Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
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四种马蹄莲叶绿体基因组的比较分析：IR 区域的扩展和收缩、系统发育分析和 SSR 遗传多样性评估
DOI：
10.7717/peerj.9132
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发表时间：
2020-05-22
期刊：
影响因子：
2.7
通讯作者：
Wu, Hongzhi
中科院分区：
文献类型：
--
作者：
He, Shuilian;Yang, Yang;Wu, Hongzhi
马蹄莲属（天南星科）由8种多年生草本植物组成。本文对四种花椒属植物（Z. aethiopica、Z. odorata、Z. elliottiana和Z. rehmannii）的叶绿体基因组进行了测序、组装和分析，探讨了花椒属植物叶绿体基因组的结构。根据我们的研究结果，Zantedeschia的cp基因组大小在169,065 bp （Z. aethiopica）到175,906 bp （Z. elliottiana）之间。共鉴定出112个独特基因，包括78个蛋白质编码基因、30个转移RNA （tRNA）基因和4个核糖体RNA （rRNA）基因。与天南星科其他物种cp基因组的比较表明，马蹄莲cp基因组相对较大的大小可能是由于反向重复序列（IR）区域扩展所致。在我们的系统发育分析中，采样的花篮属植物形成了一个单系统发育的分支。此外，马蹄莲属植物的长单拷贝区（LSC）和短单拷贝区（SSC）差异大于同属植物的IR区，非编码区差异普遍高于编码区。共鉴定出410个cpSSR位点。基于对134个马蹄莲品种4个多态性SSR标记的遗传多样性分析表明，马蹄莲品种具有较高的遗传多样性（I = 0.934; Ne = 2.371）。cpSSR区域具有较高的遗传多态性，表明cpSSR可作为马蹄莲品种遗传多样性评价和鉴定的有效工具。
The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.