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.

Keywords: Nematoda; genome annotation; genome assembly; genomics; long reads.

FIGURE 1

Initial analyses of the long reads. (A) Quality and length of Nanopore and PacBio HiFi reads. (B) k-mer analysis of the ploidy of the genomes using PacBio HiFi reads.

FIGURE 2

Draft assembly statistics of PacBio HiFi reads (red), Nanopore reads (blue) and the two combined (purple) with assembly size (in Mb), N50 (in kb) and BUSCO completeness against the Metazoa and Nematoda lineages.

FIGURE 3

Comparison of assemblies based on TE (top) count and BUSCO ortholog (bottom) statistics for the protein annotations (against the Metazoa and Nematoda lineages) shows higher repeat and gene completeness of the new assemblies.

FIGURE 4

Ortholog analysis of Panagrolaimus sp. PS1159 collapsed and phased assemblies supports triploidy. The histograms represent the number of orthologs with their copy number from the lineages Metazoa and Nematoda identified in the protein-coding genes annotated for P. sp. PS1159. In the collapsed assembly, the majority of orthologs are present in a single copy, while most orthologs are in three copies in the phased assembly.