A new haplotype-resolved turkey genome to enable turkey genetics and genomics research

Author:

Barros Carolina P1ORCID,Derks Martijn F L1ORCID,Mohr Jeff2,Wood Benjamin J23ORCID,Crooijmans Richard P M A1ORCID,Megens Hendrik-Jan1ORCID,Bink Marco C A M4ORCID,Groenen Martien A M1ORCID

Affiliation:

1. Wageningen University and Research , P.O. Box 338, 6700 AH, Wageningen , The Netherlands

2. Hybrid Turkeys , 650 Riverbend Drive Suite C, Kitchener, ON N2K 3S2 , Canada

3. School of Veterinary Science, University of Queensland , Gatton, QLD 4343 , Australia

4. Hendrix Genetics Research, Technology & Services , Boxmeer, AC 5830 , The Netherlands

Abstract

Abstract Background The domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of M. gallopavo is essential for turkey genomics and genetics research and the breeding industry. Results By adopting the trio-binning approach, we were able to assemble a high-quality chromosome-level F1 assembly and 2 parental haplotype assemblies, leveraging long-read technologies and genome-wide chromatin interaction data (Hi-C). From a total of 40 chromosomes (2n = 80), we captured 35 chromosomes in a single scaffold, showing much improved genome completeness and continuity compared to the old assembly build. The 3 assemblies are of higher quality than the previous draft quality assembly and comparable to the chicken assemblies (GRCg7) shown by the largest contig N50 (26.6 Mb) and comparable BUSCO gene set completeness scores (96–97%). Comparative analyses confirm a previously identified large inversion of around 19 Mbp on the Z chromosome not found in other Galliformes. Structural variation between the parent haplotypes was identified, which poses potential new target genes for breeding. Conclusions We contribute a new high-quality turkey genome at the chromosome level, benefiting turkey genetics and other avian genomics research as well as the turkey breeding industry.

Funder

NWO

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

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