Abstract
BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.ResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.ConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
Highlights
The Hemiptera are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics
We thereby identify genes with potentially restricted life history expression in Oncopeltus and that are unique to the Hemiptera, clarify evolutionary patterns of zinc finger protein family expansion, categorize predictors of insect gene structure, and identify lateral gene transfer and amino acid metabolism features that correlate with feeding biology
We find several lateral gene transfer (LGT) potentially involved in bacterial or plant cell wall metabolism that were acquired from different bacterial sources at different times during hemipteran lineage evolution, including 2 distinct LGTs that are unique to Oncopeltus and implicated in the synthesis of peptidoglycan, a bacterial cell wall constituent (Additional file 1: Supplemental Note 2.2)
Summary
The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, and to elucidate patterns of molecular evolution and physiology. Lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera prompted the evaluation of lineage and genome size as predictors of gene structure evolution. We identify enzymatic gains and losses that correlate with feeding biology, for reductions associated with derived, fluid nutrition feeding
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