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Rabbit genome sequencing update: genes of immunological interest found in the 2x genome assemblies, ENCODE, and the 7x trace archive
Author(s) -
Mage Rose G
Publication year - 2008
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.22.2_supplement.559
Subject(s) - ensembl , biology , genome , genetics , in silico , gene , reference genome , whole genome sequencing , shotgun sequencing , computational biology , genomics
Rabbits are a major source of polyclonal and monoclonal antibodies because the rabbit immune system has unique characteristics that contribute to production of diverse polyclonal antibodies of high affinity and specificity. Both gene conversion and somatic hypermutation diversify rearranged H and L chain genes, favorable amino acid replacements are selected during clonal expansion in germinal centers, and germline encoded V‐kappa vary in length of CDR3. The whole genome shotgun (WGS) “unfinished Oryctolagus cuniculus database” has serious gaps, yet the information has already proven useful for immunological as well as in silico studies. Deeper 7x coverage started in September 2007. The NCBI Rabbit Genome Resources site has links to searches for genes in the assemblies of the 2x WGS sequence at Ensembl and UCSC useful for designing primers for PCR by predicting mRNA sequences and exon boundaries. The “Thorbecke Inbred Rabbit” chosen for sequencing at Broad Institute is less heterozygous than outbred NZW but the Trace Archive of Oryctolagus cuniculus (WGS) contains matches to known sequences of both VH1a1 and VH1a2. Deep sequencing of the rabbit genome will provide comparative genomic data, aid discovery of variants of genes of immunological interest, and reveal genetic contributions to animal and human disease susceptibilities. This research was supported by the Intramural Research Program of the NIH, NIAID