Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.
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DOI：
10.1038/ng.3802
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发表时间：
2017-04
期刊：
影响因子：
30.8
通讯作者：
Smith TP
中科院分区：
文献类型：
--
作者：
Bickhart DM;Rosen BD;Koren S;Sayre BL;Hastie AR;Chan S;Lee J;Lam ET;Liachko I;Sullivan ST;Burton JN;Huson HJ;Nystrom JC;Kelley CM;Hutchison JL;Zhou Y;Sun J;Crisà A;Ponce de León FA;Schwartz JC;Hammond JA;Waldbieser GC;Schroeder SG;Liu GE;Dunham MJ;Shendure J;Sonstegard TS;Phillippy AM;Van Tassell CP;Smith TP
测序成本的降低和用于短读段平台的组装算法的增加的复杂性已经导致具有基因组组装的物种的数量急剧增加。然而，这些组件是高度分散的，有许多差距，模糊性和错误，阻碍下游应用。我们展示了目前最先进的从头组装使用国内山羊（山羊），基于重叠群形成的长读段，共识验证的短读段，和支架光学和染色质相互作用映射。这些技术的结合产生了迄今为止最连续的从头哺乳动物组装，具有染色体长度的支架和只有649个缺口。我们的组装代表了约400倍的连续性改善，由于正确组装的差距相比，以前公布的C。hircus组装，并更好地解决了长度超过1 kb的重复结构，代表了最大的重复家族和免疫基因复合物曾经产生的反刍动物物种的个体。
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ~400-fold improvement in continuity due to properly assembled gaps compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex ever produced for an individual of a ruminant species.
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DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
DOI：
10.1534/g3.114.011825
发表时间：
2014-05-22
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Burton JN;Liachko I;Dunham MJ;Shendure J
通讯作者：
Shendure J
影响因子：
12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.