Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.
Panfilio KA., Vargas Jentzsch IM., Benoit JB., Erezyilmaz D., Suzuki Y., Colella S., Robertson HM., Poelchau MF., Waterhouse RM., Ioannidis P., Weirauch MT., Hughes DST., Murali SC., Werren JH., Jacobs CGC., Duncan EJ., Armisén D., Vreede BMI., Baa-Puyoulet P., Berger CS., Chang C-C., Chao H., Chen M-JM., Chen Y-T., Childers CP., Chipman AD., Cridge AG., Crumière AJJ., Dearden PK., Didion EM., Dinh H., Doddapaneni HV., Dolan A., Dugan S., Extavour CG., Febvay G., Friedrich M., Ginzburg N., Han Y., Heger P., Holmes CJ., Horn T., Hsiao Y-M., Jennings EC., Johnston JS., Jones TE., Jones JW., Khila A., Koelzer S., Kovacova V., Leask M., Lee SL., Lee C-Y., Lovegrove MR., Lu H-L., Lu Y., Moore PJ., Munoz-Torres MC., Muzny DM., Palli SR., Parisot N., Pick L., Porter ML., Qu J., Refki PN., Richter R., Rivera-Pomar R., Rosendale AJ., Roth S., Sachs L., Santos ME., Seibert J., Sghaier E., Shukla JN., Stancliffe RJ., Tidswell O., Traverso L., van der Zee M., Viala S., Worley KC., Zdobnov EM., Gibbs RA., Richards S.
BACKGROUND: The 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. RESULTS: The 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. CONCLUSIONS: With 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.