Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome.

ABSTRACT: It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling

SUBMITTER: Li R 

PROVIDER: S-EPMC6874019 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature