Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations

doi:10.17520/biods.2020263

Abstract

Abstract:

Aims: Firmiana kwangsiensis and F. danxiaensis are endemic plant species with narrow distribution and small population in southern China, which have important ecological and economic value. However, our knowledge of the chloroplast genome level of F. kwangsiensis and F. danxiaensis are still limited. Also, the phylogenetic relationships among the Firmiana genus remain unclear.
Methods: The genome skimming sequencing data of F. kwangsiensis and F. danxiaensis were obtained by using the high-throughput sequencing, and the complete chloroplast genomes were assembled and then the structures were analyzed by bioinformatics methods.
Results: The results revealed that complete chloroplast genomes of the F. kwangsiensis and F. danxiaensis show a typical quadripartite structure of 160,836 bp and161,253 bp in length, consisting of a large single copy region (89,700 bp and 90,142 bp) and a small single copy region (19,970 bp and20,067 bp) that were separated by a pair of inverted repeat regions (25,583 bp and 25,522 bp each). The annotation results showed that chloroplast genomes of both species contain 131 genes, including 86 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. In F. kwangsiensis, 26 forward repeats, two reverse repeats, 21 palindromic repeats, 23 tandem repeats, and 98 simple sequence repeats were found, and 23 forward repeats, five reverse repeats, 21 palindromic repeats, 30 tandem repeats, and 107 simple sequence repeats were found in F. danxiaensis. Phylogenetic analyses revealed that five Firmiana species were clustered into two branches with strong supports. Firmiana kwangsiensis, F. pulcherrima and F. colorata formed a branch, and the F. kwangsiensis was a sister relationship to F. pulcherrima in this branch, the other branch was F. danxiaensis and F. major.
Conclusion: The structures, gene arrangement and repeat sequences in F. kwangsiensis and F. danxiaensis chloroplast genome were high similar. Phylogenetic analyses revealed that five Firmiana species were clustered into two clades, F. kwangsiensis was closely related to F. pulcherrima, and F. danxiaensis was closely related to F. major. In addition, the SSRs in this study will provides important genetic information for phylogenetic, evolution for Firmiana species.

Key words: Firmiana kwangsiensis, Firmiana danxiaensis, chloroplast genome, high-throughput sequencing, repeat sequence, phylogenetic analysis

Qifeng Lu, Zhihuan Huang, Wenhua Luo. Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations[J]. Biodiv Sci, 2021, 29(5): 586-595.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2020263

https://www.biodiversity-science.net/EN/Y2021/V29/I5/586

Figures/Tables 5

Fig. 1 Gene map of the Firmiana kwangsiensis and F. danxiaensis chloroplast genome

Table 1 Comparison of chloroplast genome characteristics of Firmiana kwangsiensis and F. danxiaensis

基因组特征 Genome characteristics	广西火桐 F. kwangsiensis	丹霞梧桐 F. danxiaensis
序列全长 Genome size (bp)	160,836	161,253
LSC区长度 LSC length (bp)	89,700	90,142
SSC区长度 SSC length (bp)	19,970	20,067
IR区长度 IR length (bp)	25,583	25,522
GC含量 GC content (%)	37.04	36.87
LSC区GC含量 GC content of LSC (%)	34.92	34.68
SSC区GC含量 GC content of SSC (%)	31.46	31.24
IR区GC含量 GC content of IR (%)	42.93	42.97
A碱基占比 A base content (%)	30.98	31.13
T碱基占比 T base content (%)	31.98	31.99
C碱基占比 C base content (%)	18.87	18.61
G碱基占比 G base content (%)	18.17	18.26
基因总数 Total genes	131	131
编码蛋白基因数 No. of protein coding sequences	86	86
tRNA	37	37
rRNA	8	8

Fig. 2 SSR analysis of the chloroplast genomes of Firmiana kwangsiensis and F. danxiaensis. (A) Number of SSRs in different types; (B) Number of SSRs in the LSC (large single copy), SSC (small single copy), and IR (inverted repeat region); (C) Number of SSRs in the intergenic regions (IGS), protein-coding gene (CDS) and introns.

Fig. 3 Repeat sequences analysis of Firmiana kwangsiensis and F. danxiaensis chloroplast genome. (A) Number of different types of repeats; (B) Size of tandem repeats in specific range; (C) Size of forward, reverse and palindromic repeats in specific range.

Fig. 4 Phylogenetic tree of 15 species based on chloroplast genome using maximum likelihood (ML) method

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