The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast

Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.

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Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

PeerJ ◽

10.7717/peerj.7210 ◽

2019 ◽

Vol 7 ◽

pp. e7210 ◽

Cited By ~ 6

Author(s):

Wan Zhang ◽

Yunlin Zhao ◽

Guiyan Yang ◽

Jiao Peng ◽

Shuwen Chen ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Evolutionary History ◽

Evolutionary Relationship ◽

Hainan Island ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Phylogenetic Studies ◽

Chloroplast Genome Sequence

Camellia oleiferais one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study usedC. oleiferathat was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies ofCamelliaplants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of HainanC. oleifera. The results showed that the whole chloroplast genome ofC. oleiferain Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of HainanC. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of HainanC. oleiferawere compared with mainlandC. oleiferaand those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of HainanC. oleifera, and allCamelliaplants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that HainanC. oleiferahad a similar evolutionary relationship withC. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.

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