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The complete chloroplast genome sequence of watercress (Nasturtium officinale R. Br.): Genome organization, adaptive evolution and phylogenetic relationships in Cardamineae

文献类型： 外文期刊

作者： Yan, Chao 1 ; Du, Jianchang 2 ; Gao, Lu 1 ; Li, Ying 1 ; Hou, Xilin 1 ;

作者机构： 1.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, Key Lab Biol & Genet Improvement Hort Crops East, Minist Agr & Rural Affairs PR China, Nanjing 210095, Jiangsu, Peoples R China

2.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Jiangsu, Peoples R China

关键词： Nasturtium officinale R. Br.; Chloroplast genome; Genomic structure; Comparative analysis; Phylogeny

期刊名称：GENE （ 影响因子：3.688； 五年影响因子：3.329 ）

ISSN： 0378-1119

年卷期： 2019 年 699 卷

页码：

收录情况： SCI

摘要： Watercress (Nasturtium officinale R. Br.), an aquatic leafy vegetable of the Brassicaceae family, is known as a nutritional powerhouse. Here, we de novo sequenced and assembled the complete chloroplast (cp) genome of watercress based on combined PacBio and Illumina data. The cp genome is 155,106 bp in length, exhibiting a typical quadripartite structure including a pair of inverted repeats (IRA and IRB) of 26,505 bp separated by a large single copy (SSC) region of 84,265 bp and a small single copy (SSC) region of 17,831 bp. The genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNAs and 4 rRNAs, with 20 duplicate in the IRs. Compared with the prior cp genome of watercress deposited in GenBank, 21 single nucleotide polymorphisms (SNPs) and 27 indels were identified, mainly located in noncoding sequences. A total of 49 repeat structures and 71 simple sequence repeats (SSRs) were detected. Codon usage showed a bias for A/T-ending codons in the cp genome of watercress. Moreover, 45 RNA editing sites were predicted in 16 genes, all for C-to-U transitions. A comparative plastome study with Cardamineae species revealed a conserved gene order and high similarity of protein-coding sequences. Analysis of the Ka/Ks ratios of Cardamineae suggested positive selection exerted on the ycf2 gene in watercress, which might reflect specific adaptations of watercress to its particular living environment. Phylogenetic analyses based on complete cp genomes and common protein-coding genes from 56 species showed that the genus Nasturtium was a sister to Cardamine in the Cardamineae tribe. Our study provides valuable resources for future evolution, population genetics and molecular biology studies of water-cress.

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