Complete plastome of a subtropical tree Eriobotrya malipoensis (Rosaceae) in Yunnan

Abstract

Eriobotrya malipoensis Kuan is an important wild woody evergreen tree within the genus Eriobotrya Lindl belonging the family Rosaceae. To better determine its phylogenetic location with respect to the other Eriobotrya species, the complete plastome of E. malipoensis was sequenced. The whole plastome is 159,313 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,344 bp, one large single-copy (LSC) region of 87,270 bp, and one small single-copy (SSC) region of 19,355 bp. The overall G + C content of the whole plastome is 36.7%. Further, maximum likelihood phylogenetic analyse (TVM + F+R2 model) was conducted using 14 complete plastome of the Rosaceae. Our phylogeny supports the relationships: sisterhood of the E. malipoensis and E. fragrans Champ, flowed E. japonica Lindl.

Eriobotrya malipoensis Kuan is a narrowly distributed species at high altitudes in Southeast Yunnan of SW China. It was assigned to the genus Eriobotrya in the family Rosaceae (http://foc.iplant.cn/). E. malipoensis owns the largest leaves among the reported species in the genus Eriobotrya (Yang et al. 2017). Previous moleculae studies, using the RAPD, AFLP, internal transcribed spacer (ITS) and RAD sequencing technologies, reported close relationship between E. malipoensis and E. japonica (Li et al. 2009; Yang et al. 2009a, 2009b; Yang et al. 2017). Zhao et al. (2011), however, used ITS region to investigate sisterhood of E. malipoensis and E. seguinii rather than E. japonica. This raises the question, is there sister relationship between E. malipoensis and E. japonica? Here, we selected E. malipoensis to determine the entire plastid genome sequence.

The total genomic DNA was extracted from the fresh and healthy leaves of a single individual of E. malipoensis, which was collected from Malipo County (Yunnan, China; Long. 104.852021 E, Lat. 23.146254N, 1292 m), using the modified CTAB method (Shen et al. 2016). The voucher specimen was preserved in the Herbarium of Southwest Forestry University (Accession Number: SWFU-SY35055). The GetOrganelle software (Jin et al. 2018) was used to assemble the complete plastome of E. malipoensis with the publicly available plastome of E. japonica (GenBank accession number KT633951) as the reference (Huang 2019). Geneious R8.1.3 software (Biomatters Ltd, Auckland, New Zealand) was used for initial plastome annotation.

The plastome of E. malipoensis (LAU10002), with a length of 159,313 bp, was 176 bp and 27 bp larger than that of E. japonica (159,137 bp, KT633951) and E. fragrans (159,286 bp, LAU10001). It was also 844 bp and 926 bp smaller than that of Pyrus ussuriensis Maxim (160,157 bp, MK172841) and Malus prattii (Hemsl.) Schneid (160,239 bp, MH929090). The length of the inverted repeats (IRs), large single-copy (LSC), and small single-copy (SSC) regions of E. malipoensis was 26,344 bp, 87,270 bp, and 19,355 bp, respectively. The overall G + C content is 36.7% (LSC, 34.5%; SSC, 30.2%; IR, 42.7%). The plastid genome includes 112 unique genes, including 4 rRNA genes, 30 tRNA genes, and 78 protein-coding genes, of which 17 are duplicated in IR regions.

Furthermore, based on 13 published plastomes, we reconstructed a phylogenetic tree (Figure 1) to confirm the relationship between E. malipoensis and E. fragrans or E. japonica, with Crataegus kansuensis Wils (MF784433) as outgroup. Maximum likelihood (ML) phylogenetic analyses were performed based on TVM + F+R2 model in the iqtree version 1.6.7 programme with 1000 bootstrap replicates (Nguyen et al. 2015). The ML phylogenetic tree with 43-100% bootstrap values at each node supported the fact that E. malipoensis and E. fragrans instead of E. japonica were located in the same clade.

Figure 1.

The ML phylogenetic tree for E. malipoensis based on other thirteen species (two in Eriobotrya, three in Pyrus, one in Docynia, one in Chaenomeles, one in Cydonia, one in Sorbus, three in Malus, and one in Crataegus) plastid genomes.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability

The plastome data of the E. malipoensis will be submitted to Rosaceae Chloroplast Genome Database (https://lcgdb.wordpress.com). Accession numbers are LAU10002.