Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.
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DOI：
10.1101/gr.213660.116
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发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Larkin DM
中科院分区：
文献类型：
--
作者：
Damas J;O'Connor R;Farré M;Lenis VPE;Martell HJ;Mandawala A;Fowler K;Joseph S;Swain MT;Griffin DK;Larkin DM
最新的重新测序和组装新物种基因组的计划未能实现产生重叠群的最终终点，每个重叠群代表一个完整的染色体。即使是最好的组装基因组（使用当代技术）由亚染色体大小的支架组成。为了解决这个问题，我们开发了一种新的方法，该方法结合了计算算法将支架合并为染色体片段，基于PCR的支架验证和染色体的物理映射。多基因组比对引导的探针选择导致了一组通用禽类BAC克隆的开发，其允许将多个支架快速锚定到所有禽类基因组上的染色体。作为原则的证明，我们组装了鸽子（哥伦比亚利维亚）和游隼（隼peregrinus）的染色体水平相当，在连续性，鸟类参考基因组的基因组。这两个物种的利益为育种，文化，食品，和/或环境的原因。鸽子具有典型的鸟类核型（2n = 80），而猎鹰（2n = 50）与鸟类祖先相比高度重排。通过使用染色体断裂点数据，我们建立了鸟类染色体间断裂点出现在保守的非编码元件（CNEs）的低密度区域，染色体分裂位点进一步限于长CNE "沙漠"。这与裂变是鸟类基因组进化中最罕见的重排类型相对应。使用当前BAC集的高通量多重杂交和快速捕获策略为组装许多鸟类（以及可能的其他爬行动物）物种提供了基础，而支架组装和映射的总体策略为可以应用于任何动物基因组的方法（提供中期分裂相）提供了基础。
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.