Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Yang, Jiaxin; Hu, Guo‐Xiong; Hu, Guang‐Wan

doi:10.1186/s12864-021-08259-w

Cited by 15 publications

(10 citation statements)

References 115 publications

(140 reference statements)

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“…Overall, the 31 plastid genomes of Linderniaceae showed size differences mainly in the LSC region ( Table 2 ). Consistent with previous studies ( Yang et al., 2022 ; Bai et al., 2023 ; Peng et al., 2023 ), the non-coding and single copy (SC) regions were more divergent than the coding and IR regions ( Supplementary Figure 3 ). We, therefore, speculated that the size variation of Linderniaceae plastomes was mainly attributed to the LSC region, especially in the non-coding regions, similar to the results of studies of Gao et al.…”

Section: Discussionsupporting

confidence: 90%

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Yan,

Geng,

Jia

et al. 2023

Front. Plant Sci.

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IntroductionThe recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae.MethodsIn this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses.ResultsThe plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic.DiscussionComparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

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Section: Discussionsupporting

confidence: 90%

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Yan,

Geng,

Jia

et al. 2023

Front. Plant Sci.

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“…Drymosphace showed high consistency and similarity in terms of their gene structure, order, and content. These results are consistent with other plastomes of Lamiaceae [26][27][28]33,51] and are also as conservative as most of the angiosperms that have been previously reported [52][53][54][55][56].…”

Section: Plastome Features Of Sect Drymosphacesupporting

confidence: 92%

Chloroplast Genome of Salvia Sect. Drymosphace: Comparative and Phylogenetic Analysis

Geng

Xiang

et al. 2022

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Sect. Drymosphace is one of eight sections of Salvia subg. Glutinaria and includes 13 species and one dubious species that hold great economic value. Although the section is well supported, interspecific relationships remain unresolved. Moreover, most of this section’s plastome information remains unknown. In this study, we sequenced and assembled eight sect. Drymosphace plastomes and conducted comparative analyses within this section. The length of plastid genome sequences ranged from 151,330 bp to 151,614 bp, with 80 protein-coding, 30 tRNA, and four rRNA genes being annotated. The plastomes were found to be as conservative as other Lamiaceae species, showing high consistency and similarity in terms of gene content, order, and structure. Within the sect. Drymosphace, single-copy regions were more variable than IR regions, and the intergenic regions were more variable than the coding regions; nine hypervariable regions were detected, and some of them may be useful for the phylogenetic analysis of Salvia. The topologies inferred from all of the data sets indicated that sect. Drymosphace was monophyletic and that S. honania was sister to S. meiliensis. Compared to previous studies involving more sect. Drymosphace species, phylogenomic analyses can improve the phylogenetic resolution considerably.

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“…According to our findings, ndhD-psaC and rpl16-rps3 were found to be divergent hotspots in the cp genome of T. fargesii , and have also been reported in other studies on the plastome of Thalictrum ( Xiang et al., 2022 ). The same phenomenon has been witnessed for numerous other taxa such as Lagerstroemia and Adrinandra ( Cui et al., 2019 ; Dong et al., 2021 ; Nguyen et al., 2021 ; Ren et al., 2022 ; Yang et al., 2022 ). In addition, these mutational hotspots might aid researchers in studying population genetics and identifying Thalictrum species.…”

Section: Discussionsupporting

confidence: 71%

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

Chen,

Safiul Azam,

Akter

et al. 2024

Front. Plant Sci.

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IntroductionThalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety.MethodsThe present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussionThe cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium.ConclusionConsidering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.

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Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

Cited by 15 publications

References 115 publications

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Chloroplast Genome of Salvia Sect. Drymosphace: Comparative and Phylogenetic Analysis

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

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