Complete plastid genome of <i>Rhododendron griersonianum</i>, a critically endangered plant with extremely small populations (PSESP) from southwest China

Liu, Detuan; Fu, Chao‐Nan; Yin, Ling-Juan; Ma, Yongpeng

doi:10.1080/23802359.2020.1800427

Cited by 5 publications

(6 citation statements)

References 9 publications

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“…Among them, the number of mononucleotide-repeat SSRs was 57, dinucleotide-repeat SSRs was 3, and trinucleotide-repeat SSRs was 2. Phylogenetic analysis revealed that genus Rhododendron was sister to genus Vaccinium and they were both highly supported as monophyletic, which agreed with previous phylogenetic studies (Shen et al 2019 ; Liu, Fu, et al 2020 ; Liu, Chen, et al 2020 ; Ma et al 2021 ). Within the genus Rhododendron , R. datiandingense was clearly separated from the other six Rhododendron species and shown in the basal position ( Figure 1 ).…”

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confidence: 89%

“…PhyloSuite is an integrated phylogenetic analysis platform. Our performance, which used it, included sequence alignment with MAFFT 7.313 (Katoh et al 2002 ), alignment trimming with trimAl 1.2 (Capella-Gutiérrez et al 2009 ), model selection with ModelFinder (Kalyaanamoorthy et al 2017 ), and maximum-likelihood phylogenetic inference with MrBayes 3.2.6 (Ronquist et al 2012 ) using Nymphaea thermarum and Oryza sativa as outgroup species (Liu, Fu, et al 2020 ).…”

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confidence: 99%

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The complete chloroplast genome of Rhododendron datiandingense (Ericaceae)

Wang

Feng

et al. 2021

Mitochondrial DNA Part B

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Rhododendron datiandingense is newly reported and endemic to China. The genome of R. datiandingense is 207,311 bp in length, including a large single-copy region of 190,689 bp and a small single-copy region of 2582 bp, a pair of inverted repeat regions (IRA) of 7020 bp each. The genome encodes 110 genes, comprising 77 protein-coding genes, four ribosomal RNA genes, and 29 transfer RNA genes. Repeat analysis revealed 62 simple sequence repeats (SSRs) in the genome. Phylogenetic analysis revealed that R. datiandingense is clearly separated from the other Rhododendron species and shown in the basal position.

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confidence: 89%

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confidence: 99%

The complete chloroplast genome of Rhododendron datiandingense (Ericaceae)

Wang

Feng

et al. 2021

Mitochondrial DNA Part B

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“…According to Liu et al and Kim et al, the GC content in the IR regions of two Ericaceae species (Rhododendron griersonianum Balf. f. & Forrest and Vaccinium oldhamii Miquel) is significantly lower than that of the other six species (Table 1) [48,49], which may lead to more variations in length and gene number in their chloroplast genomes than other species in Ericales. Table 1.…”

Section: Chloroplast Genome Featuresmentioning

confidence: 86%

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Ding

Dong

Yang

et al. 2021

Forests

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Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced and assembled the complete chloroplast genome of C. fargesii. We also analyzed the chloroplast genome features and compared them to Clethra delavayi and other closely related species in Ericales. The complete chloroplast genome is 157,486 bp in length, including a large single-copy (LSC) region of 87,034 bp and a small single-copy (SSC) region of 18,492 bp, separated by a pair of inverted repeat (IR) regions of 25,980 bp. The GC content of the whole genome is 37.3%, while those in LSC, SSC, and IR regions are 35.4%, 30.7%, and 43.0%, respectively. The chloroplast genome of C. fargesii encodes 132 genes in total, including 87 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. A total of 26,407 codons and 73 SSRs were identified in C. fargesii chloroplast genome. Additionally, we postulated and demonstrated that the structure of the chloroplast genome in Clethra species may present evolutionary conservation based on the comparative analysis of genome features and genome alignment among eight Ericales species. The low Pi values revealed evolutionary conservation based on the nucleotide diversity analysis of chloroplast genome in two Clethra species. The low selection pressure was shown by a few positively selected genes by adaptive evolution analysis using 80 coding sequences (CDSs) of the chloroplast genomes of two Clethra species. The phylogenetic tree showed that Clethraceae and Ericaceae are sister clades, which reconfirm the previous hypothesis that Clethra is highly conserved in the chloroplast genome using 75 CDSs of chloroplast genome among 40 species. The genome information and analysis results presented in this study are valuable for further study on the intraspecies identification, biogeographic analysis, and phylogenetic relationship in Clethraceae.

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“…The published Rhododendron spp. are as follows: R. pulchrum (MN182619, 146,941 bp), R. simsii (MW030509, 152,214 bp), R. delavayi (MN413198, 193,798 bp), R. mole (MZ073672, 197,877 bp), R. platypodum (MT985162, 201,047 bp), R. griersonianum (MT533181, 206,467 bp), R. datiandingense (MW381788, 207,311 bp), and R. kawakamii (MW762686, 230,777 bp) (Shen et al, 2020;Xu et al, 2021;Liu et al, 2020b;Liu et al, 2021;Ma et al, 2021;Liu et al, 2020a;Wang et al, 2021b;Wang et al, 2021a). Considering the numerous Rhododendron species, the cp genome data of Rhododendron spp.…”

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confidence: 99%