Sequencing and De Novo Assembly of the Transcriptome of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)

Abstract

BackgroundThe glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce’s disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference.ResultsHere we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1−5) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements.ConclusionsOur data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.

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

“…1 and 2). The distribution of GO terms within the ontology categories is consistent with other insect transcriptomes (Hull et al 2013;Nandety et al 2013). These sequences were then grouped into 58 subcategories (Fig.…”

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…Velvet and Oases, common assembly programs in de novo transcriptomic studies using Illumina reads, were employed to assemble the processed reads [7,10,14,21,22,34,35,42,43]. It should be noted that the quality of the de novo transcriptome assembly is reliant on the user-defined k-mer value characterized as the length parameter defining the sequence overlap between two reads forming a contiguous sequence (referred as a contig) [44,45].…”

“…(Table 1). Velvet and Oases, common assembly programs successfully used in previous Illumina based de novo transcriptome studies, were employed to perform the assembly [7,10,14,21,22,34,35]. The paired-end sequence reads were assembled into 254,446 contigs with an N50 length of 1,324 bp and average contig length of 831.68 bp ( Table 2).…”

“…The first is the reduction fishery that turns the menhaden into fish oil omega-3 supplements for example, and into fishmeal for livestock and aquaculture consumption [4,5]. The second is the bait fishery that uses the menhaden as bait for bluefish, crab, and lobster [6][7][8][9][10][11][12][13][14][15]. They have been rarely studied at the genetic level most likely due to the lack of genomic and transcriptome data.…”

Emerging strategies for RNA interference (RNAi) applications in insects

“…Additionally transcript information and annotation of novel transcriptome data can be obtained through BLAST homology and annotations from Gene Ontology databases. 62 Halyomorpha halys 63 and the references there after. After target selection, further consideration must be given to many factors including size of the RNAi inducer (short vs long), distal vs. proximal ends of the target match (5', 3' or in the central region of the target), etc.…”