Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering.
Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering.
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DOI：
10.1155/2014/675158
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发表时间：
2014
影响因子：
--
通讯作者：
Hare MP
中科院分区：
文献类型：
--
作者：
Ilut DC;Nydam ML;Hare MP
下一代测序在非模式物种的野生种群中应用地理学、景观遗传学和种群基因组学方面有很大的希望，但推断的鲁棒性取决于仔细的实验设计和有效的生物信息学去除可预测的伪影。为了解决这个问题，我们使用已发表的基因组从被囊动物，刺鱼，和大豆来说明生物信息学文物的潜力，并引入一个协议，以尽量减少两个来源的错误预期从相似性为基础的从头聚类的堆叠读取：分裂的等位基因到不同的集群，这会产生假纯合性，和分组的旁系同源到同一个集群，这会产生假杂合性。我们提出了一个经验的应用程序，重点是玻璃海鞘，具有非常高的SNP杂合性（~0.05），因为高多样性的挑战，大多数现有的非模型管道的计算效率，同时也可能加剧parabolic文物的被囊动物。模拟和经验数据说明了使用更高的序列差异聚类阈值比典型的优势，并证明了我们的协议的效用，有效地确定一个最佳的阈值，从数据中没有杂合性的先验知识。经验的玻璃海鞘数据还突出了空等位基因作为基于限制的简化代表性基因组数据中假纯合性的潜在大来源。
Next generation sequencing holds great promise for applications of phylogeography, landscape genetics, and population genomics in wild populations of nonmodel species, but the robustness of inferences hinges on careful experimental design and effective bioinformatic removal of predictable artifacts. Addressing this issue, we use published genomes from a tunicate, stickleback, and soybean to illustrate the potential for bioinformatic artifacts and introduce a protocol to minimize two sources of error expected from similarity-based de-novo clustering of stacked reads: the splitting of alleles into different clusters, which creates false homozygosity, and the grouping of paralogs into the same cluster, which creates false heterozygosity. We present an empirical application focused on Ciona savignyi, a tunicate with very high SNP heterozygosity (~0.05), because high diversity challenges the computational efficiency of most existing nonmodel pipelines while also potentially exacerbating paralog artifacts. The simulated and empirical data illustrate the advantages of using higher sequence difference clustering thresholds than is typical and demonstrate the utility of our protocol for efficiently identifying an optimum threshold from data without prior knowledge of heterozygosity. The empirical Ciona savignyi data also highlight null alleles as a potentially large source of false homozygosity in restriction-based reduced representation genomic data.
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影响因子：
7
作者：
Swigonov치, Z;Lai, JS;Messing, J
通讯作者：
Messing, J
影响因子：
3.7
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3.7
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作者：
Bao, Ergude;Jiang, Tao;Girke, Thomas
通讯作者：
Girke, Thomas
影响因子：
64.8
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Jones, Felicity C.;Grabherr, Manfred G.;Chan, Yingguang Frank;Russell, Pamela;Mauceli, Evan;Johnson, Jeremy;Swofford, Ross;Pirun, Mono;Zody, Michael C.;White, Simon;Birney, Ewan;Searle, Stephen;Schmutz, Jeremy;Grimwood, Jane;Dickson, Mark C.;Myers, Richard M.;Miller, Craig T.;Summers, Brian R.;Knecht, Anne K.;Brady, Shannon D.;Zhang, Haili;Pollen, Alex A.;Howes, Timothy;Amemiya, Chris;Lander, Eric S.;Di Palma, Federica;Lindblad-Toh, Kerstin;Kingsley, David M.
通讯作者：
Kingsley, David M.