Preprint on two new Neotoma genomes is out!
Using the trio binning technique first employed in Bos cattle, we generated reference genomes for Neotoma bryanti and Neotoma lepida using PacBio reads from a single F1 hybrid female. Dr. Robert Greenhalgh (Post-Doctoral Fellow) led the assembly and annotation processes over the past several months, and we recently released these as the first draft chromosome-level genomes in this genus. This work has revealed a complex evolutionary history for cytochrome P450 genes involved with dietary detoxification in Neotoma spp. One particularly notable discovery from these new resources lies in the CYP2B and 3A detoxification repertoires of these rodents, which appear to have undergone recent, lineage-specific expansions.
A preprint of this work is available from bioRxiv at: https://www.biorxiv.org/content/10.1101/2021.03.08.434435v1
The genomes and annotations are hosted with OSF at:
https://osf.io/xck3n/
Outline of the trio binning approach. Neotoma woodrats of different species are crossed to generate a hybrid F1 female, and all individuals in the cross are sequenced. Sequences unique to each parent are identified in Illumina short-read data and used to partition PacBio reads from the hybrid by haplotype. Each parental haplotype is then assembled separately, yielding genomes for each species involved in the cross. These assemblies were aligned against existing Peromyscus genomes to generate chromosome-length scaffolds. (Figure based on schematic presented in Koren et al. 2018. Photo credits: N. bryanti – M. Doolin, N. lepida – K. Kohl, hybrid – JCMDI.)
CYP Expansion Example. One of the CYP expansions we discovered was in this CYP2B island, which is found only in New World rodents. Neotoma lepida has a greatly increased number of intact and pseudogenized CYP2B genes in this region.
