Copy Cats: Improved Cat Genomes Highlight Remarkable Similarities Within the Feline Family
Monday, January 11, 2021
Felix, Garfield, Leo the Lion — despite their differences, the genomes of these frisky felines are highly conserved across the family, even among its most divergent members.
A new set of highly contiguous haploid Felis and Prionailurus assemblies provides further proof that although the genomes appear karyotypically distinct, they are grossly collinear, and any cytogenetic differences represent centromere repositioning rather than chromosomal rearrangements.
A team of researchers at Texas A&M University, led by Kevin R Bredemeyer, Andrew Harris and William J Murphy, worked with colleagues in the United States, China and Russia to create a de novo assembly of a Bengal hybrid cat, as well as phased haplotypes of its parents, a random-bred domestic cat (Felis catus) and an Asian leopard cat (Prionailurus bengalensis).
As reported in the Journal of Heredity, the assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in one or two large contigs.
Previous diploid-based genome assemblies for the domestic cat suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable, the authors noted.
“These difficult to assemble regions are increasingly understood as playing important roles in disease biology, genome organization, gene regulation, and speciation,” they added.
By using highly contiguous PacBio long reads, the team was able to capture complex repetitive regions previously un-spanned due to insufficient read lengths and/or high haplotype divergence, as well as resolve multicopy gene families with high allelic diversity (such as the Major Histocompatibility Locus and olfactory receptors).
“Furthermore, we have provided a genome assembly from a random-bred domestic cat, which is more representative of the domestic cat pet population,” they wrote.
Adding to a growing collection of assembly methods, they also demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available — an important ability, since F1 interspecies hybrids are rare biological resources, and in many cases it may be logistically impossible to obtain the actual parents of the cross.
As they noted in their paper, cats are not only some of the most popular companion animals — species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease– but the study of domestic cats can also help in the conservation of their wild cousins.
“These novel genome resources will empower studies of feline precision medicine, adaptation and speciation,” the authors wrote.
To hear from fellow scientists about their latest plant & animal discoveries, register to attend PAGBio Day, a virtual half-day event on January 19th. Explore how to use PacBio whole genome sequencing for your project.