The American lobster genome reveals insights on longevity, neural, and immune adaptations

Abstract

The American lobster, Homarus americanus, is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the H. americanus genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.

The NGS Magic Pudding: A Nanopore-Led Long-Read Genome Assembly for the Commercial Australian Freshwater Crayfish, Cherax destructor

“…The number of predicted proteins with InterPro signatures is very similar to other species of decapod crustaceans ( Tan et al, 2016 ). While the total number of predicted protein-coding genes is large (45,673) relative to those that have an Interpro signature, this number does not differ greatly from the recently published genome for the clawed lobster, Hommarus americanus , which identified 40,732 peptides ( Polinski et al, 2021 ). This high proportion of unique genes is most likely a function of the evolution of a large repetitive genome and the limited genomic data for crayfish and lobsters as pointed out by Polinski et al (2021) in their recent study of he American lobster ( Polinski et al, 2021 ).…”

“…While the total number of predicted protein-coding genes is large (45,673) relative to those that have an Interpro signature, this number does not differ greatly from the recently published genome for the clawed lobster, Hommarus americanus, which identified 40,732 peptides (Polinski et al, 2021). This high proportion of unique genes is most likely a function of the evolution of a large repetitive genome and the limited genomic data for crayfish and lobsters as pointed out by Polinski et al (2021) in their recent study of he American lobster (Polinski et al, 2021). Significantly, Cherax destructor harbours the highest number of cellulase genes among the currently sequenced decapod crustaceans (Figure 3A) with a substantially higher number of GH9 cellulase genes comparable to its close relative, C. quadricarinatus, which was previously highlighted in an earlier transcriptomic study (Tan et al, 2016).…”

“…The assembled genome size was ∼27.0% smaller than the genome size estimate. This is quite a common outcome for decapod genome assemblies due to sequencing bias and their repetitive genomes (Tan et al, 2020a;Polinski et al, 2021) and was reflected in the uneven distribution of read depths across scaffolds in our study. Over 3,000 scafolds have over 300x coverage, compared with an average read depth of 111x, consistent with the occurence of a significant proportion of repeat regions and potentially contributing to the discrepency between the assembled genome size and the genome size estimate.…”

“…Then, the predicted C. destructor proteins that formed orthologous clusters with at least one of the decapod species were used for subsequent annotation and analysis. Specific comparisons of peptide homology were made with several decpod crustaceans including the recently published clawed lobster genome (clawed lobsters are from the clade most closely related to the freshwater crayfish) ( Polinski et al, 2021 ), the southern hemisphere crayfish ( Cherax quadricarinatus ) using NCBI’s blastx (evalue 1e −10 ). Putative protein functions were inferred using InterproScan v5.35-74.0 ( Jones et al, 2014 ) with the options “—iprlookup –goterms --dp”.…”

The salmon louse genome may be much larger than sequencing suggests

“…Similarly, genome assembly based on k-mer analysis of the lobster Homarus americanus is believed to be missing approximately 28% of the genome [59]. The salmon louse genome is among the crustaceans with highest occurrence of repetitive elements; ≈60% of the assembly annotated as repeats [40], suggesting that such underestimation of size may not be implausible.…”