Evaluation and Application of the New Chicken Genome Version GGswu1

Abstract:

The integrity and accuracy of the chicken genome hold significant implications for the study of vertebrate evolution and the understanding of avian biological characteristics. Additionally, it plays an essential role in deciphering the genetic mechanisms of poultry and in the improvement of genetic breeding. The nearly complete chicken genome map was recently published, but genetic variation studies using this genome as a reference have not been widely conducted.This study aims to evaluate the differences and advantages of GGswu1 and the current chicken reference genome GRCg7b. Based on 60 publicly available chicken wholegenome resequencing data and 103 chicken transcriptome data collected, a comprehensive assessment and comparison of the two reference genomes were conducted in terms of assembly quality, alignment rate, SNPs detection capability, and completeness of gene assembly.The results indicate that, compared to GRCg7b, GGswu1 has achieved a significant improvement in assembly quality and has also improved the completeness of gene assembly to some extent, demonstrating considerable potential in genetic variation analysis. These findings aid with a more precise understanding of the differences and advantages between these two genome assembly versions and offer a reference for future functional research of the chicken genome and indepth exploration of poultry genetic resources.