College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, China.
Sci Rep. 2020 Sep 25;10(1):15799. doi: 10.1038/s41598-020-72769-y.
The chloroplast genome is an integral part of plant genomes in a species along with nuclear and mitochondrial genomes, contributing to adaptation, diversification, and evolution of plant lineages. In the family Caricaceae, only the Carica papaya chloroplast genome and its nuclear and mitochondrial genomes were sequenced, and no chloroplast genome-wide comparison across genera was conducted. Here, we sequenced and assembled the chloroplast genome of Vasconcellea pubescens A.DC. using Oxford Nanopore Technology. The size of the genome is 158,712 bp, smaller than 160,100 bp of the C. papaya chloroplast genome. And two structural haplotypes, LSC_IRa_SSCrc_IRb and LSC_IRa_SSC_IRb, were identified in both V. pubescens and C. papaya chloroplast genomes. The insertion-deletion mutations may play an important role in Ycf1 gene evolution in family Caricaceae. Ycf2 is the only one gene positively selected in the V. pubescens chloroplast genome. In the C. papaya chloroplast genome, there are 46 RNA editing loci with an average RNA editing efficiency of 63%. These findings will improve our understanding of the genomes of these two crops in the family Caricaceae and will contribute to crop improvement.
叶绿体基因组是物种基因组的一个组成部分，与核基因组和线粒体基因组一起，有助于植物谱系的适应、多样化和进化。在 Caricaceae 科中，仅对 Carica papaya 叶绿体基因组及其核基因组和线粒体基因组进行了测序，而没有对属间的叶绿体基因组进行全基因组比较。在这里，我们使用 Oxford Nanopore Technology 对 Vasconcellea pubescens A.DC. 的叶绿体基因组进行了测序和组装。基因组大小为 158712bp，小于 C. papaya 叶绿体基因组的 160100bp。在 V. pubescens 和 C. papaya 叶绿体基因组中均鉴定出两种结构单倍型，LSC_IRa_SSCrc_IRb 和 LSC_IRa_SSC_IRb。插入缺失突变可能在 Caricaceae 科的 Ycf1 基因进化中发挥重要作用。Ycf2 是 V. pubescens 叶绿体基因组中唯一受到正选择的基因。在 C. papaya 叶绿体基因组中，有 46 个 RNA 编辑位点，平均 RNA 编辑效率为 63%。这些发现将提高我们对这两种 Caricaceae 科作物基因组的理解，并有助于作物改良。
