Investigating the genome of a female hihi (Notiomystis cincta)

Abstract

A reference genome can be a valuable resource for threatened species as it can be used to assess overall genetic diversity and the evolutionary potential of species to adapt to future pressures such as environmental. Using Oxford Nanopore Technologies long-read sequence data, we assembled the genome of a female hihi (Notiomysits cincta), a threatened avian species endemic to Aotearoa New Zealand. The assembled female genome is 1.06 Gb, and is of high quality and highly contiguous, with an N50 of 61 Mb and a BUSCO completeness of 96.4%. A high-quality male assembly was generated in parallel, which allowed us explore sex differences in the density of microsatellites and transposable elements. Using comparisons of male and female genomic depth of coverage and homology to the sex chromosomes of other passerine species we identified 31 candidate W-linked and 27 candidate Z-linked contigs with a total length of 14,975,707 bp and 75,165,712 bp, respectively. We used Oxford Nanopore Technologies extended basecalling to detect 5mC CpG methylation in the male and female which revealed that the level of methylation was highly correlated in both sexes, but that the W chromosome was more highly methylated than the autosomes and Z chromosome. A female hihi genome assembly provides us with sequence information from the female-specific W chromosome, enabling genome-wide diversity to be captured more completely for females and the investigation of female-specific evolutionary processes. Ultimately, the generation of a female hihi genome can help us to broaden our understanding of avian evolution which contributes to the understanding of how all species evolved, will form the basis for fine-scale assessment of the impacts of low genetic diversity and inbreeding on the adaptive potential of the species, and will therefore enable more tailored and informed conservation management of this threatened taonga species.