From listmaster animalgenome.org Wed Mar 11 11:43:12 2020
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From: "Cheng, Hans" <hans.chengusda.gov>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Requesting input on proposed strain for chicken
genome assembly
Date: Wed, 11 Mar 2020 11:43:12 -0500
The chicken genome reference, GRCg6a, has been of great tool to many labs as
a computational starting point for a broad spectrum of studies. We have
continued to improve this resource over the years since 2004. In an effort to
better meet the needs of the community and further improve the completeness
of the chicken genome reference, we have recently completed de novo
assemblies of a representative broiler and layer birds. A trio of samples was
collected to create a high-quality reference genome for two haplotypes. The
female offspring (bGalGal1) is a cross between a modern commercial broiler
mother (bGalGal2) and a modern commercial White leghorn layer father
(bGalGal3). In collaboration with Erich Jarvis, the Genome Reference
Informatics Team, and as part of the Vertebrate Genomes Project (VGP), we
have manually curated the maternal (broiler) haplotype of bGalGal1 that we
plan to use as the new chicken genome reference. In this bGalGal1 reference,
we have accurately resolved many regions that were errors in GRCg6a such as
false interchromosomal fusions and intrachromosomal inversions.
In detail, we have:
• replaced the Jungle Fowl genome assembly with a strain relevant to the
domestic poultry industry,
• made 22 large structural corrections,
• removed significant misassemblies, leaving the new genome as the ideal
substrate for further michrochromosome classification,
• created an assembly where – in contrast to GRCg6a - no known chromosomal
markers fail to map to the correct chromosomes. Some chromosomes, e.g.,
chromosome 16 gain chromosomal markers that previously didn’t map,
• reduced the number of gaps by two-thirds compared to GRCg6,
• extended chromosome W by adding to the pseudoautosomal region (PAR),
• preserved existing correct sequence as shown by Hi-C comparisons, marker
mapping, and BUSCO scores that reflect gene completeness,
• resolved poor quality assembly structures typically around chromosome, as
evidenced by an 8x increase in correctly placed telomeres.
Importantly, you will still have access to the GRCg6a reference through the
NCBI assembly archive. However, we wish to hear your input regarding these
efforts and the decision to change the strain of the reference genome
assembly. Thus, please contact Wes Warren (warrenwcmissouri.edu) or Hans
Cheng (hans.chengusda.gov) if you have any questions or concerns.
========================================
Hans H. Cheng
Research Geneticist
USDA-ARS
Avian Disease and Oncology Laboratory
4279 E. Mount Hope Rd.
East Lansing, MI 48823
Tel: (517) 337-6758
FAX: (517) 337-6829
E-mail: hchengmsu.edu
or Hans.Chengusda.gov
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