From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).
From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).
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DOI：
10.1534/g3.117.040055
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发表时间：
2017-05-05
期刊：
影响因子：
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通讯作者：
Stevens KA
中科院分区：
文献类型：
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作者：
Crepeau MW;Langley CH;Stevens KA
我们研究了新的读取云技术的实用性和可扩展性，以改善庞大的，并且在很大程度上重复的针叶树基因组的基因组组装草图。自基因组组装开始以来，合成长读段技术已经以各种形式存在，作为降低复杂性和解析重复序列的手段。最近，大规模地将高分子量DNA的亚单倍体库与条形码化联合收割机组合的技术为样品制备和数据生成带来了新的效率。当与廉价的轻鸟枪测序相结合时，所得到的数据可以用于构建大基因组。该协议是足够有效的，即使是最大的基因组常规考虑。针叶树代表了迄今为止执行的最大的参考基因组计划。其中最大的是针叶树Pinus lambertiana（糖松），基因组大小为310亿bp。在本文中，我们报告了使用10× Genomics的文库技术构建P. lambertiana基因组的分子和计算方案。在247，000 bp处，现有参考序列的NG 50是目前公布的针叶树组装体中最高的支架邻接;这个新组装体的NG 50为194万bp，增加了8倍。
We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly’s NG50 is 1.94 million bp, an eightfold increase.