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6种君子兰叶绿体基因组比较分析
Comparative analysis of chloroplast genomes of six species of Clivia
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摘要: 为理解君子兰叶绿体全基因组的基本特征，开发种质资源利用分析的分子标记，选取了6种君子兰属植物为研究对象，进行了叶绿体基因组的精细拼接和高效组装，以及全面的基因注释。结果表明：花园、黄花、彩叶、沼泽、有茎和大花君子兰的叶绿体基因组长度分别为158 156、158 112、157 689、157 130、157 130、158 149 bp和158 114 bp，分别注释了130、130、133、128、128、133个基因。在花园、黄花、彩叶、沼泽、有茎和大花君子兰的叶绿体基因组中分别鉴定出54、60、61、63、71个和61个简单重复序列（SSRs）。在编码区中，ycf4-cemA基因的核苷酸多样性值最高（Pi=
0.0152 ），以及rrn23基因的核苷酸多样性值大于0.0100 ，可视为多样性较高的基因。Rpl22基因在LSC（大单拷贝区）与IRb（反向重复区b）的交界处，6个种间仅存在1 bp的差异。ndhF基因跨越了IRb与SSC的边界区域，它们的序列差异仅有6 bp。其中花园君子兰、沼泽君子兰和有茎君子兰相同，而另外3种大花君子兰、黄花君子兰和彩叶君子兰相同，观察到2个差异性较大的基因（rpoC2和ycf2）和8个高变区（rps19-psbA、rps16-trnS-GCU、atpF-atpH、trnT-UGU-trnF-GAA、rps2–rpoC2、petA-psbL、trnI-CAU-ycf2、rps12-rrn16）。通过君子兰叶绿体基因组比较，可以利用差异性较大的基因和高变区域，以开发出具有高度特异性的分子标记。Abstract: In order to understand the basic features of the whole chloroplast genome of Clivia and to develop molecular markers for germplasm utilization analysis, the data obtained were finely spliced and efficiently assembled. The acquired data were subjected to fine splicing and efficient assembly of the chloroplast genome and comprehensive gene annotation. The results were as follows:(1) The chloroplast genome lengths of C. gardenii, C. miniata var.citrina, C. miniata var. Variegata, C. robusta, C. caulescens and C. miniata were 158 156, 158 112, 157 689, 157 130, 157 130, 158 149, and 158 114 bp, respectively. 130, 130, 133, 128, 128, and 133 genes were annotated, respectively.(2) 54, 60, 61, 63, 71, and 61 SSRs were identified in the chloroplast genomes of C. gardenii, C. miniata var.citrina, C. miniata var. Variegata, C. robusta, C. caulescens and C. miniata, respectively.(3) Among the coding regions, the ycf4-cemA gene had the highest nucleotide diversity value(Pi=0.0152 ), as well as the rrn23 gene, which had a nucleotide diversity value greater than0.0100 and can be considered as genes with higher diversity.(4) The Rpl22 gene is located at the junction between the LSC(Large Single Copy region) and IRb(Inverted Repeat region b), with a difference of only 1 bp among 6 species. Specifically, the ndhF gene spans the border region between the IRb and the SSC and is only 6 bp different in sequence among these species. Among them, C. gardenii, C. robusta, C. caulescens are the same, while the other three species of C. miniata, C. miniata var. citrina, and C. miniata var. variegata are the same.(5) Two highly differentiated genes(rpoC2 and ycf2) and eight highly variable regions(rps19-psbA, rps16-trnS-GCU, atpF-atpH, trnT-UGU-trnF-GAA, rps2-rpoC2, petA-psbL, trnI-CAU- ycf2, rps12-rrn16). Comparative analysis of the monarch chloroplast genome allows for the utilization of highly divergent genes and highly variable regions in order to develop highly specific molecular markers that can be implemented for precise species identification and in-depth phylogenetic exploration.
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