De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis

Abstract

BackgroundThis study aimed at enhancing the transcriptomic resources for two sibling species of moths, Ostrinia scapulalis (Adzuki bean borer) and Ostrinia nubilalis (European corn borer), as a foundation for future researches on their divergence history. Previous works on these species had shown that their genetic divergence was low, while they were reproductively isolated in natura and specialized on different host plants. Comparative genomic resources will help facilitate the understanding of the mechanisms involved in this isolation and adaptation to the host plants. Despite their fundamental interest, these species still lack the genomic resources to thoroughly identify candidate genes for functions of interest. We present here a high throughput sequencing and de novo transcriptome assembly for these two sibling species in line with this objective of comparative genomics.ResultsBased on 322,504 and 307,622 reads of 454 sequencing for O. scapulalis and O. nubilalis respectively, we reconstructed 11,231 and 10,773 transcripts, of which 40% were functionally annotated by BLAST analyzes. We determined the level of completeness of both assemblies as well as the recovery level of published Ostrinia genomic resources. Gene ontology (GO) of common and species-specific de novo transcripts did not reveal GO terms significantly enriched in one or the other species. By applying stringent homology searches on transcripts common to O. scapulalis and O. nubilalis, we identified a set of homologous transcripts, with a mean nucleotide identity value of 98.1%. In this set, the most divergent transcripts revealed candidate genes involved in developmental, sensorial and pathogen defense processes.ConclusionsThis data greatly increases the genomic resources of Ostrinia species and constitute a solid skeleton for future comparative analyzes of expression or diversity, despite we show that the transcriptomes for both species have not been assembled at full completion. In addition, we provide a set of homologous transcripts together with their annotation as a source of candidate genes for comparative analyzes.

Transcriptome Comparison Analysis of Ostrinia furnacalis in Four Developmental Stages

“…The rapid development of next-generation sequencing, such as Illumina sequencing, has provided cost-effective methods for the transcriptomic characterization of insect species that lack a fully-sequenced genome. Many insects have been sequenced, including the ACB 12 13 14 15 and its sibling species, the European corn borer 16 17 . The deeper sequencing coverage of Illumina sequencing combined with de novo transcriptome assembly will facilitate the characterization of genes in the absence of a reference genome.…”

De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)

“…Further comparative analysis of the reference transcripts with the Lepbase [23] reference protein set detected probable homologs for 20,835 transcripts. OHR analyzes [12] on the best matches indicated that 61% of the CDS were reconstructed at least at 60% of the corresponding reference lepidopteran protein homolog, whereas 43% of the transcript CDS were assembled at full length.…”

“…To further investigate the host adaptation and divergence between these two sibling species at a pangenomic scale, we have elaborated new genomic and transcriptomic resources consisting of an OSCA draft genome and a related reference transcriptome. The latter extends a published transcriptomic set generated with Roche 454 sequencing technology [12] .…”

Transcriptomic response of female adult moths to host and non-host plants in two closely related species

“…First, we applied default parameters and the normalization procedure of the Trinity package (version r20140413p1 [ 28 ]) to assemble high quality reads of the 12 ECB libraries and of the 12 ABB libraries separately into two comprehensive transcriptomes. Then, for each of the resulting ECB and ABB assemblies, we included a 454 de novo transcript set previously obtained by Gschloessl et al [ 27 ] from four ECB and four ABB adults, respectively. Such meta-assemblies that combine different technologies of sequencing reads have been proved to increase contig length and coverage in other studies [ 50 , 61 ].…”