The complete chloroplast genome of Ottelia acuminata var. songmingensis, an Endangered aquatic macrophyte in China

Abstract

Ottelia acuminata var. songmingensis is an Endangered freshwater submerged macrophyte occupying only a portion of a stream ca. 300 meters long in Songming County of the Yunnan Province, China. Here, we report and characterize the complete chloroplast genome sequence of O. acuminata var. songmingensis to provide genomic resources useful for promoting its conservation. The complete chloroplast genome is 157,645 bp in length, consisting of a pair of inverted repeat (IR) regions (24,973 bp), a small single copy (SSC) region (20,055 bp), and a large single copy (LSC) region (87,644 bp). The chloroplast genome contained 116 genes, including 71 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome is 36.6%. Phylogenetic analysis of 19 selected chloroplast genomes revealed that O. acuminata var. songmingensis was closely related to Elodea canadensis of Hydrocharitaceae.

Keywords:

• Ottelia acuminata var.songmingensis
• chloroplast genome
• Endangered species

Ottelia acuminata (Gagnepain) Dandy (Hydrocharitaceae) is an endemic submerged perennial in China (Wang et al. 2010). It has been categorized as vulnerable with a status ‘A2c’ in the China Species Red List (Qin et al. 2017). During the past 30 years, O. acuminata has disappeared from 12 lakes or rivers where it previously had been common (Guo et al. 2019). Unfortunately, the rapid disappearance of populations continues. Ottelia acuminata (Gagnepain) Dandy var. songmingensis Z. T. Jiang, H. Li et Z. L. Dao (Jiang et al. 2005) is a variant that only occurs in Songming County of the Yunnan Province occupying a portion of a stream ca. 300 meters long. Here, we reported the complete cp genome of O. acuminata var. songmingensis, to provide a genomic resource for further conservation genetics and phylogenetic analysis.

The fresh leaves of O. acuminata var. songmingensis were collected from Songming County (25°16′23.2″N, 102°52′52.7″E), Yunnan province and voucher specimens (Guo SM01) were deposited in Herbarium of Yunnan Normal University. A sequence library was constructed and sequencing was performed using the Illumina HiSeq 2500-PE150 platform (Illumina, San Diego, CA, USA). All raw reads were filtered by using NGS QC Toolkit_v2.3.3 with default parameters to obtain clean reads (Patel and Jain 2012). The plastome was de novo assembled using NOVOPlasty (Dierckxsens et al. 2017). The complete cp genome was annotated with the online annotation tool GeSeq (Tillich et al. 2017).

The complete chloroplast genome of O. acuminata var. songmingensis was a quadripartite circular and 157,645 bp in length (GenBank accession No.: MK604184), comprising a large single copy (LSC) of 87,644 bp and a small single copy (SSC) of 20,055 bp, separated by two inverted repeat (IR) regions of 24,973 bp. It contained 116 genes, including 71 protein-coding, 8 ribosomal RNA, and 37 tRNA genes. The base compositions of the chloroplast genome were uneven (31.2% A, 18.7% C,18.0%G, 32.1% T), with an overall GC content of 36.6%. A total of 79 SSRs were discovered by the online software IMEx (Mudunuri and Nagarajaram 2007). Among them, the numbers of mono-, di-, tri-, tetra-, penta- and hexa- nucleotides SSRs are 24, 33, 8, 11, 2, and 1, respectively.

To determine the phylogenetic location of O. acuminata var. songmingensis, the published chloroplast genomes, including Elodea canadensis (NC_018541, Huotari and Korpelainen 2012) from Hydrocharitaceae and 14 species from Alismatales were used, with 3 Acorus species from Acorales as outgroups. The total of 19 chloroplast genomes were aligned using MAFFT 7.308 (Katoh and Standley 2013). The maximum likelihood (ML) tree was reconstructed by RAxML 8.2.11 (Stamatakis et al. 2008) with the nucleotide substitution model of GTR + G and node support was estimated by means of bootstrap analysis with 1000 replicates. The phylogenetic tree showed that O. acuminata var. songmingensis and Elodea canadensis from Hydrocharitaceae formed a monophyletic clade with 100% bootstrap value (Figure 1). The complete chloroplast genome of O. acuminata var. songmingensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Hydrocharitaceae.

Figure 1. Phylogenetic tree reconstruction of 19 samples using Maximum Likelihood based on complete chloroplast genome. Bootstrap support values >50% are indicated next to the branches.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study is supported by the National Natural Science Foundation of China [31760048, 31560062] and Grants from the Open Foundation of Key Laboratory for Pollution Process and Watershed Management of Plateau Lakes in Yunnan Province [2014530117].