Complete chloroplast genome of <i>Vaccinium oldhamii</i> and phylogenetic analysis

Kim, Sang-Chul; Baek, Seung-Hoon; Lee, Jei-Wan; Hyun, Hwa Ja

doi:10.1080/23802359.2019.1579067

Cited by 14 publications

(18 citation statements)

References 5 publications

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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: 84%

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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Section: Chloroplast Genome Featuresmentioning

confidence: 84%

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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“…However, most of the reported conserved plastid genomes are usually 120-160 kb in length (Orton, Burke & Duvall, 2019;Twyford & Ness, 2017;Xue et al, 2019). In addition, ycf1, which is common in conserved plastid genomes, is missing from R. delavayi, and from other photosynthetic Ericaceae (Kim et al, 2019;Logacheva et al, 2016;Martinez-Alberola et al, 2013). Plastid sequences usually have a lower repeat rate than nuclear and mitochondrial genomes, especially for long repeats, and most of the short repeats are mononucleotide A/T (Marechal & Brisson, 2010;Twyford & Ness, 2017).…”

Section: Discussionmentioning

confidence: 99%

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

Guo

et al. 2020

PeerJ

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Background Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. Methods The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. Results The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.

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“…Compared with exclusively autotrophic Ericaceae species (photosynthetic, Vaccinieae and Rhododendron), the cp genomes of mycoheterotrophic species (nonphotosynthetic, Monotropeae) are substantially smaller in size (ca. 33-41 kb) and gene content [10,11,42]. The R. pulchrum cp genome was found to have 73 functional genes, 110 and 133 genes were annotated in those of Vaccinium macrocarpon and Vaccinium oldhamii, whereas 40-45 genes were annotated in species of Monotropeae respectively-suggesting that Ericaceae cp genomes are highly variable.…”

Section: Discussionmentioning

confidence: 99%

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Jia

Zhu

Huang

et al. 2020

Forests

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Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.

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Complete chloroplast genome of Vaccinium oldhamii and phylogenetic analysis

Cited by 14 publications

References 5 publications

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

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

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

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