The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

Evans, Jay D.; Brown, Susan J.; Hackett, Kevin J.; Robinson, Gene E.; Richards, Stephen; Lawson, Daniel; Elsik, Christine G.; Coddington, Jonathan A.; Edwards, Owain; Emrich, Scott J.; Gabaldón, Toni; Goldsmith, Marian R.; Hanes, Glenn; Misof, Bernard; Muñoz-Torres, Monica; Niehuis, Oliver; Papanicolaou, Alexie; Pfrender, Michael E.; Poelchau, Monica F.; Purcell-Miramontes, Mary; Robertson, Hugh M.; Ryder, Oliver A.; Tagu, Denis; Torres, Tatiana Teixeira; Zdobnov, Evgeny M.; Zhang, Guojie; Zhou, Xin

doi:10.1093/jhered/est050

Cited by 335 publications

(131 citation statements)

References 3 publications

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“…Efforts are underway to sequence and annotate the genomes of many insects and crustacea because of their important impact on disease and food production (i5K Consortium 2013). With readthrough so abundant in these species, it is important to recognize and annotate readthrough genes in order to complete the reference annotations of these genomes for use in studies to elucidate gene function.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Dynamics of Abundant Stop Codon Readthrough

et al. 2016

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Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.

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Section: Discussionmentioning

confidence: 99%

Evolutionary Dynamics of Abundant Stop Codon Readthrough

et al. 2016

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“…However, some measures to minimize the chance of harmful effects on non-target organisms, such as avoiding very conserved regions of the target gene, could already be taken for these insects of which the genome has not been sequenced. Furthermore, efforts in filling this sequence data gap are ongoing and increasing at a rapid rate, for instance with the i5k project43.…”

Section: Discussionmentioning

confidence: 99%

RNA interference: a promising biopesticide strategy against the African Sweetpotato Weevil Cylas brunneus

Christiaens

Prentice

Pertry

et al. 2016

Sci Rep

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The African sweetpotato weevil Cylas brunneus is one of the most devastating pests affecting the production of sweetpotatoes, an important staple food in Sub-Saharan Africa. Current available control methods against this coleopteran pest are limited. In this study, we analyzed the potential of RNA interference as a novel crop protection strategy against this insect pest. First, the C. brunneus transcriptome was sequenced and RNAi functionality was confirmed by successfully silencing the laccase2 gene. Next, 24 potential target genes were chosen, based on their critical role in vital biological processes. A first screening via injection of gene-specific dsRNAs showed that the dsRNAs were highly toxic for C. brunneus. Injected doses of 200ng/mg body weight led to mortality rates of 90% or higher for 14 of the 24 tested genes after 14 days. The three best performing dsRNAs, targeting prosα2, rps13 and the homolog of Diabrotica virgifera snf7, were then used in further feeding trials to investigate RNAi by oral delivery. Different concentrations of dsRNAs mixed with artificial diet were tested and concentrations as low as 1 μg dsRNA/ mL diet led to significant mortality rates higher than 50%.These results proved that dsRNAs targeting essential genes show great potential to control C. brunneus.

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“…[50]. We additionally screened genomes of the following species for IBP-coding genes (see Additional file 2: Table S1 for accession numbers): Drosophila wilistoni [51], Aedes aegypti [52], Anopheles gambiae (Diptera) [53], Bombyx mori (Lepidoptera) [54], Limnephilus lunatus (Trichoptera), Machilis hrabei (Archaeognatha), Catajapyx aquilonaris (Diplura), Ephemera danica (Ephemeroptera), and Ladona fulva (Odonata) [55]. …”

Section: Methodsmentioning

confidence: 99%

Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

et al. 2016

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BackgroundBody plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods.ResultsOur study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection.ConclusionsOur results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3205-1) contains supplementary material, which is available to authorized users.

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The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

Cited by 335 publications

References 3 publications

Evolutionary Dynamics of Abundant Stop Codon Readthrough

Evolutionary Dynamics of Abundant Stop Codon Readthrough

RNA interference: a promising biopesticide strategy against the African Sweetpotato Weevil Cylas brunneus

Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

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