The complete chloroplast genome of <i>Rhododendron calophytum</i> Franch (Ericaceae)

Ma, Wenqi; Yu, Tao; Wang, Wanjiang; Wang, Fei; Ji, Huijuan; Chang-long, MU

doi:10.1080/23802359.2022.2106161

Cited by 3 publications

(2 citation statements)

References 8 publications

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“…This resulted in the chloroplast genome of R. calophytum Franch. (OM373082.1 (Ma et al ., 2022)) and R. shanii W.P. Fang (MW374796 (Yu et al ., 2022)) being the closest.…”

Section: Methodsmentioning

confidence: 99%

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

Worth,

Kikuchi,

Kanetani

et al. 2023

Preprint

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The Japanese subalpine zone is dominated by a distinct and ecologically important conifer rich forest biome, subalpine coniferous forests, that are an outlier of the extensive boreal forests of Eurasia. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small populations size effects. However, there is a severe lack of genetic resources available for the study of this biome’s major constituent plant species. This study aims to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species via genome skimming of whole genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled viade novo-based methods from 4-10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 to 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpumandVaccinium vitis-idaea) characterized by large chloroplast genomes,de novoassembly failed, but single nucleotide polymorphisms could be identified using reference mapping. This data will be useful for genetic studies of the taxonomic relationship of populations within Japan and to other parts of northeast Asia, investigating phylogeographic patterns within species, conservation genetics and has potential application for studies of environmental and ancient DNA.

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“…This resulted in the chloroplast genome of R. calophytum Franch. (OM373082.1 (Ma et al ., 2022)) and R. shanii W.P. Fang (MW374796 (Yu et al ., 2022)) being the closest.…”

Section: Methodsmentioning

confidence: 99%

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

Worth,

Kikuchi,

Kanetani

et al. 2023

Preprint

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“… 2021 ), Rhododendron calophytum NC061396 (Ma et al. 2022 ), Rhododendron huadingense NC063113 (An et al. 2022 ), Arbutus unedo JQ067650 (Fernando et al.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic relationship and characterization of the complete chloroplast genome of Rhododendron przewalskii subsp. przewalskii Maximowicz 1877, an ornamental and medicinal plant in China

Wang,

Tang,

Chen

et al. 2023

Mitochondrial DNA Part B

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As one of the top 10 famous flowers in Chinese tradition, Rhododendron przewalskii subsp. przewalskii known as ‘beauty in flowers,’ which has high ornamental and medicinal value. The complete chloroplast (cp) genome of R. przewalskii subsp. przewalskii was determined in this study. The complete chloroplast genome of R. przewalskii subsp. przewalskii was 201,233 bp in length and contained a large single-copy region (LSC, 108,077 bp), and a small single-copy region (SSC, 2624 bp) and a pair of inverted repeat regions (IRa and IRb, 45,266 bp). A total of 142 functional genes were observed in this cp genome, including 91 protein-coding genes (PCGs), 43 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The R. przewalskii subsp. przewalskii cp genome has an A + T content of 64.06% and presents a positive AT-skew (0.53%) and a negative GC-skew (−1.56%). The maximum likelihood phylogenetic analysis based on the concatenated nucleotide sequences of 13 PCGs strongly supported the monophyletic relationship of R. przewalskii subsp. przewalskii the clade of R. henanense subsp. lingbaoense . This study provides genomic evidence for the vegetation classification of Rhododendron .

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Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement

Rawat,

Jugran,

Sharma

2024

3 Biotech

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The complete chloroplast genome of Rhododendron calophytum Franch (Ericaceae)

Cited by 3 publications

References 8 publications

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

Chloroplast genome-based genetic resources for Japan’s threatened subalpine forests via genome skimming

Phylogenetic relationship and characterization of the complete chloroplast genome of Rhododendron przewalskii subsp. przewalskii Maximowicz 1877, an ornamental and medicinal plant in China

Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement

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