Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea).
Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea).
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DOI：
10.1093/molbev/msu154
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发表时间：
2014-08
影响因子：
10.7
通讯作者：
Vogler AP
中科院分区：
文献类型：
--
作者：
Gillett CP;Crampton-Platt A;Timmermans MJ;Jordal BH;Emerson BC;Vogler AP
完整的线粒体基因组已被证明是不同动物群体之间同源性重建的可靠标记。然而，获得从头完整的有丝分裂基因组的相对困难和高成本往往导致在随后的研究中明显低的分类群采样。在这里，我们报告了成功使用一种经济和方便的方法来组装完整或接近完整的有丝分裂基因组，通过鸟枪下一代测序的一个单一的库，从汇集的总DNA提取物的许多目标物种。为了避免使用单独的索引库为每个标本，以及相关的成本增加，我们将标准的聚合酶链反应为基础的“诱饵”序列，以确定组装的有丝分裂基因组。该方法被应用于研究更高层次的系统发育关系，在象甲（鞘翅目：胡蜂总科），生产92个新组装的有丝分裂基因组中获得一个单一的Illumina MiSeq运行。分析支持一个单独的起源钻木行为的亚科Scolytinae，Platypodinae，和Cossoninae。这一发现与提出前两者之间密切关系的形态学假设相矛盾，但与以前的分子研究一致，加强了有丝分裂基因组在胚胎重建中的实用性。我们的方法提供了一个技术上简单的程序，从整个有丝分裂基因组产生密集的采样树，并广泛适用于动物群体的诱饵序列是唯一需要的先验基因组知识。
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.
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影响因子：
1.3
作者：
Bouchard P;Bousquet Y;Davies AE;Alonso-Zarazaga MA;Lawrence JF;Lyal CH;Newton AF;Reid CA;Schmitt M;Slipiński SA;Smith AB
通讯作者：
Smith AB
影响因子：
3.3
作者：
Langley CH;Crepeau M;Cardeno C;Corbett-Detig R;Stevens K
通讯作者：
Stevens K
影响因子：
3.7
作者：
Finstermeier K;Zinner D;Brameier M;Meyer M;Kreuz E;Hofreiter M;Roos C
通讯作者：
Roos C
影响因子：
3.4
作者：
Kayal E;Roure B;Philippe H;Collins AG;Lavrov DV
通讯作者：
Lavrov DV
影响因子：
4.1
作者：
Bernt, Matthias;Bleidorn, Christoph;Struck, Torsten H.
通讯作者：
Struck, Torsten H.