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. 2020 Dec 2;9(12):1692.
doi: 10.3390/plants9121692.

The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Li Gu  1   2   3 , Ting Su  1   2   3 , Ming-Tai An  4 , Guo-Xiong Hu  1   2
Affiliations

The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Li Gu et al. Plants (Basel). .

Abstract

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

Keywords: Gesneriaceae; Oreocharis; Thamnocharis; complete chloroplast genome; next-generation sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Gene map of chloroplast genome of Oreocharis esquirolii. Genes outside the circle are transcribed in counterclockwise direction and those inside in clockwise direction. LSC indicates large single copy; SSC small single copy, and IR inverted repeat.
Figure 2
Figure 2
Amino acid frequencies and RSCU value of the protein-coding sequences of Oreocharis esquirolii.
Figure 3
Figure 3
Simple Sequence Repeats (SSRs) in cp genomes of Oreocharis esquirolii and O. mileensis. (A,B) Frequencies of identified SSRs in LSC, IR, and SSC regions; (C) Numbers of SSRs.
Figure 4
Figure 4
Repeat sequences in the chloroplast genome of Oreocharis esquirolii and O. mileensis. (A,B) Percentages of repeats in LSC, IR, and SSC regions; (C) Numbers of repeat types detected (F: forward, P: palindrome, R: reverse).
Figure 5
Figure 5
Comparisons of LSC, SSC, and IR border regions among five chloroplast genomes of Gesneriaceae.
Figure 6
Figure 6
Mauve multiple alignment of five chloroplast genomes of Gesneriaceae, with Oreocharis esquirolii as the reference.
Figure 7
Figure 7
Nucleotide diversity (Pi) in the complete chloroplast genomes of five species of Gesneriaceae. Sliding window analysis with a window length of 600 bp and a step size of 200 bp.
Figure 8
Figure 8
Visualization of genome alignment of five chloroplast genomes of Gesneriaceae using Oreocharis mileensis as reference.
Figure 9
Figure 9
Phylogenetic relationships of 28 species based on complete chloroplast genome sequence. ML bootstrap values are given above branches and posterior probabilities are indicated below.
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