A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei

Abstract

BackgroundFor more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it.FindingsWe assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei.ConclusionsWe built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei’s genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

“…Consistently with previous reports from other mytilid species (12,13), the mussel genome is highly heterozygous. The contribution of heterozygosity to the overall intraspecific genomic variation was estimated in Lola and in the resequenced genomes by analyzing common regions in all individuals, in order to overcome the limitations of k-mer-based methods.…”

“…As a matter of fact, bivalve genomes are generally complex, relatively large and highly heterozygous, harboring numerous mobile elements (9)(10)(11)(12)(13). These factors have proved to be particularly challenging in previous assembly efforts in M. galloprovincialis, resulting in extremely fragmented and poorly contiguous genome sequences (8,14).…”

Identification of suitable reference genes for qPCR expression analysis on the gonads of the invasive mussel Limnoperna fortunei

“…The selection was based on the premise that the more stable the gene, the lower the LogFC and CV% values. Transcripts for which the TMM count was zero in at least one of the samples, as well as those which did not match any gene in the reference genome, [9] were not considered.…”

“…Primers were designed to span exon-exon junctions, except for HS6ST3B, which is a single-exon gene. This was based on the exon-intron structure predicted for each gene in the golden mussel reference genome [9]. The presence of secondary structures (hairpin and dimers) in the primers was evaluated using the Oligoanalyzer tool (IDT).…”

“…An important milestone for understanding the biology of this species was the sequencing of its genome [9]. In addition, transcriptomic (RNA-seq) analyses have been performed for tissues such as the digestive glands, foot, mantle, muscle [9,10,11], and, more recently, for tissue from the gonads of both sexes [12]. This latest work characterized the gene expression profile of adult male and female gonads and revealed almost 4000 sex-biased transcripts in this tissue.…”