to the nuclear genomes in Taxus and Welwitschia, individually. We also show that similar to the pattern observed in angiosperms, multiple tRNA genes and introns have been lost in some lineages of gymnosperms, but gene clusters in gymnosperms could be less conserved than those of angiosperms. In addition, we show that number of introns and genes could be positively correlated with number of RNA editing sites.

Abbreviations

EGT

Endosymbiotic gene transfer

GC1/2/3

GC content of the first, second and third codon positions, respectively

HGT

Horizontal gene transfer

MHH

Mutational hazard hypothesis

mitogenome

Mitochondrial genome

MTPTs

Plastid-derived mtDNA

NCBI

National Center for Biotechnology Information

NGS

Next-generation sequencing

ORF

Open reading frame

TCR

Transcription-coupled repair

Authors’ contributions

JHR and XQW conceived and designed the study. SLK carried out the laboratory work, data treatment and data analysis. TTS and PG participated in the data analysis. JHR and SLK drafted the manuscript. XQW helped revising the manuscript. All authors read and approved the manuscript.

Funding

This study was supported by the National Key R&D Program of China (2017YFA0605100), the Key Research Program of Frontier Sciences, CAS (QYZDJ-SSW-SMC027), the National Natural Science Foundation of China (grant nos. 31330008, 31370250, and 31770238), and the Youth Innovation Promotion Association, Chinese Academy of Sciences (2012070).

Availability of data and materials

The raw data were deposited in the Short Read Archive database under accession numbers SRR10305024-SRR10305026 (BioProject: PRJNA578185) and the assembled and annotated Taxus mitogenome has been deposited in GenBank under accession number MN593023. Homologous transcripts of eight lost mitochondrial genes of Taxus cuspidata have been submitted to GenBank, with accession numbers MN886610-MN886617.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12862-020-1582-1.