Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica

Abstract

The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better understanding of its gene expression and develop genomic resources for future work. We sequenced and explored the characteristics of the de novo transcriptome of T. japonica using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end clean reads were assembled into 61 141 unigenes using the trinity software; the mean unigene size was 771 bp, and the N50 length was 1238 bp. A total of 29 225 unigenes were functionally annotated to the NCBI nonredundant protein sequences (Nr), NCBI nonredundant nucleotide sequences (Nt), a manually annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of putative genes that are potentially involved in pigment pathways, juvenile hormone (JH) metabolism and signalling pathways were identified in the T. japonica transcriptome. Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms occurred in the adult and larvae transcriptomes, respectively, and a total of 3162 simple sequence repeats were detected in this assembly. This comprehensive transcriptomic data for T. japonica will provide a usable resource for gene predictions, signalling pathway investigations and molecular marker development for this species and other pygmy grasshoppers.

Contrasting patterns of neutral and functional genetic diversity in stable and disturbed environments

“…A transcriptomic analysis on Tetrix japonica —a closely related pygmy grasshopper species (see Figure S1 in Forsman, )—has identified several putative pigment‐related genes and differential expression patterns of them between adults and larval phases in this species (Qiu, Liu, Lu, & Huang, ). Moreover, putative genes involved in juvenile hormone metabolism and signaling pathways that regulate the body color and flight activity in insects are available for the same species (Qiu et al., ). A genomic approach taking advantage of advances in sequences technologies such as restriction site‐associated DNA sequencing (e.g., RADseq) and of the available genome‐wide sequencing data and protein expression profiles from related species can generate a more comprehensive understanding of the genes/loci under selection.…”

Ommochromes in invertebrates: biochemistry and cell biology

“…More recently, developmental biologists have used ommochromes of butterfly wings to tackle the mechanisms and the diversity of colour patterning (Sekimura & Nijhout, ). Today, ommochromes are also involved in transcriptomic studies of grasshoppers, butterflies, damselflies and spiders (Croucher et al, ; Chauhan et al, ; Connahs, Rhen & Simmons, ; Qiu et al, ; Wang et al, ), as well as in clustered regular interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9)‐mediated genome editing (Khan, Reichelt & Heckel, ; Xue et al, ; Zhang & Reed, ). Unfortunately, biochemical knowledge did not keep pace with this increase in functional studies.…”

De novo transcriptome characterization of a sterilizing trematode parasite (Microphallus sp.) from two species of New Zealand snails

“…After these steps, PrimerPro V.1.0 outputs the putative microsatellites, the primer sequences, their transcriptomic locations, and the primer properties. Following Qiu et al (2016), we allowed for a minimum of ten repeats for mononucleotide repeats, six for dinucleotide repeats, five for trinucleotide repeats, four for tetranucleotide repeats, three for pentanucleotide repeats, and three for hexanucleotide repeats, and identified compound microsatellites as instances where there was more than one microsatellite separated by less than or equal 150 nucleotides.…”