Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking.
https://doi.org/10.1186/s12859-021-04118-3

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.
https://doi.org/10.1126/sciadv.abg4216

Homologous recombination plays a fundamental role in the evolution of organisms. It serves as a DNA repair mechanism which, in sexual organisms, contributes to genetic diversity through the shuffling of alleles during meiosis. Here we investigate the two functions of homologous recombination in the bdelloid rotifer Adineta vaga, an ancient asexual species also known for its tolerance to extreme genotoxic stresses. Genomic analyses reveal that A. vaga retained meiotic recombination mechanisms, both for DNA repair and occurrence of spontaneous crossovers during oogenesis. Our study introduces a novel transgenerational DNA repair mechanism termed break-induced homologous extension repair (BIHER). BIHER operates on single DNA ends, enabling the repair of fragmented chromosomes. Our findings suggest that the BIHER mechanism, combined with a holocentric structure of chromosomes and a modified meiosis, constitutes a key adaptation for life in extreme environments. Identifying such a mechanism in bdelloid rotifers sheds a new light on the strategies that evolved to maintain genome structure in asexually reproducing species.
GitHub
https://doi.org/10.1101/2024.01.25.577190

This tool assesses the haploidy H of a given assembly. H is defined as the fraction of the bases of the genome that are in the collapsed peak C. This metrics is calculated as H=C/(C+U/2), where C is the size (area) of the collapsed peak and U the size of the uncollapsed peak in the per-base coverage histogram of the assembly. For more information, see: Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
GitHub
https://doi.org/10.5281/zenodo.4292076