Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

Abstract

High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation, and prediction when compared to those obtained with short-read technologies, but also allow to understand haplotype divergence. Advances in long-read sequencing technologies in the last years have made it possible to produce such high-quality assemblies for non-model organisms. This allows us to revisit genomes, which have been problematic to scaffold to chromosome-scale with previous generations of data, and assembly software. Nematoda, one of the most diverse, and speciose animal phyla within metazoans, remains poorly studied, and many previously assembled genomes are fragmented. Using long reads obtained with Nanopore R10.4.1 and PacBio HiFi, we generated highly contiguous assemblies of a diploid nematode of the Mermithidae family, for which no closely related genomes are available to date, as well as a collapsed assembly and a phased assembly for a triploid nematode from the Panagrolaimidae family. Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions.

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

“…Thus, a rise in population genomic studies can be associated with the increasing availability of high-quality reference genomes due to advances in long-read sequencing technologies (Guiglielmoni et al 2023; The Darwin Tree of Life Project Consortium 2022; Blaxter et al 2022). Chironomus riparius , a non-biting midge, commonly known as the harlequin fly and distributed in Europe, has been the focus of many molecular genomic studies (e.g.…”

Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha

“…The sizes of few published genomes range from 250-500 Mb and the genomes overall exhibit a reduced gene content when compared to metazoan orthologs. (Cunha et al 2023;Eleftheriadi et al 2023;Guiglielmoni et al 2024;Bhattarai et al 2024;Kirangwa et al 2023). A comprehensive comparative analysis of these genomes within an evolutionary framework remains an unexplored aspect.…”