Artiodactyl MYADM-like Repeat Region: BAC Sequence Identifies 7 Open Reading Frames with Differing Lengths Between Reference Genome and Alternate Allele

We recently identified multiple phenotypes associated with a genomic region under strong historical selection, including red blood cell (RBC) traits and ewe lifetime weight of lamb weaned. This region contained an expanded repeat locus, unique to the artiodactyl lineage, comprising approximately 40 highly divergent (<87% average pairwise nucleotide identity) MYADM-like open reading frames (ORFs). Within this region, resequencing suggested an apparent deletion of a single full-length ORF MYADM-like repeat (Rpt-29) in strong linkage disequilibrium with the best marker. To further characterize this region, a bacterial artificial chromosome (BAC) from a non-reference allele homozygote was sequenced to >500X minimum Pac Bio read depth. The BAC region spans 17 MYADM-like ORFs relative to the reference genome, including 11 downstream and 6 upstream ORFs surrounding Rpt-29. This span was confirmed by BAC end sequencing and by maximum sequence identity of the individual ORFs. Two ORFs in the reference appear deleted in the BAC assembly, full length Rpt-29 as expected and truncated Rpt-33 (133 bp). Five additional MYADM-like ORFs (Rpts- 22, 28, 31, 32, 34) appear larger (>100 bps) in the BAC assembly compared to reference. The BAC assembly contained a short inserted segment in place of Rpt-29, and PCR sequencing confirmed inclusion of this alternate sequence in BAC and genomic DNA bearing the non-reference allele, but not in reference allele homozygotes.  Additional genomic testing of this region is ongoing, and further phenotypic characterization will include susceptibility to Anaplasma ovis and RBC morphologic investigation.