Comparative Chloroplast Genomics and Phylogenetic Analysis of Thuniopsis and Closely Related Genera within Coelogyninae (Orchidaceae)

Li, Lin; Wu, Qiuping; Fang, Lin; Wu, Kunlin; Li, Mingzhi; Zeng, Songjun

doi:10.3389/fgene.2022.850201

Cited by 16 publications

(32 citation statements)

References 41 publications

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“…We compared the CPGs of six species within the subgenus Gynopodium . The results indicated that the SSC and LSC regions were more divergent than IR regions, and sequences in non-coding regions were more divergent than that in coding regions, which were consistent with previous findings in Magnolia species [ 29 ] and other flowering plants [ 42 , 43 ] In this study, we identified six regions presenting significant variations in the CPGs of subgenus Gynopodium species, such as five intergenic regions: trnH - psbA , rps2 - rpoC2 , ycf4 - cemA , petA - psbJ , and ccsA - ndhD , and one gene ycf1 (Fig. 2 ).…”

Section: Discussionsupporting

confidence: 91%

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Xie

Zhang

et al. 2022

BMC Genomics

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Background The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. Results The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). Conclusion The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

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Section: Discussionsupporting

confidence: 91%

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Xie

Zhang

et al. 2022

BMC Genomics

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“…Unsurprisingly, sequence variations mainly occurred within the non-coding regions and located predominantly in the intergenic spacer regions (IGS). Similar results have been shown in other chloroplast genomes of angiosperms [17,29].…”

Section: Plastome Polymorphisms and Mutation Hotspots Of Pholidotasupporting

confidence: 90%

“…Pleione bulbocodioides and P. pleionoides (Accession Nos. NC036342 and MK810725) were included as outgroups based on previous study [17]. All the genome sequences were aligned using MAFFT v7.313 [53] and adjusted manually by BioEdit [54].…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes

Wang

Zhang³

et al. 2022

Preprint

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Background The orchid genus Pholidota Lindl. ex Hook. is ecologically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, the taxonomy of Pholidota remains controversial and only limited genomic information has been available. In this study, the complete chloroplast (cp) genomes of thirteen Pholidota species were sequenced and analyzed to gain insight into the phylogeny of Pholidota and mutation patterns in their cp genomes. Results All examined thirteen Pholidota cp genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genome studies. Phylogenetic analyses confirm that the genus Pholidota is polyphyletic, with species grouped into four main clades: Pholidota s.s. was well-supported as the sister to a clade comprising two members of Coelogyne; the other two clades clustered together with species of Bulleyia and Panisea, respectively; species P. ventricosa was placed at basal position, deviated from those three clades. Conclusion This is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution of Pholidota based on plastid genome data. These findings contribute to a better understanding of plastid genome evolution of Pholidota and provide new insights into the phylogeny of Pholidota and its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.

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“…This is consistent with the codon preference of other genera in the Orchidaceae, such as Thuniopsis and Polystachya. (Jiang et al, 2022;Li et al, 2022). Contraction and expansion of the IR region is usually observed in most angiosperms (Li et al, 2019), including Renanthera.…”

Section: Discussionmentioning

confidence: 99%

“…This is consistent with the codon preference of other genera in the Orchidaceae, such as Thuniopsis and Polystachya . ( Jiang et al, 2022 ; Li et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Xiao

Zhang

et al. 2022

Front. Genet.

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Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design and in landscape gardens. Two species of Renanthera are categorized as endangered and critically endangered in China’s Red List and international trade in these orchids is currently strictly monitored by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). This paper reports on the de novo assembled and annotated plastome of four species of Renanthera; R. citrina, R. coccinea, R. imschootiana, and R. philippinensis. The length of the plastome sequences ranged from 144,673 bp (R. imschootiana) to 149,007 bp (R. coccinea) with GC content of 36.6–36.7%. The plastomes showed a typical quadripartite structure, including a large single-copy (84,241–86,404 bp), a small single-copy (11,468–12,167 bp), and a pair of inverted repeats (24,482–25,715 bp) regions. Of the 120 genes detected, 74 were protein coding, 38 were tRNA, and eight were rRNA genes. The plastome of Renanthera is rather conserved, but nucleotide variations that could distinguish them apart are noticeable—the total number of tandem repeats ranged from 62 (in R. imschootiana) to 74 (in R. citrina); while the number of long repeats ranged from 21 (in R. imschootiana and R. philippinensis) to 43 (in R. citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) were identified. Phylogenetic analyses based on the CDS using maximum likelihood (ML) and Bayesian inference (BI) revealed that Renanthera is closely related to Holcoglossum, Neofinetia, Pendulorchis, and Vanda. The relationship between the four species of Renanthera was fully resolved; a monophyletic clade was formed and R. coccinea was recorded as the first to diverge from the rest. The genetic data obtained from this study could serve as a useful resource for species identification in Renanthera as well as contribute to future research on the phylogenomics of Orchidaceae.

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Comparative Chloroplast Genomics and Phylogenetic Analysis of Thuniopsis and Closely Related Genera within Coelogyninae (Orchidaceae)

Cited by 16 publications

References 41 publications

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

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