Insights into the genomic evolution of insects from cricket genomes

Abstract

<jats:title>Abstract</jats:title><jats:p>Crickets are currently in focus as a possible source of animal protein for human consumption as an alternative to protein from vertebrate livestock. This practice could ease some of the challenges both of a worldwide growing population and of environmental issues. The two-spotted Mediterranean field cricket <jats:italic>Gryllus bimaculatus</jats:italic> has traditionally been consumed by humans in different parts of the world. Not only is this considered generally safe for human consumption, several studies also suggest that introducing crickets into one’s diet may confer multiple health benefits. Moreover, <jats:italic>G. bimaculatus</jats:italic> has been widely used as a laboratory research model for decades in multiple scientific fields including evolution, developmental biology, neurobiology, and regeneration. Here we report the sequencing, assembly and annotation of the <jats:italic>G. bimaculatus</jats:italic> genome, and the annotation of the genome of the Hawaiian cricket <jats:italic>Laupala kohalensis.</jats:italic> The comparison of these two cricket genomes with those of 14 additional insects supports the hypothesis that a relatively small ancestral insect genome expanded to large sizes in many hemimetabolous lineages due to transposable element activity. Based on the ratio of observed versus expected CpG sites (CpG<jats:sub>o/e</jats:sub>), we find higher conservation and stronger purifying selection of typically methylated genes than of non-methylated genes. Finally, our gene family expansion analysis reveals an expansion of the <jats:italic>pickpocket</jats:italic> class V gene family in the lineage leading to crickets, which we speculate might play a relevant role in cricket courtship behavior, including their characteristic chirping.</jats:p>

Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

“…Given the deep divergence of Eumastacoidea and Acridoidea (~197 mya [33]), the two Orthopteran superfamilies to which the viatica species group and the locusts grasshoppers belong, respectively, these findings suggest that large repeatomes are widespread in grasshoppers. The S. gregaria genome assembly has 18,815 annotated genes, and the L. migratoria genome assembly has a similar number of annotated genes (17,307) to those recently reported in two cricket species with genome assembly sizes of 1.6 Gb (TE content 40 %; [75]), indicating the absence of partial or whole genome duplication events in these orthopteran lineages. Additionally, there was no evidence for such large-scale genome duplication events in the viatica species group because only 3-5 % of BUSCO genes were duplicated.…”

Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

“…We found that 14 of the 17 primary optimal codons (one per amino acid) that were previously identified using a partial transcriptome from one pooled tissue sample (embryos/ovaries [10]), were identical to those observed here, marking a strong concordance between studies and datasets (the differences herein were CAA for Gln, TTA for Leu, and AGA for Arg as optimal codons, and the presence of an optimal codon AAA for Lys, which had no optimal codon using previous embryonic/ovary data [10]). Thus, the present analysis using largescale RNA-seq from nine divergent tissues (Additional file 1: Table S1) and using a complete annotated genome [65] support a strong preference for AT3 codons in this cricket. Importantly, the expression datasets herein (Additional file 1: Table S1) allowed us to conduct an assessment of whether the identity of optimal codons varied with tissue type or sex.…”

“…For our study, codon and amino acid use in G. bimaculatus was assessed using genes from its recently available annotated genome [65]. We included all 15,539 G. bimaculatus protein-coding genes (CDS, longest CDS per gene) that had a start codon and were >150bp.…”

“…G. bimaculatus comprises a model for investigations in genetics [59,60], germ line formation and development [61][62][63] and for molecular evolutionary biology [10,64]. In the present study, we rigorously assess codon and amino acid use in highly transcribed genes of G. bimaculatus using its recently available annotated genome [65] and large-scale RNA-seq data from tissues of the male and female reproductive and nervous systems [64]. From our analyses, we demonstrate that optimal codons, those preferentially used in highly expressed genes, occur in this organism, are largely shaped by selection pressures, and are nearly identical across tissues.…”

Evolutionary dynamics of sex-biased genes expressed in cricket brains and gonads

“…Unlike Drosophila, Gryllus is currently an emerging model genus with few genomic resources outside the aforementioned recent G. bimaculatus genome [59]. Thus, to measure dN/dS, we generated and assembled novel RNA-seq data for its sister species G. assimilis to obtain a CDS list for that organism (Additional file 1: Table S2).…”