Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

Wang, Yifei; Wen, Fang; Hong, Xia; Li, Zhenglong; Mi, Yaolei; Zhao, Bo

doi:10.3389/fpls.2022.1019831

Cited by 18 publications

(15 citation statements)

References 84 publications

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“…A previous study also reported the loss of the trnH -GUG genes was one of the major differences between the plastomes of the two subgenera Siphisia and Aristolochia ( Li et al., 2019 ). These sequence variations might be the result of boundary contraction and expansion between the LSC/IR regions in plants ( Wang et al., 2022 ). Plastid genomes have the characteristics of high conservation and slow evolutionary rate, thus the special characteristics presented in their structure are often phylogenetically informative ( Pascual-Diaz et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome

et al. 2023

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IntroductionThe Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers.MethodsIn this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes.ResultsThe 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia.DiscussionThis research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.

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Section: Discussionmentioning

confidence: 99%

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome

et al. 2023

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“…The high conservatism of plastome has also been observed in other Gesneriaceae genera. For instance, Wang et al. (2022) found that the plastomes length of Paraboea ranged from 153,166–154,245 bp and exhibited similar structure, gene order, and gene content.…”

Section: Discussionmentioning

confidence: 99%

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

et al. 2023

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Trichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified the phylogenetic relationships within this tribe on several DNA markers, including the generic relationships within subtribes. Recently, plastid phylogenomics have been successfully employed to resolve the phylogenetic relationships at different taxonomic levels. In this study, plastid phylogenomics were used to explore the relationships within Trichosporeae. Eleven plastomes of Hemiboea were newly reported. Comparative analyses, phylogeny and morphological character evolution within Trichosporeae were conducted on 79 species representing seven subtribes. The Hemiboea plastomes range from 152,742 bp to 153,695 bp in length. Within Trichosporeae, the sampled plastomes range from 152,196 bp to 156,614 bp and GC content from 37.2% to 37.8%. A total of 121–133 genes were annotated in each species, including 80–91 protein-coding genes, 34–37 tRNA genes, and 8 rRNA genes. The contraction and expansion of IR borders were not detected, and gene rearrangements and inversions did not occur. The 13 hypervariable regions were proposed as the potential molecular markers for species identification. A total of 24,299 SNPs and 3,378 indels were inferred, and most of the SNPs were functionally missense and silent variations. There were 1968 SSRs, 2055 tandem repeats and 2802 dispersed repeats. The RSCU and ENC values indicated that the codon usage pattern was conserved in Trichosporeae. Both the phylogenetic frameworks based on the whole plastome and 80 CDSs were basically concordant. The sister relationships between Loxocarpinae and Didymocarpinae were confirmed, and Oreocharis was a sister group of Hemiboea with high support. The morphological characters showed a complex evolutionary pattern of Trichosporeae. Our findings may contribute to future research on genetic diversity, morphological evolutionary patterns, and conservation of the tribe Trichosporeae.

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“…The chloroplast genome sequences were used to study systematic evolutionary relationships between species of Swertia L. It was found that rpoC1, ccsA, ndhI, ndhA, and rps15 protein-coding genes had large variations [21]. The complete chloroplast genomes of Paraboea (Gesneriaceae) plants were used to study their phylogeny and adaptive evolution [22]. The complete chloroplast genomes of Ipomoea were used to construct a phylogenetic tree in our study.…”

Section: Organellar Phylogenetic Relationshipmentioning

confidence: 99%

Comparing sweet potato chloroplast genome and mitochondrial genome reveals organelle gene transfer

li¹,

qiu²

2022

Preprint

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The increasing number of plant mitochondrial genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast (cpDNA) and nuclear genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato Fucaishu18 better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of Fucaishu18 (OM808940) is 161387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269578 bp in length and contained 70 functional genes, including 41 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome; 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.

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Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

Cited by 18 publications

References 84 publications

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

Comparing sweet potato chloroplast genome and mitochondrial genome reveals organelle gene transfer

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