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.
Highlights
Each species inhabits a specific environment, a niche, that shapes its unique genome sequence and its expression
Red List categories (Table 1): sea otter (Enhydra lutris), cheetah (Acinonyx jubatus), clouded leopard (Neofelis nebulosa), giant otter (Pteronura brasiliensis), red panda (Ailurus fulgens), Asian small-clawed otter (Aonyx cinereus), American bison (Bison bison), and Eurasian river otter (Lutra lutra). Each of these species was represented by two genome assemblies: the initial draft assembly and a chromosome-level assembly generated from the draft using high-throughput chromosome conformation capture (Hi-C)-scaffolding [23]
Our analysis demonstrates that even using a large set (66) of mustelid STR markers developed in the five studies of the pre-genomic era with previously unknown localization, some of the chromosomes were missed in the analysis (Figure 5, chromosomes shaded in grey)
Summary
Each species inhabits a specific environment, a niche, that shapes its unique genome sequence and its expression. The resulting patterns of variation provide a backdrop for natural selection, enabling adaptation [4,5], and it is generally thought that preserving genetic diversity is required for adaptability: a species that has lost all its reserves of genetic diversity is doomed to extinction [6,7,8,9,10,11,12]. In this context, adaptability is generally understood to depend on the existing genetic variation within each species. Among many endangered and threatened species, genome-wide genetic diversity has been severely reduced, which is usually seen as a critical sign of vulnerability, as genetically diverse populations should be more resilient to environmental change due to a higher adaptive potential [6,13,14,15]
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