Multiple chicken (Gallus gallus) genome references to advance genetic variation studies

Authors: WARREN, WESLEY - University Of Missouri; FEDRIGO, OLIVIER - Rockefeller University; TRACEY, ALLEN - Wellcome Trust Sanger Institute; MASON, ANDREW - York University; FORMENTI, GIULOLIO - Rockefeller Foundation; PERINI, FRANCESCO - University Of Perugia; WU, ZHOU - University Of Edinburgh; MURPHY, TERRANCE - National Institutes Of Health (NIH); SCHNEIDER, VALERIE - National Institutes Of Health (NIH); STIERS, KYLE - University Of Missouri; RICE, EDWARD - University Of Missouri; COGHILL, LYNDON - University Of Missouri; ANTHONY, NICK - Cobb-Vantress, Inc; OKIMOTO, RON - Cobb-Vantress, Inc; CARROLL, RACHEL - University Of Missouri; MOUNTECASTLE, JACQUELYN - Rockefeller University; BALACCO, JENNIFER - Rockefeller University; HAASE, BETTINA - Rockefeller University; YANG, CHENTAO - Bgi Shenzhen; ZHANG, GUOJIE - Zhejiang University; SMITH, JACQUELYN - University Of Edinburgh; DRESCHLER, YVONNE - Western University Of Health Sciences; Cheng, Hans; HOWE, KERSTIN - Wellcome Trust Sanger Institute; JARVIS, ERICH - Rockefeller University

Submitted to: Cytogenetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2023
Publication Date: 6/26/2023
Citation: Warren, W.C., Fedrigo, O., Tracey, A., Mason, A.S., Formenti, G., Perini, F., Wu, Z., Murphy, T., Schneider, V., Stiers, K., Rice, E.S., Coghill, L., Anthony, N., Okimoto, R., Carroll, R., Mountecastle, J., Balacco, J., Haase, B., Yang, C., Zhang, G., Smith, J., Dreschler, Y., Cheng, H.H., Howe, K., Jarvis, E. 2023. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Cytogenetics and Genome Research. https://doi.org/10.1159/000529376.
DOI: https://doi.org/10.1159/000529376

Interpretive Summary: In the modern era of biology, high quality genome assemblies of your organism of interest are essential especially for understanding complex traits like growth, reproduction, and disease resistance. In 2004, chicken was the first farm animal to generate a draft genome assembly, which was based Red Jungle Fowl, the ancestor of domestic chickens. Since then, a number of improvements have been made. In this publication, two new reference genomes were assembled that were based on a commercial broiler (meat-type bird) and commercial layer (egg-type bird). These references are more complete and likely more suitable for studies in commercial birds. These references should enable more precise studies especially those involving genetic improvement, which will ultimately aid poultry producers and consumers.

Technical Abstract: We present two phased chromosome-scale assemblies of chicken, a layer (GRCg7w) and broiler (GRCg7b), that better meet research demands to characterize important for traits of interest in commercial birds. Annotation with existing long- and short-read RNAseq data improved contiguity, accuracy, and protein-coding and non-coding gene counts, when compared to the existing Red Jungle Fowl reference, GRCg6a. Most striking were the improvements in placed telomeres, corrections for erroneous microchromosome fusions, and gap reduction in these phased assemblies. We add six putative microchromosomes that were previously missing in GRCg6a. Using a pairwise genome comparison of the parental genomes, and two independent cohorts of sequenced chickens, we show small discernable differences in mapping rates of whole genome sequence (WGS) and RNAseq data, gene annotation, and called single nucleotide variants (SNVs) or indels. Structurally, some regional differences suggest future assembly curation will further improve variant ascertainment. These Gallus references also enabled a new genome-wide review of endogenous Avian Leukosis Virus (ALVE) integrations, exemplifying the improved representation of chicken genomic diversity by these phased genomes. Our genome references will collectively improve our computational outcomes when testing multiple variant hypotheses that are at the core of our understanding of avian biology.