Biology subjects

Derzelle, A.

Publications and source records attributed to Derzelle, A..

2 recordsLinked to original sources

bioRxiv2020

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

The several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloid A. vaga validated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescent in situ hybridization (FISH), we demonstrate that the A. vaga genome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure of A. vaga and the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonal A. vaga suggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.

evolutionary biology↗

bioRxiv2020

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

BackgroundThird-generation sequencing, also called 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 also error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Although failure to properly collapse haplotypes results in fragmented and/or structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, 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. ResultsTo fill this gap, we tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering out shorter reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups. ConclusionsTesting these strategies separately and in combination revealed several approaches able to generate haploid assemblies with genome sizes, coverage distributions, and completeness close to expectations.

genomics↗