Genomic signatures of local adaptation to the degree of environmental predictability in rotifers

Abstract

Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)

“…With a total span of ca. 260 Mb, its size is within the range reported for bdelloids [67,68] but larger than draft genomes in monogononts [144][145][146][147]149]. In addition, the repetitive portion of the P. laevis genome (63%) is higher than corresponding values published for monogononts and bdelloids [68,146].…”

“…The total size of the P. laevis draft genome ranges within according estimates for other parasitic taxa such as Platyhelminthes (104-1,259 Mb) and Nematoda (42-700 Mb) [148]. The nuclear genome size additionally meets the expectations obtained from closer phylogenetic relatives of acanthocephalans, i.e., bdelloids and monogononts [67,68,146,149]. According to flow cytometry measurements, for example, haploid genomes should have about 117-225 Mb in the monogonont genus Brachionus (1 pg = 978 Mb; [150,151]).…”

“…In fact, cytofluorometric measurements suggest that Adineta vaga and Philodina roseola have haploid genomes of about 245 Mb and 1,193 Mb, respectively (1 pg = 978 Mb;[151,154]). However, more revealing should be the comparison with size estimates of haploid genomes according to de novo assemblies, which span 129.6 Mb in B. calyciflorus and 51-115 Mb in the B. plicatilis species complex[144,146,149]. The corresponding estimates for bdelloids are in a higher range once more, with up to 217.9 Mb (A. vaga), 201.3 Mb (Adineta ricciae), 295.4 Mb (Rotaria macrura), and 337.6 Mb (R. magnacalcarata)[67,68].…”

Adaptación e incertidumbre ambiental

“…Thus, a «draft» rotifer genome was created from sequencing data in a new study (Franch-Gras et al, 2018) and compared to previously sequenced populations that were differentially adapted to environmental unpredictability in order to analyse divergence between these genomes. Using genotyping by sequencing (GBS) and subsequent bioinformatic analysis, genetic divergence (single nucleotide polymorphisms, SNPs) were found in a large number of nucleotide positions, even when applying very conservative methods.…”

Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

“…The B. plicatilis complex is one of the most extensively studied rotifer groups and has long been recognized as a model of ecological adaptation and speciation (23,25,26). Increasing genomic resources and tools make it a promising model for studying the evolution of genome size (27,28 Table 1). The phylogenetic relationships among the studied clones and species are summarised in Figure 1.…”