The complete chloroplast genome sequence of Berchemiella wilsonii (Rhamnaceae), an endangered endemic species

Abstract

Berchemiella wilsonii (Rhamnaceae) is an endangered endemic tree to China. Here, the chloroplast genome was characterized by next-generation Illumina paired-end sequencing. The complete genome comprised 160,076 bp in length, with an inverted repeat region of 26,514 bp, a small single copy (SSC) region of 18,717 bp, and a large single copy region of 88,331 bp. A total of 132 genes were identified, including 83 protein-coding genes, 37 transfer RNA genes, and eight rRNA genes. The overall GC content of the whole genome was 37.23%. Phylogenetic analysis showed that B. wilsonii was most closely related to Berchemiella berchemiifolia.

Keywords:

• Berchemiella wilsonii
• chloroplast genome
• endangered plant
• phylogenetic analysis

Berchemiella wilsonii, a member in the family Rhamnaceae, is one of the most critically endangered plants in China. The species has not been found for almost a hundred years since the first specimen collected originally by E. H. Wilson in the Xingshan county, Hubei Province, central China in 1907 and is treated as an extinct taxon, listed on the China Plant Red Data Book (Fu and Jin 1992). Due to anthropogenic activities such as habitat loss and deforestation, all taxa of the genus Berchemiella have been designated as nationally endangered species (Kang et al. 1991; Fu and Jin 1992; Iwatsuki et al. 1999). According to botanic expedition covering all recorded sites throughout its distribution range, five isolated adult trees of B. wilsonii were found in three sites in Hubei province(Kang et al. 2006). Therefore, it is an urgent need for effective conservation of endangered species, the critical importance for retaining the comprehensive genomics information of the species would definitely be used in attempting to formulate any conservation strategy. Thus, our study had got and the complete cp genome of B. wilsonii (GenBank accession number MH938366) to retrieve valuable resources for the conservation and phylogeny of B. wilsonii.

Four individual of B. wilsonii representing an isolated population was sampled from Wudaoxia Nature Reserve, Hubei, China (110.08 E, 31.40 N). The specimen of B. wilsonii was stored in the Harvard University Herbaria, its DNA was also stored in the Plant Gene Bank of Three Gorges Endangered Plant Species Resource Bank. Total genomic DNA was extracted from young and healthy leaves with the DNeasy Tissue Kit (Tiangen, Beijing, China), and then used to construct a library for sequencing with Illumina Hiseq 2500 platform (Illumina, San Diego, CA). The paired-end reads were trimmed for quality using the CLC Genomics Workbench version 9.0 (CLC Bio, Aarhus, Denmark) and NGSQCToolkit_version 2.3.3 with default parameters (Patel and Jain 2012). Additionally, MITObim version 1.8 (Hahn et al. 2013) was used to assemble the complete circular cp genome sequence. The cp genome was annotated and manually adjusted with CpGAVAS (Liu et al. 2012). The assembled genome was then manually checked for start and stop codons as well as intron/exon boundaries. The transfer RNA (tRNA) genes were further confirmed by tRNAscan-SE and ARAGORN (Lowe and Eddy 1997; Laslett and Canback, 2004; Schattner et al. 2005). Finally, the circular plastid genome map was completed using the online program OrganellarGenome DRAW (OGDRAW) (Lohse et al. 2013).

The complete cp genome of B. wilsonii was 160,076 bp in length presenting a typical quadripartite structure and contained an inverted repeat region (IR, 26,514 bp), a small single copy (SSC) region and a large single copy region (LSC) (18,717, 88,331 bp, respectively). Moreover, the cp genome encoded 132 genes, including 83 (62.88%) protein-coding genes (PCGs), 37 (28.03%) tRNA genes, and eight (6.06%) rRNA genes. Four genes (3.03%) were inferred to be pseudogenes. Fourteen genes (rpoC1, trnL-UAA, trnV-UAC, rpl22, rp12, ycf2, ycf15, trnI-GAU, ndhB, trnA-UGC, ndhA, trnA-UGC, trnI-GAU, and rps12) contained one intron, while three genes (ycf3, clpP, and ycf1) contained two introns. The overall GC content of the B. wilsonii cp genome was 37.23%, and the corresponding values in LSC, SSC, and IR regions were 35.09, 31.89, and 42.69%, respectively.

Phylogenetic analysis was performed using the chloroplast genome sequences of B. wilsonii and other 49 available cp genomes. A neighbour-joining phylogenetic tree was reconstructed with MEGA version 7 (Kumar et al. 2016) with 1000 bp replicate using the concatenated coding sequences of cp PCGs. The phylogenetic tree (Figure 1) showed that Rhamnaceae were monophyletic and sister to Elaegnaceae. Specifically, we observed that B. wilsonii was most closely related to Berchemiella berchemiifolia.

Figure 1. Phylogenetic tree reconstruction of 49 taxa using maximum likelihood based on complete chloroplast genome sequences. The bootstrap values were based on 1000 replicates, and are indicated next to the branches.

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Funding

This research was supported by Scientific Research Foundation for the introduction of talent of Pingdingshan University (No. PXY-BSQD2016018), Key Research Project of Colleges, and Universities of Henan Province (No. 16A210035).