The salmon louse genome may be much larger than sequencing suggests

Abstract

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3–1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.

A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

“…It is apparent that the size of draft genome assembly is almost twice as large as the estimated genome size based on 17-mer analysis. The most plausible explanation for the genome assembly size deviation may be that the presence of a large number of repetitive elements (87.03%) and high heterozygosity (2.85%) of S. leurokolo genome might induce the assembly has multiple copies of the same genomic region and even contained two divergent haplotypes (Pflug et al ., 2020; Hu et al ., 2022; Wyngaard et al ., 2022). The average GC content of S. leurokolos assembled genome was about 36.12%.…”

Lake Baikal amphipods and their genomes, great and small

“…Genome Size Database (http://www.genomesize.com/) (Gre gory et al, 2007). When comparing data obtained using different methods, it is worth keeping in mind that crustacean genome size estimates obtained with FIAD are typically slightly lower than those obtained with FCM (Wyngaard et al, 2022). Notably, genome size differences accumulate quite rapidly, as evidenced by the differing genome sizes of E. verrucosus lineages (6.1 pg for the E, 6.9 pg for the W, and 8.0 pg for the S lineage) (Drozdova et al, 2022).…”

Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others

“…L. salmonis crustacean has transposons as its largest major content, 55% of 1000 Mb genomic DNA or 1300 Mb by flow cytometry (Wyngaard et al 2022), versus 630 Mb of two recent assemblies (lesal21ncbi_chr, lesal21ioa_chr). However, the L. salmonis assemblies also under-assemble SatDNA contents by a large order (22 Mb repeats assembled of 80-90 Mb in genomic DNA).…”