Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
复制标题
全球红豆杉 (红豆杉) 中异构质体的普遍性和质体超级条形码的有效性
DOI：
10.1038/s41598-019-39161-x
复制
发表时间：
2019-02-26
影响因子：
4.6
通讯作者：
Gao, Lian-Ming
中科院分区：
文献类型：
--
作者：
Fu, Chao-Nan;Wu, Chung-Shien;Gao, Lian-Ming
红豆杉是红豆杉科中种类最丰富、分类最困难的属。到目前为止，还没有研究阐明质体基因组（质体组）的复杂性，或者研究整个质体作为全世界红豆杉物种的超级条形码的可能性。在这项研究中，我们测序了16个公认的红豆杉物种（包括三个潜在的密码子）和白的两到三个人的质体。我们的比较分析发现了几个基因丢失事件，独立发生在红豆杉，导致较低的质体基因数比其他红豆杉属。在红豆杉属和红豆杉属中，我们发现了两种异构体排列，它们的不同之处在于侧翼为“trnQ-IR”的35 kb片段的方向。这两种安排存在于不同的比例在每个采样的个人，和种内移位的主要异构体的安排首次在这里报道的红豆杉。此外，我们证明，整个塑性体可以用来成功地区分所有红豆杉物种与100%的支持，这表明他们是有用的超级条形码物种识别。我们还建议accD和rrn 16-rrn 23是有希望的特殊条形码，以区分红豆杉物种。我们新开发的红豆杉质体组序列为几种濒危红豆杉的超级条形码和保护遗传学提供了资源，并作为全面的数据，以改善整个红豆杉科的质体组复杂性模型和鉴定红豆杉物种。
Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by “trnQ-IRs”. These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate Taxus species.