Genomic Features of Parthenogenetic Animals

Abstract

Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.

Convergent consequences of parthenogenesis on stick insect genomes

“…We tested these predictions by comparing the genomes of five independently derived parthenogenetic stick insect species in the genus Timema with their close sexual relatives ( Figure 1). These replicate comparisons allowed us to solve the key problem in understanding the consequences of parthenogenesis for genome evolution: separating the consequences of parthenogenesis from lineage specific effects ( 17 ) . Timema are wingless, plant-feeding insects endemic to western North America.…”

First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

“…The genome-wide heterozygosity of D. stevensoni matches to some extent an earlier study on intra-individual divergence in three nuclear genes of D. stevensoni . The finding of almost 1% heterozygosity in D. stevensoni is remarkable, given that all previous genome-wide estimates for asexual arthropods that did not evolve via hybridization revealed extremely low levels of heterozygosity (Jaron et al 2020). Yet heterozygosity is clearly less than the estimates for parthenogenetic species with known hybrid origin (1.73-8.5%) or polyploidy (1.84%-33.21%) (Jaron et al (2020), supporting the view that D. stevensoni is neither a hybrid nor a polyploid.…”

“…The finding of almost 1% heterozygosity in D. stevensoni is remarkable, given that all previous genome-wide estimates for asexual arthropods that did not evolve via hybridization revealed extremely low levels of heterozygosity (Jaron et al 2020). Yet heterozygosity is clearly less than the estimates for parthenogenetic species with known hybrid origin (1.73-8.5%) or polyploidy (1.84%-33.21%) (Jaron et al (2020), supporting the view that D. stevensoni is neither a hybrid nor a polyploid. Asexual reproduction in ostracods is thought to be apomictic (Chaplin et al 1994), implying that observed heterozygosity levels are largely depend on the relative impact of heterozygosity losses from gene conversion and heterozygosity gains from new mutations.…”

“…Genome-wide estimates of heterozygosity are especially interesting for asexual taxa because the absence of recombination is expected to cause accumulation of mutations, resulting in increasing allelic divergences within individuals (Birky 1996). Jaron et al (2020) identified three factors driving intragenomic heterozygosity in asexuals: how the transition to parthenogenesis occurred, which cytological mechanism underlies parthenogenesis and how long asexual reproduction has been ongoing. Based on sequencing reads from individual ostracods, we estimate heterozygosity of the putative ancient asexual ostracod D. stevensoni to be 0.92-0.99% ( Figure S1 A-B) and 1.32-1.43% for the sexual N. monacha ( Figure S1 C-D).…”

“…effects (Jaron et al 2020). For many animal groups in which asexuality is frequent, genomic data are limited to a few representatives only (Tvedte et al 2019) or are totally absent like in the Ostracoda.…”