title: Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence.
abstract: The complexity of eukaryote genomes makes assembly errors inevitable in the process of constructing reference genomes. Next-generation sequencing (NGS) could provide an efficient way to validate previously assembled genomes. Here, we exploited NGS data to interrogate the chicken reference genome and identified 35 pairs of nearly identical regions with >99.5 % sequence similarity and a median size of 109 kb. Several lines of evidence, including read depth, the composition of junction sequences, and sequence similarity, suggest that these regions present genome assembly errors and should be excluded from forthcoming genomic studies.
authors.affiliation: Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, 02138, USA, quzhang@post.harvard.edu.
authors.forename: Qu
authors.initials: Q
authors.lastname: Zhang
authors.forename: Niclas
authors.initials: N
authors.lastname: Backström
mesh_terms: D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D005260:Female; D020440:Gene Duplication; D016678:Genome / Q000235:genetics*; D008297:Male; D020080:Tandem Repeat Sequences / Q000235:genetics*