Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.
Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.
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DOI：
10.1093/sysbio/syv035
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发表时间：
2015-09
影响因子：
6.5
通讯作者：
Blattner FR
中科院分区：
文献类型：
--
作者：
Brassac J;Blattner FR
多倍化是大麦属重要的物种形成机制。为了分析异源多倍化后的进化变化，亲本关系的知识至关重要。通过聚合酶链式反应 (PCR)，在所有大麦属和 6 个外群物种中扩增了 1 个叶绿体和 12 个核单拷贝基因座。来自 96 个个体的扩增子被汇集、剪切、用个体特异性条形码标记，并在 454 平台上单次运行进行测序。通过对九个补充个体的所有基因座进行克隆和桑格测序获得参考序列。 454 个读数被组装成代表 13 个基因座的重叠群，对于多倍体，也代表同源体。分别对所有基因座和所有基因座的串联数据矩阵进行系统发育分析。对于二倍体类群，从所有基因树中推断出贝叶斯一致性分析和基于合并的约会物种树。叶绿体 matK 用于确定异源多倍体类群中的母本。还评估了在不完整谱系分选和杂交的情况下不同多位点分析的相对性能。由此产生的多位点系统发育首次揭示了单次分析中所有二倍体和多倍体大麦类群的物种系统发育和祖先衍生关系。我们的研究证明，通过将 PCR 与下一代测序相结合，可以获得二倍体和多倍体类群的多位点物种水平系统发育，而无需克隆，也无需创建大量序列数据。
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.