OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Abstract

BackgroundNasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N. vitripennis and two sibling species were published in 2010, yet a considerable amount of transcriptiome data have since been produced thereby enabling improvements to the original (OGS1.2) annotated gene set. We describe and apply the EvidentialGene method used to produce an updated gene set (OGS2). We also carry out comparative analyses showcasing the usefulness of the revised annotated gene set.ResultsThe revised annotation (OGS2) now consists of 24,388 genes with supporting evidence, compared to 18,850 for OGS1.2. Improvements include the nearly complete annotation of untranslated regions (UTR) for 97 % of the genes compared to 28 % of genes for OGS1.2. The fraction of RNA-Seq validated introns also grow from 85 to 98 % in this latest gene set. The EST and RNA-Seq expression data provide support for several non-protein coding loci and 7712 alternative transcripts for 4146 genes. Notably, we report 180 alternative transcripts for the gene lola.Nasonia now has among the most complete insect gene set; only 27 conserved single copy orthologs in arthropods are missing from OGS2. Its genome also contains 2.1-fold more duplicated genes and 1.4-fold more single copy genes than the Drosophila melanogaster genome. The Nasonia gene count is larger than those of other sequenced hymenopteran species, owing both to improvements in the genome annotation and to unique genes in the wasp lineage.We identify 1008 genes and 171 gene families that deviate significantly from other hymenopterans in their rates of protein evolution and duplication history, respectively. We also provide an analysis of alternative splicing that reveals that genes with no annotated isoforms are characterized by shorter transcripts, fewer introns, faster protein evolution and higher probabilities of duplication than genes having alternative transcripts.ConclusionsGenome-wide expression data greatly improves the annotation of the N. vitripennis genome, by increasing the gene count, reducing the number of missing genes and providing more comprehensive data on splicing and gene structure. The improved gene set identifies lineage-specific genomic features tied to Nasonia’s biology, as well as numerous novel genes.OGS2 and its associated search tools are available at http://arthropods.eugenes.org/EvidentialGene/nasonia/, www.hymenopteragenome.org/nasonia/ and waspAtlas: www.tinyURL.com/waspAtlas.The EvidentialGene pipeline is available at https://sourceforge.net/projects/evidentialgene/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2886-9) contains supplementary material, which is available to authorized users.

The Evolution of Venom by Co-option of Single-Copy Genes

“…To determine the venom composition of these four species, we generated proteomes from the venom reservoir, which stores venom prior to injection into the host, and assembled de novo transcriptomes from the venom gland plus reservoir. These data are compared to existing [30–32] and our de novo expression and genome data (see STAR Methods for details).…”

“…For whole body adult transcriptomes, any contigs with expression <2 FPKM were removed. Contigs were ranked from 1 to n based on highest to lowest FPKM and assigned annotations by BLASTp to N. vitripennis genome [30] (OGS2 http://arthropods.eugenes.org/genes2/nasonia/genes/) and NCBI nr database (accessed Feb, 2014). RNAseq produced high quality transcriptomes with each library averaging 97.7% of their reads >90 bp, 44% GC content, and a Phred score of 37.…”

Functional characterization of CYP4G11—a highly conserved enzyme in the western honey bee Apis mellifera

“…Many insects with less sophisticated social behavior have larger genomes, with a greater number of functional protein‐coding genes. Among species within the Hymenoptera, which generally have smaller genomes than species in other holometabolous orders, the eusocial Argentine ant ( Linepithema humile ) has a genome size of about 251 Mb and 16,123 protein‐coding genes (Smith et al, ) and the solitary parasitoid wasp Nasonia vitripennis has a genome 295.78 Mb in size, with approximately 24,388 annotated genes (Rago et al, ), almost 36 more genes per Mb than the honey bee.…”

Evaluating the evolution and function of the dynamic Venom Y protein in ectoparasitoid wasps

“…A). This was considerably smaller than the predicted size of 11.4 kDa for the translated messenger RNA (mRNA) sequence based on de novo transcriptome assembly from venom reservoirs (Martinson et al ., ) and the gene model from the N. vitripennis official gene set (Rago et al ., ). We sequenced the ~5 kDa fragment, which confirmed that the band corresponds to a 5.55 kDa portion of the predicted VenY B protein.…”