The complete chloroplast genome sequence of <i>Tainia cordifolia</i> (Orchidaceae)

Zheng, Qing-Dong; Zhou, Jie; Ma, Shan-Hu; Chen, Ming-Kun; Xie, Tai-Xiang; Chen, Juan; Ai, Ye

doi:10.1080/23802359.2019.1693304

Cited by 3 publications

(1 citation statement)

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“…The high diversity of morphological characteristics such as vegetative and floral variations within Collabieae has made it difficult for systematists to infer their evolutionary relationships. Despite this, based on a revision by Chase (7), among the Collabieae tribe the chloroplast genome has been reported for several taxa, such as Calanthe (8)(9)(10)(11) and Tainia (12)(13)(14). Although the group has approximately 450-500 known species, scarce genomic data are available and there are few reports of taxonomic conflicts (9,15,16).…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae

Talkah,

Jasim,

Nordin

et al. 2023

Preprint

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The yellow–floweredSpathoglottis aurea(tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship betweenS. aureaand the geographically isolatedS. microchilinafrom Borneo that has encouraged further study of theS. aureapopulations, but the genomic resource forS. aureahas not yet been reported. The present study reports the first work to characterize a chloroplast genome among theSpathoglottisgenus. The complete chloroplast (cp) genome ofS. aureawas assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome ofS. aureais 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite chloroplast genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of theS. aureacp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed thatS. aureahas a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such asPhaiusandCephalantheropsis.

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Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae

Talkah,

Jasim,

Nordin

et al. 2023

Preprint

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The complete chloroplast genome of Chrysoglossum ornatum (Epidendroideae, Orchidaceae) and its phylogenetic analysis

Tan,

Yan,

et al. 2024

Mitochondrial DNA Part B

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Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae

Talkah,

Jasim,

Nordin

et al. 2024

PLoS ONE

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The yellow–flowered Spathoglottis aurea (tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship between S. aurea and the geographically isolated S. microchilina from Borneo that has encouraged further study of the S. aurea populations, but the genomic resource for S. aurea has not yet been reported. The present study reports the first work to characterize a chloroplast (cp) genome among the Spathoglottis genus. The complete cp genome of S. aurea was assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome of S. aurea is 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite cp genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of the S. aurea cp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed that S. aurea has a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such as Phaius and Cephalantheropsis.

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The complete chloroplast genome sequence of Tainia cordifolia (Orchidaceae)

Cited by 3 publications

References 6 publications

Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae

Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae

The complete chloroplast genome of Chrysoglossum ornatum (Epidendroideae, Orchidaceae) and its phylogenetic analysis

Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae

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