The complete chloroplast genome of <i>Firmiana danxiaensis</i>, an endangered species endemic to Danxia landform in Southern China

Lu, Qifeng; Wei, Luo; Huang, Zhihuan

doi:10.1080/23802359.2019.1689861

Cited by 2 publications

(1 citation statement)

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“…Earlier studies of F. danxiaensis mainly focus on its distribution, growth [24][25][26][27], and cultivation [28][29][30]. In recent years, some studies have performed phylogenetic [31,32] and comparative genomics analyses [33] based on F. danxiaensis cp genomes. However, only the cp genome of F. danxiaensis individuals from the DX location have been sequenced.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Firmiana danxiaensis chloroplast genomes and comparative analysis of Firmiana: insight into its adaptive evolution and phylogenetic relationships

Nie

Deng

et al. 2023

Preprint

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Background Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Therefore, we sequenced its complete chloroplast (cp) genome from four locations and conducted comparative genomics analyses at both interspecific and intrageneric levels. Results The F. danxiaensis cp genomes are about 160,972 bp in size, with 112 unique genes encoded. The genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels, respectively. Selection pressure analysis revealed that Ka/Ks values of F. danxiaensis cp genomes were less than one at the interspecific level. Seven (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) positively selected genes were identified when comparing F. danxiaensis cp genomes to Sterculia monosperma and other Firmiana species, respectively. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, our cp genomes did not cluster phylogenetically according to their habitat types. Conclusions The F. danxiaensis cp genomes reveal both possible environmental associated adaptation and random genetic effects in the species, which encourages further integration of geographical distances, environmental factors, and SNPs on the adaptive evolution study of F. danxiaensis.

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Section: Introductionmentioning

confidence: 99%

Characterization of Firmiana danxiaensis chloroplast genomes and comparative analysis of Firmiana: insight into its adaptive evolution and phylogenetic relationships

Nie

Deng

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution

Li,

Nie,

Deng

et al. 2024

BMC Genomics

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Background Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies. Results The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types. Conclusions The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.

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The complete chloroplast genome of Firmiana danxiaensis, an endangered species endemic to Danxia landform in Southern China

Cited by 2 publications

References 6 publications

Characterization of Firmiana danxiaensis chloroplast genomes and comparative analysis of Firmiana: insight into its adaptive evolution and phylogenetic relationships

Characterization of Firmiana danxiaensis chloroplast genomes and comparative analysis of Firmiana: insight into its adaptive evolution and phylogenetic relationships

Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution

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