Plastid Genome Evolution in the Subtribe Calypsoinae (Epidendroideae, Orchidaceae)

Zhang-hai, LI; Jiang, Yan; Ma, Xiao; Li, Jianwu; Yang, Jun‐Bo; Wu, Jiang; Jin, Xiao‐Hua

doi:10.1093/gbe/evaa091

Cited by 23 publications

(30 citation statements)

References 26 publications

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“…The monograph indicated that the mentum is one of the characters to distinguish C. striata and other congeneric species ( Freudenstein, 1997 ), thus the character presents a possible synapomorphy for the clade. Our phylogenetic result is consistent with the previous studies ( Kim et al., 2020 ; Li et al., 2020 ), that Corallorhiza is not a monophyletic group, because the genus Oreorchis is nested within the clade of Corallorhiza with strong bootstrap support (BS = 100) and posterior probability (PP = 1.00). In the Calypsoinae, however, phylogenetic analysis based on the nrDNA sequence suggests that Corallorhiza is a monophyletic group and strongly supports C. sinensis as sister to Corallorhiza (ML: BS = 98; BI: PP = 1.00).…”

Section: Discussionsupporting

confidence: 92%

“…A total of 109 unique genes were identified in the plastome, which contains 68 protein-coding genes, 30 tRNAs, and four rRNAs. C. sinensis further shows evidence of some photosynthesis-related genes either lost or pseudogenized, which is consistent with some previous studies of Corallorhiza ( Barrett and Davis, 2012 ; Kim et al., 2020 ; Li et al., 2020 ). In the current study, a common feature of the plastome of Corallorhiza and Oreorchis species was that IR regions were more conserved than the LSC and SSC regions .…”

Section: Discussionsupporting

confidence: 91%

“…An earlier study based upon combined ITS, plastid datasets, and morphological character matrix strongly support Oreorchis and Corallorhiza are both monophyletic groups, but the Corallorhiza is far from Oreorchis ( Zhai et al., 2013 ). In recent molecular phylogenetic studies based on the plastomes, however, Corallorhiza is still non-monophyletic, and the Oreorchis and Corallorhiza were nested together and formed a single clade ( Kim et al., 2020 ; Li et al., 2020 ). In the taxonomic revision of Oreorchis ( Pearce and Cribb, 1997 ), except for Kitigorchis itoana , the remaining species of Kitigorchis were transferred into Oreorchis .…”

Section: Introductionmentioning

confidence: 99%

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Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

et al. 2021

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Corallorhiza sinensis , a new species of mycoheterotrophic orchid from western Sichuan, China, is described and illustrated based on molecular and morphological evidence. It is morphologically similar to Corallorhiza trifida , but can be distinguished by bigger flowers, both sepals and petals with 3 veins, and longer lateral lobes of lip. To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae, this study employed sequences of the nuclear ribosomal DNA (nrDNA) and whole plastome assembled from the genome skimming approach. The plastome is 148,124 bp in length, including a pair of inverted repeats (IRs) of 26,165 bp, a large single-copy region (LSC) of 82,207 bp, and a small single-copy region (SSC) of 13,587 bp. Further, phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences (CDSs) from 26 complete plastomes of subtribe Calypsoinae. The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group, and strongly support C. sinensis as sister to the rest species of Corallorhiza . The plastid tree showed that 10 Corallorhiza species grouped into two clades and C. sinensis is most closely related to the North American C . striata and C. bentleyi instead of Oreorchis foliosa and O . angustata in the same clade. The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic. Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C. sinensis , it is still the most closely related to Corallorhiza . Comparative analysis showed that C. sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis . The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza .

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

et al. 2021

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“…(2020a) , for example, utilized the chloroplast genomes of 124 species of orchids to evaluate the phylogenomics and relationship within the Orchidaceae family. Moreover, the whole cp genome phylogeny that was generated at different taxonomical level in several groups of Orchidaceae, such as subtribe Aeridinae ( Kim et al., 2020b ), subtribe Calypsoinae ( Li et al., 2020 ), and Holcogloss um ( Li et al., 2019 ). Considering that most species-level diversity of Orchidaceae, a whole cp genome phylogeny is highly desired for Bulbophyllum .…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Tang

Shao

et al. 2021

Plant Diversity

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Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia . The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum . All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum . Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum . The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.

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“…Paired-end sequencing (100-bp read lengths) was performed on an Illumina HiSeq 2500 platform at Majorbio in Beijing, which generated 5 GB of raw data. We assembled the plastome according to previously described methods ( Feng et al., 2016 ; Li et al., 2020a , Li et al., 2020b ). The filtered paired reads were mapped to the plastome of G. elata (GenBank accession number: MF163256 ) using Geneious v.10.1.2.…”

Section: Methodsmentioning

confidence: 99%

New taxa of tribe Gastrodieae (Epidendroideae, Orchidaceae) from Yunnan, China and its conservation implication

Liu

et al. 2021

Plant Diversity

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Gastrodia longistyla , a new species of Orchidaceae from Yunnan Province, China, is described and illustrated. It is morphologically similar to Gastrodia peichatieniana , but can be easily distinguished from the latter by having a rhombic epichile, long column (6.0–7.5 mm long), and a needle-shaped appendage (1.8–3.2 mm in length) at the base of the stigma. Identification key and colour photographs are provided. A preliminary risk-of-extinction assessment, according to the IUCN Red List Categories and Criteria, is given for the new species. The plastome of G. longistyla is 30464 bp in length with GC content approximately 24.8%, and the plastome does not contain some housekeeping genes, such as mat K, rpl16 , or all photosynthesis genes. In addition, the G. longistyla plastome lacks an IR region. This indicates that the plastome is in the last stage of degradation.

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Plastid Genome Evolution in the Subtribe Calypsoinae (Epidendroideae, Orchidaceae)

Cited by 23 publications

References 26 publications

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

New taxa of tribe Gastrodieae (Epidendroideae, Orchidaceae) from Yunnan, China and its conservation implication

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