Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Abstract

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

“…Assessment of variation among genome assemblies of closely related species is also strongly impacted by the contiguity and completeness of the analysed assemblies (Gurevich et al, 2013; Totikov et al, 2021). This needs to be accounted for when examining variation among discontiguous genome assemblies.…”

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

“…Highly contiguous assemblies provide a more complete understanding of historical and contemporary diversity and demographics, and can enable the precise estimation of parameters relevant for the study, management, and conservation of endangered species ( Robinson et al . 2021 ; Totikov et al . 2021 ).…”

Genomics of Adaptation and Speciation

“…Answering questions about speciation, adaptation, and extinction does not require the newest and most advanced sequencing technologies, and limited sets of data can be used. The examples in this issue included studies of large structural and chromosomal variation [9,13] However, newer, more contiguous assemblies may allow for a better estimation of the genetic diversity, localization, and visualization of the distribution of genome diversity in the evolutionary context of adaptation and speciation [21] (Totikov et al, 2021).…”

“…The examples in this issue included studies of large structural and chromosomal variation [ 9 , 13 ] (Beklemisheva et al, 2020; Galindo et al, 2021), mtDNA and/or limited nuclear marker approaches to phylogenetics [ 24 ] (Kolchanova et al, 2021), hybridogenesis [ 10 ] (Miura et al, 2021), comparative transcriptomics [ 14 ] (Zhao and Kishino, 2020), and genome-wide studies of SNP variation using a combination of low-coverage sequencing and genotyping [ 15 , 16 ] (de La Torre et al, 2021; Mahtani-Williams et al, 2020). However, newer, more contiguous assemblies may allow for a better estimation of the genetic diversity, localization, and visualization of the distribution of genome diversity in the evolutionary context of adaptation and speciation [ 21 ] (Totikov et al, 2021).…”

“…By visualizing genome diversity among high-quality genome assemblies, Totikov et al (2021) [ 21 ] demonstrated how technological breakthroughs in genomics could provide conservation biology with valuable new approaches. Chromosome maps can also be used to investigate the distribution of genetic diversity in different parts of genomes of endangered and threatened species.…”