Initial Assembly and Analysis of the MHC B-Locus of the Ocellated Turkey

The ocellated turkey (Meleagris ocellata) is a distinctive galliform native to the Yucatan Peninsula of Mexico, Guatemala and Belize.  Due to hunting and habitat loss, the range of the ocellated turkey has been reduced to less than 50,000 sq. miles. Therefore, unlike their widespread relative, the wild turkey (M. gallopavo), ocellated turkeys have a near-threatened conservation status.  Understanding the structure and diversity of the major histocompatibility complex (MHC) can have important implications for conservation efforts and lead to hypotheses on MHC evolution.  Whole genome sequencing (WGS) was performed on the Illumina HiSeq, producing 100bp paired-end reads.  After trimming and filtering, approximately 168M paired-reads remained, of which over 3M read pairs and 4M single reads aligned to the domestic turkey MHC B-locus (MHC-B).  Alignment resulted in an average sequence depth of 1,659 reads/reference nucleotide, due to areas of extremely high sequence coverage in repetitive regions.  Twenty known gene families from the MHC-B were represented in the assembled sequences.  Contigs were aligned and compared to the domestic turkey and other galliforms; a number of polymorphism and insertions unique to the ocellated turkey were identified.  This analysis provides insight into gene content and evolutionary conservation of the ocellated turkey MHC and provides a framework for further investigation of MHC variability.