Grogan Kathleen E, McGinnis Gwendolyn J, Sauther Michelle L, Cuozzo Frank P, Drea Christine M
University Program in Ecology, Duke University, Durham, NC, USA.
Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.
BMC Genomics. 2016 Mar 8;17:204. doi: 10.1186/s12864-016-2503-y.
Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes.
In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1-7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies.
In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species.
在所有物种中，主要组织相容性复合体（MHC）的多样性对于抗病能力和种群健康至关重要；然而，MHC基因中发现的极端变异阻碍了利用MHC多样性来量化种群的遗传健康状况。新一代测序（NGS）技术能够产生足够的数据来对即使是多样性最高的物种进行基因分型，但区分人工产物和等位基因的工作流程仍在开发中。我们使用NGS评估了300多只圈养和野生环尾狐猴（狐猴属：灵长目：哺乳纲）的MHC多样性。我们修改了已发表的工作流程以解决深度测序个体时出现的错误，并测试了在多样性最高的MHC基因上的选择证据。
除了评估454 Titanium和Ion Torrent PGM对高变基因进行大群体基因分型的准确性外，我们还提出了改进当前等位基因分型方法的修改建议。使用这些修改，我们对319只个体中的302只进行了基因分型，每个扩增子的平均测序深度超过1000次读取。我们鉴定出55个MHC-DRB等位基因，其中51个是先前未描述的，并提供了另外五个MHC基因的首个序列：DOA、DOB、DPA、DQA和DRA。另外五个MHC基因每个都有一两个等位基因，序列变异很少；然而，55个MHC-DRB等位基因显示出高dN/dS比率和跨物种多态性，表明存在正选择历史。由于每个个体拥有1-7个MHC-DRB等位基因，我们认为环尾狐猴有四个假定具有功能的MHC-DRB拷贝。
未来，针对NGS数据的准确基因分型方法对于评估非模式物种的遗传变异至关重要。我们建议未来的NGS研究增加重复样本的比例，包括在平台内和跨平台，特别是对于像MHC这样的高变基因。量化非模式物种内的MHC多样性是评估功能位点的遗传多样性与个体适应性和种群生存力之间关系的第一步。由于MHC-DRB的多样性和拷贝数，环尾狐猴可能是估计遗传多样性、适应性和环境之间相互作用的理想模型，特别是对于濒危物种。
Zotero 插件
