Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
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DOI：
10.1111/1755-0998.12328
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发表时间：
2015-05
影响因子：
7.7
通讯作者：
Brady SG
中科院分区：
文献类型：
--
作者：
Faircloth BC;Branstetter MG;White ND;Brady SG
要想从基因组的角度了解系统发育，需要从整个基因组中许多假定独立的基因座收集数据。在昆虫中，收集这类数据的一种日益普遍的方法涉及转录组测序，因为很少有昆虫拥有高质量的基因组序列；组装新的基因组仍然是一个限制因素；基因组的转录部分是基因组的一个合理的、减少的子集；从基因组的转录部分收集的数据在组成上类似于生物学家传统上处理的数据类型(例如外显子)。然而，需要以RNA为模板的分子技术，包括转录组测序，仅限于使用非常高质量的来源材料，而这些材料往往无法从很大比例的具有重要生物学意义的昆虫样本中获得。最近的研究表明，基于DNA的保守基因组元件的靶向浓缩为收集跨昆虫分类群的系统发育数据提供了另一条途径，前提是保守元件存在于昆虫基因组中并可以从昆虫基因组中收集。在这里，我们识别了昆虫目膜翅目共享的一大组超服务元素(UCES)(n=11510)。我们在计算机分析中使用了这些基因座来表明这些基因座准确地重建了基因组使能的膜翅目之间的关系，并设计了一组RNA诱饵(n=2749)来丰富这些基因座，研究人员可以与从各种来源提取的DNA模板一起使用。我们用我们的UCE诱饵集丰富了30个膜翅目分类群的平均721UCE基因座，并利用这些UCE基因座重建了膜翅目各谱系之间跨越非常古老(≥220 Ma)到非常年轻(≤1 Ma)的系统发育关系。与最近一项利用转录组数据研究膜翅目系统发育的研究不同，我们发现蚂蚁是所有剩余的针形谱系的姐妹，完全支持，尽管这一结果可以用分类单元采样等因素来解释。我们在阐明最多样和最特殊的动物目之一的进化史的背景下，讨论了这种方法和我们的结果。
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
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DOI：
10.1073/pnas.0605858103
发表时间：
2006-11-28
影响因子：
11.1
作者：
Brady, Sean G.;Schultz, Ted R.;Ward, Philip S.
通讯作者：
Ward, Philip S.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
9.8
作者：
Ahituv N;Zhu Y;Visel A;Holt A;Afzal V;Pennacchio LA;Rubin EM
通讯作者：
Rubin EM
影响因子：
12.3
作者：
Fisher S;Barry A;Abreu J;Minie B;Nolan J;Delorey TM;Young G;Fennell TJ;Allen A;Ambrogio L;Berlin AM;Blumenstiel B;Cibulskis K;Friedrich D;Johnson R;Juhn F;Reilly B;Shammas R;Stalker J;Sykes SM;Thompson J;Walsh J;Zimmer A;Zwirko Z;Gabriel S;Nicol R;Nusbaum C
通讯作者：
Nusbaum C
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T