The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation John C. Schwartz, Mark S. Gibson, Dorothea Heimeier, Sergey Koren, Adam M. Phillippy, Derek M. Bickhart, Timothy P.L. Smith, Juan F. Medrano, John A. Hammond

Introduction Natural killer cells are lymphocytes – have a range of biological functions (including essential immune functions). NK cell diversity is created by the differential expression of cell surface receptors Modulate activation and function Multiple subfamilies of C-type lectin receptors encoded within the NK complex Encoded within two unrelated gene complexes – LRC (encoding immunoglobulin- like receptors) and NKC (lectin-like receptor genes (KLR). Both complexes evolve rapidly and vary in gene content between and within species

Rationale Little is known about gene content of natural kill cells beyond rodents and primates – appears to be variable between the groups. Research suggests that cattle are unique in having expanded and diversified NK cell receptor genes. At least seven KLRC, two KLRD, and a single, polymorphic KLRA + 8 functional KIR genes in the LRC Relies largely on current public genome assembly – immune gene complexes are often highly repetitive, however – very similar genes with interspersed repetitive elements, close together

methods New draft assemblies for cattle and goat (Artiodactyla: Bovidae); re-annotated Sheep (Artiodactyla: Bovidae), Pig (Artiodactyla: Suidae), Horse (Perissodactyla: Equidae); and published human (Primates: Hominidae), rat (Rodentia: Muridae), and mouse lemur (Primates: Cheirogaleidae). NKC region upstream of KLRA to downstream of KLRE extracted from current genome builds within Ensembl. Additional scaffolds for goat and cattle generated using long reads – specifics yet to be published/published in Bickhart et al. 2016 – first livestock genomes assembled de novo from PacBio reads alone Genes within NKC identified using BLAST agains GenBank and other NKC genes

results Major NKC genes are largely in the same positions in all eight species Significant independent expansions and deletions between species Cattle and goats – second KLRC locus flanked by KLRA and KLRJ, plus KLRH-like gene with an activating tail (duplicated several times within cattle – other activating receptor genes have been disrupted selectively) Allelic polymorphism between the NKC genes (in cattle), concentrated in extracellular ligand-binding domains. Genes under strong selection

Questions? Wouldn’t sequencing just the NKC and LRC regions reveal just as much about the region? Are there other methods in genome assembly techniques to counter assembly problems like NKC? Why not use those?