Targeted PacBio Sequencing of Zebrafish NLR Exons
The NLR (nucleotide-binding leucine-rich repeat) gene family encodes a class of immune receptors that has expanded to hundreds of copies in many phylogenetic clades, including fish. However, not much is known about the within-species variability of this family. Here we used the model animal zebrafish to study copy number variation of the NLRs in two laboratory strains and four wild populations sampled from the native range of species. We combined de novo assembly with orthology clustering to generate a partial NLRome that consists of a set of unique sequences for two major exon types found in those genes. To our knowledge, this is the first time that such a large-scale study of copy number variation in a large multi-copy gene family has been conducted in fish. Our pan-NLRome can be used for further studies on zebrafish NLR diversity and we hope that it will be a valuable resource for many future studies conducted across the world.