Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae)

Liu, Ding-Kun; Tu, Xiong-De; Zhao, Zhuang; Zeng, Meng-Yao; Zhang, Sai; Ma, Liang; Zhang, Guoqiang; Wang, Miaomiao; Liu, Zhong‐Jian; Lan, Siren; Li, Minghe; Chen, Shi-Pin

doi:10.1016/j.ympev.2019.106729

Cited by 44 publications

(56 citation statements)

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“…The chloroplast (cp) genome is one of the three DNA genomes (with nuclear and mitochondrial genomes) in plants with a relatively conserved quadripartite circular structure ranging from 115 to 165 kb [23,24]. Because of their relatively stable genome structure, the complete cp genome sequences have been widely accepted to provide a valuable and informative data source for understanding evolutionary biology and have become a powerful tool for resolving plant phylogenies [24][25][26][27][28][29][30][31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

et al. 2021

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Background Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity. Results In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836–34,706 bp) separated by a large single-copy region (LSC: 76,657–103,161 bp) and a small single-copy region (SSC: 17,433–21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum. Conclusions Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

et al. 2021

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“…J.J.Sm., Vanda undulata Lindl. ; Liu et al, 2020). This was done to maintain the genus Vandopsis Pfitzer monophyletic.…”

Section: Introductionmentioning

confidence: 99%

“…Morphological characteristics of Cymbilabia are similar to those of Vandopsis with respect to the monopodial habit, distichous leaves, resupinate flowers and 3-lobed lip. However, the genus is differentiated from the latter by its less branching stem, verrucose basal sheaths and subovate to triangular labellum side lobes (Liu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Cymbilabia sourioudongii (Orchidaceae), a new species from Lao PDR Souvannakhoummane

S.¹,

Rakthai²,

Kumar³

et al. 2021

Rheedea

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“…japonicum by GENEIOUS v11.1.5 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al 2012). According to Zou et al (2015) and Liu et al (2020), a matrix of 18 representative species of Aeridinae and three outgroup species (Calanthe triplicata, C. davidii and Cattleya crispata) were aligned using MAFFT v7.307 (Katoh and Standley 2013). The phylogenetic tree was constructed by the maximum likelihood software IQ-TREE (Nguyen et al 2015) based on the complete plastid genomes, and branch supports with the ultrafast bootstrap (Hoang et al 2018).…”

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confidence: 99%

The complete plastid genome of Thrixspermum centipeda (Orchidaceae, Aeridinae)

Chi

Liu

Zhou

et al. 2021

Mitochondrial DNA Part B

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The complete plastid genome of the type species of Thrixspermum, Th. centipeda, was determined and analyzed in this work. The plastome was 147,888 bp in length with 85,899 bp of the large single-copy (LSC) region, 11,055 bp of the small single-copy (SSC) region and 25,467 bp of the invert repeats (IR) regions. The genome contained 120 genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis divided 18 Aeridinae plastomes into four groups, and Th. centipeda was sister to Th. tsii.

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Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae)

Cited by 44 publications

References 51 publications

Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

Cymbilabia sourioudongii (Orchidaceae), a new species from Lao PDR Souvannakhoummane

The complete plastid genome of Thrixspermum centipeda (Orchidaceae, Aeridinae)

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