Tian Shoubo, Lu Panling, Zhang Zhaohui, Wu Jian Qiang, Zhang Hui, Shen Haibin
Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
Nanjing Agricultural University, NanJing, 210095, China.
BMC Genomics. 2021 Mar 18;22(1):194. doi: 10.1186/s12864-021-07467-8.
Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited.
The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. lunatus Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found significant variation, the intergenic regions of trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11-rsp19, ndhF-ccsA was found in a high degree of divergence. A phylogenetic analysis showed that P. lunatus appears to be more closely related to P. vulgaris, V.unguiculata and V. radiata.
The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research.
利马豆（Phaseolus lunatus L.）是豆科菜豆亚科的成员，是人类饮食中植物蛋白的重要来源。众所周知，利马豆具有重要的经济价值和丰富的多样性。然而，我们对利马豆叶绿体基因组水平的了解有限。
首次通过Illumina测序技术获得了利马豆的叶绿体基因组。该叶绿体基因组长度为150,902 bp，包括一对反向重复序列（IRA和IRB各26,543 bp）、一个大单拷贝区（LSC 80,218 bp）和一个小单拷贝区（SSC 17,598 bp）。在利马豆叶绿体基因组中总共鉴定出124个独特基因，包括82个蛋白质编码基因、34个tRNA基因和8个rRNA基因。在利马豆叶绿体基因组中总共检测到61个长重复序列和290个简单序列重复（SSR）。它具有豆科植物典型的50 kb倒位以及与菜豆亚族相关的70 kb倒位。发现编码区的rpl16、accD、petB、rsp16、clpP、ndhA、ndhF和ycf1基因存在显著变异，trnk-rbcL、rbcL-atpB、ndhJ-rps4、psbD-rpoB、atpI-atpA、atpA-accD、accD-psbJ、psbE-psbB、rsp11-rsp19、ndhF-ccsA的基因间隔区存在高度差异。系统发育分析表明，利马豆似乎与普通菜豆、豇豆和绿豆关系更密切。
首次鉴定了利马豆叶绿体基因组的特征，这些结果将为物种鉴定、进化研究和分子生物学研究提供有用的见解。
