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Chicken RJF Reference Genome Sequence containing MHCY and NOR Ribosomal Genes

dataset
posted on 2024-01-27, 00:24 authored by City of Hope Beckman Research Institute
The MHCY region is a polymorphic gene region that influences immune responses in chickens. Understanding the genomics of the region will help in genetic selection of chickens raised for meat and eggs. The nucleotide sequence for the MHCY region has been especially hard to assemble due to the presence of many retroelements (principally CR1 and retroviral LTRS) and the presence of gene blocks of highly similar. Four contigs were identified. These did not assemble into a single sequence. One contig contains a portion of the NOR (Nucleolar Organizer Region) sequence. This provides sequence data for ribosomal RNA genes (and intervening sequence) closely adjacent to MHCY. The SMRT data was the first sequence data that allowed large regions of MHCY to be sequenced. Here we deposit additional PacBio data and Illumina data for some clones.

Funding

National Institute of Food and Agriculture, 2009-65119-05676 (Miller)

National Institute of Food and Agriculture, 2017-67017-26570 (Miller)

National Institute of Food and Agriculture, CA-D*-ASC-6414-RR (Delany)

Cooperative State Research, Education, and Extension Service, CALR 2005-04966 (Miller)

Caltech-City of Hope, Caltech-City of Hope Biomedical Initiative Pilot Award 2014 (Miller and Bjorkman)

US Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA), National Research Support Program-8 (NRSP-8) (Animal Genome Research Program), Funds for SMRT sequencing from Poultry Species Coordinator funds – 2016 (Miller)

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2022-02-04

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

sequence analysis

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA803548

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