The complete chloroplast genome sequence of a morphotype of <i>Goodyera schlechtendaliana</i> (Orchidaceae) with the column appendages

Oh, Sang‐Hun; Suh, Hwa Jung; Park, Jongsun; Kim, Yongsung; Kim, Sangtae

doi:10.1080/23802359.2018.1564390

Cited by 20 publications

(25 citation statements)

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“…In addition, only a few genetic differences have been explored [13], such as the chloroplast regions rps16, trnL-F, trnD-T, and nuclear ITS, but these markers were not able to give enough resolution to distinguish them all. In this context, chloroplast genomes are a valuable resource for phylogenies, and the study of their structure and content can provide clues for improving inter-and intraspecific studies, such as population biology [14], and even the discovery of new species [15]. The chloroplast genomes of most angiosperms have conserved quadripartite structure separated in Large and Small Single Copy regions (LSC and SSC, respectively) and two inverted repetitive regions (IRs) [16].…”

Section: Introductionmentioning

confidence: 99%

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

Silva

Pinheiro

Penha

et al. 2019

IJMS

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Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.

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Section: Introductionmentioning

confidence: 99%

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

Silva

Pinheiro

Penha

et al. 2019

IJMS

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“…Phylogenetic trees show that R. augusta is similar to R. rugosa with reasonable number of sequence varaitions ( Figure 1C). Chloroplast genome of candidate new species (Heo et al 2019;Kim et al 2019;Oh et al 2019)…”

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confidence: 99%

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae)

Kim¹,

Heo²,

Nam

et al. 2019

Mitochondrial DNA Part B

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Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989 bp long and has four subregions: 86,227 bp of large single copy (LSC) and 18,816 bp of small single copy (SSC) regions are separated by 25,793 bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.

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“…De novo assembly was performed using Velvet 1.2.10 (Zerbino and Birney 2008), and gap sequences were filled by SOAPGapCloser 1.12 (Zhao et al 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for genome annotation based on G. schlechtendaliana chloroplast genome (MK134679; Oh et al 2019).…”

Section: Goodyera; Chloroplast Genome; Goodyera Schlechtendaliana; Komentioning

confidence: 99%

The complete chloroplast genome sequence of Goodyera schlechtendaliana in Korea (Orchidaceae)

Suh

Park³

et al. 2019

Mitochondrial DNA Part B

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Goodyera schlechtendaliana is a common orchid species in East Asia, providing a case to study phylogeographic structure of understory plants in warm temperate forests. Here, we present the complete chloroplast genome of the Korean G. schlechtendaliana. Its length is 153,801 bp and it has four subregions; 82,683 bp of large-single-copy and 18,048 bp of small-single-copy regions are separated by 26,535 bp of inverted repeat regions, including 133 genes (86 protein-coding genes, eight rRNAs, and 39 tRNAs). Phylogenetic analyses suggest that the chloroplast genomic data should be useful in future phylogeographic and phylogenetic studies of Goodyera. ARTICLE HISTORY

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The complete chloroplast genome sequence of a morphotype of Goodyera schlechtendaliana (Orchidaceae) with the column appendages

Cited by 20 publications

References 4 publications

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae)

The complete chloroplast genome sequence of Goodyera schlechtendaliana in Korea (Orchidaceae)

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