期刊
NATURE GENETICS
卷 49, 期 4, 页码 643-+出版社
NATURE PORTFOLIO
DOI: 10.1038/ng.3802
关键词
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资金
- US Agency for International Development Feed the Future program
- Norman Borlaug Commemorative Research Initiative
- Livestock Improvement Program
- Agriculture and Food Research Initiative (AFRI) competitive grant from the USDA National Institute of Food and Agriculture (NIFA) Animal Genome Program [2011-67015-30183, 2015-67015-22970]
- USDA CRIS project [8042-31000-104-00, 3040-31320-012-00, 6402-31000-006-00D]
- NIH [R01HG006283, P41 GM103533]
- UW Commercialization Gap Fund and Commercialization Fellows Program
- MN Experiment Station Project [MIN-16-103]
- UK Biotechnology and Biological Sciences Research Council Institute Strategic Program on Livestock Viral Diseases award
- NIH Intramural Research Program of the National Human Genome Research Institute
- Biotechnology and Biological Sciences Research Council [BBS/E/I/00001710, BB/M027155/1] Funding Source: researchfish
- BBSRC [BB/M027155/1, BBS/E/I/00001710] Funding Source: UKRI
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 what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a similar to 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 yet produced for an individual of a ruminant species.
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