Development of genomic resources for Wenchengia alternifolia (Lamiaceae) based on genome skimming data.
Development of genomic resources for Wenchengia alternifolia (Lamiaceae) based on genome skimming data.
复制标题
互叶文成藻基因组资源开发
DOI：
10.1016/j.pld.2021.09.006
复制
发表时间：
2022-11
期刊：
影响因子：
4.8
通讯作者：
Li, Pan
中科院分区：
文献类型：
--
作者：
Zhou, Qi-Yue;Cai, Hui-Xia;Liu, Zi-Han;Yuan, Lang-Xing;Yang, Lei;Yang, Tuo;Li, Bo;Li, Pan
四轮香（唇形科），四轮香属的唯一物种，极为罕见，目前在世界自然保护联盟濒危物种红色名录中被列为极危（CR）。该物种长期以来被认为是中国海南岛特有的，曾一度被认为已灭绝，直到2010年在模式产地重新发现了一小部分残余种群。后来在海南和越南又发现了另外四个种群。为了开发基因组资源，以便对这一珍稀物种进行种群遗传学和保护生物学的进一步研究，在本研究中，我们利用分别从海南岛两个种群和越南三个种群采集的五个个体的基因组浅层测序数据，鉴定了种下分子标记。这五个个体的质体基因组长度在152,961碱基对到150,204碱基对之间，呈现出典型的被子植物四分体结构。我们鉴定出6个核苷酸多样性（Pi）> 0.01的质体热点区域（trnH - psbA、psbA - trnK、rpl22、ndhE、ndhG - ndhI和rps15 - ycf1）、1621个多态性基因组简单序列重复（gSSR），以及237个变异核基因中的1657个候选单核苷酸多态性（SNP），从而为进一步的遗传学研究提供了重要信息。
四轮香处于极危状态，且曾一度被认为已灭绝。
鉴于其极高的保护优先级，我们基于五个现存种群（两个来自海南，三个来自越南）的基因组浅层测序数据开发了种下分子标记。
在四轮香中鉴定出6个质体热点区域、1621个多态性gSSR，以及237个变异核基因中的1657个候选SNP。
此处开发的大量基因组资源将有助于对该属进行保护遗传学和生物地理学的进一步研究。
Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies. Wenchengia alternifolia is critically endangered and was once believed to be extinct. Due to its high priority of conservation, we developed intraspecific molecular markers based on genome skimming data of the five extant populations (two from Hainan, three from Vietnam). Six plastid hotspot regions, 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes, were identified within W. alternifolia. The extensive genomic resources developed here will be useful for further studies on conservation genetics and biogeography of the genus.
登录
查看更多内容
影响因子：
2.4
作者：
Bae, Kyung-Mi;Sim, Sung-Chur;Kwon, Yong-Sham
通讯作者：
Kwon, Yong-Sham
影响因子：
1.3
作者：
Paton, Alan;Phillipson, Peter B.;Suddee, Somran
通讯作者：
Suddee, Somran
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
DOI：
10.1093/bioinformatics/bts199
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kearse M;Moir R;Wilson A;Stones-Havas S;Cheung M;Sturrock S;Buxton S;Cooper A;Markowitz S;Duran C;Thierer T;Ashton B;Meintjes P;Drummond A
通讯作者：
Drummond A