UNRAVELING THE IMMUNOGLOBULIN SUPERFAMILY GENES GENOMIC ORGANIZATION IN CATFISH (ICTALURUS PUNCTATUS) BY THIRD GENERATION SEQUENCING
Sylvie Quiniou, USDA-ARS-Stoneville
Sylvie M.A. Quiniou1, Eva Bengtèn2, Christophe Klopp3, Bryan M. Musungu1 and Mekki Boussaha4
1. Warmwater Aquaculture Research Unit, USDA-ARS-Stoneville, MS
2. Department of Microbiology, University of Mississippi Medical Center, MS
3. Genotoul, INRA, France
4. UMR 1313 Génétique Animale et Biologie Intégrative, INRA, France
The Immunoglobulin Superfamily (IgSF) gene regions have been amongst the most challenging ones to sequence and assemble due to the presence of multiple duplications and repetitive regions. The advent of third generation sequencing has enabled resolving most of these issues. We undertook sequencing of the major IgSF gene loci in catfish using Pacific Biosciences long read sequencing. First, we sequenced the genome of a meotic gynogenetic fish (CCBL1) for which we already had a BAC library and a physical map. Second, to ensure accuracy and contiguity of the large IgSF gene loci, we also sequenced 180 BACs, in parallel. The de novo genomic assembly produced a map of 1319 contigs with a N50 of 4.4Mb and a L50 of 50. Currently approximately 92% of the genome is anchored by a high density linkage map. Reintegration of the genome with the physical map and its 43,000 associated BES should further increase the anchoring by several percentages. Through BAC sequencing we assembled the regions encoding the antigen receptors of adaptive immunity: Immunoglobulin Heavy chains, the σ, κ and λ Immunoglobulin Light chains, the α, β, δ, and γ T cell receptors, as well as the major histocompatibility I and II. In addition, we also assembled the loci encoding teleost specific innate immune regulatory receptor families such as the LITRs, NITRs, PIGRLs and NILTs. The genome assembly results and the structural organization of IgSF gene regions will be presented.