Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

Christopher D. Smith; Aleksey Zimin; Carson Holt; Ehab Abouheif; Richard Benton; Elizabeth Cash; Vincent Croset; Cameron R. Currie; Eran Elhaik; Christine G. Elsik; Marie-Julie Fave; Vilaiwan Fernandes; Jürgen Gadau; Joshua D. Gibson; Dan Graur; Kirk J. Grubbs; Darren E. Hagen; Martin Helmkampf; Jo-Anne Holley; Hao Hu; Ana Sofia Ibarraran Viniegra; Brian R. Johnson; Reed M. Johnson; Abderrahman Khila; Jay W. Kim; Joseph Laird; Kaitlyn A. Mathis; Joseph A. Moeller; Monica C. Muñoz-Torres; Marguerite C. Murphy; Rin Nakamura; Surabhi Nigam; Rick P. Overson; Jennifer E. Placek; Rajendhran Rajakumar; Justin T. Reese; Hugh M. Robertson; Chris R. Smith; Andrew V. Suarez; Garret Suen; Elissa L. Suhr; Shu Tao; Candice W. Torres; Ellen van Wilgenburg; Lumi Viljakainen; Kimberly K. O. Walden; Alexander L. Wild; Mark Yandell; James A. Yorke; Neil D. Tsutsui

doi:10.1073/pnas.1008617108

New Research In

Edited* by Gene E. Robinson, University of Illinois, Urbana, IL, and approved January 11, 2011 (received for review June 17, 2010)

Abstract

Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

Footnotes

↵¹To whom correspondence may be addressed. E-mail: ntsutsui{at}berkeley.edu or smithcd{at}sfsu.edu.

Author contributions: C.D.S. and N.D.T. designed research; C.D.S., A.Z., C.H., E.A., R.B., E.C., V.C., E.E., C.G.E., M.-J.F., V.F., J.G., J.D.G., D.G., D.E.H., M.H., H.H., A.S.I.V., B.R.J., R.M.J., A.K., J.W.K., J.L., M.C.M.-T., R.N., R.P.O., J.E.P., R.R., J.T.R., H.M.R., C.R.S., A.V.S., S.T., C.W.T., E.v.W., L.V., K.K.O.W., M.Y., and N.D.T. performed research; C.D.S., A.Z., C.H., C.G.E., M.C.M., S.N., H.M.R., M.Y., and N.D.T. contributed new reagents/analytic tools; C.D.S., A.Z., C.H., E.A., R.B., E.C., V.C., C.R.C., E.E., C.G.E., M.-J.F., V.F., J.G., J.D.G., D.G., K.J.G., D.E.H., M.H., J.-A.H., H. H., A.S.I.V., B.R.J., R.M.J., A.K., J.W.K., J.L., K.A.M., J.A.M., M.C.M.-T., R.N., R.P.O., J.E.P., R.R., J.T.R., H.M.R., C.R.S., A.V.S., G.S., E.L.S., S.T., C.W.T., E.v.W., L.V., K.K.O.W., A.L.W., M.Y., J.A.Y., and N.D.T. analyzed data; and C.D.S., A.Z., C.H., E.A., R.B., E.C., V.C., C.R.C., E.E., C.G.E., M.-J.F., V.F., J.G., J.D.G., D.G., D.E.H., M.H., H.H., A.S.I.V., R.M.J., A.K., K.A.M., M.C.M.-T., R.P.O., J.E.P., R.R., J.T.R., H.M.R., C.R.S., G.S., S.T., C.W.T., E.v.W., L.V., M.Y., and N.D.T. wrote the paper.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database [accession nos. 46575 (transcriptome), 45799 (genome), and 45805 (genome project)].
See Commentary on page 5477.
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