Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

摘要

Long-range and highly accurate de novo assembly from short-read data is oneof the most pressing challenges in genomics. Recently, it has been shown thatread pairs generated by proximity ligation of DNA in chromatin of living tissuecan address this problem. These data dramatically increase the scaffoldcontiguity of assemblies and provide haplotype phasing information. Here, wedescribe a simpler approach ("Chicago") based on in vitro reconstitutedchromatin. We generated two Chicago datasets with human DNA and used a newsoftware pipeline ("HiRise") to construct a highly accurate de novo assemblyand scaffolding of a human genome with scaffold N50 of 30 Mb. We alsodemonstrated the utility of Chicago for improving existing assemblies byre-assembling and scaffolding the genome of the American alligator. With asingle library and one lane of Illumina HiSeq sequencing, we increased thescaffold N50 of the American alligator from 508 kb to 10 Mb. Our method usesestablished molecular biology procedures and can be used to analyze any genome,as it requires only about 5 micrograms of DNA as the starting material.