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Research Article

Draft genome of the red harvester ant Pogonomyrmex barbatus

Chris R. Smith, Christopher D. Smith, Hugh M. Robertson, Martin Helmkampf, Aleksey Zimin, Mark Yandell, Carson Holt, Hao Hu, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Favé, Vilaiwan Fernandes, Joshua D. Gibson, Dan Graur, Wulfila Gronenberg, Kirk J. Grubbs, Darren E. Hagen, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Kaitlyn A. Mathis, Monica C. Munoz-Torres, Marguerite C. Murphy, Julie A. Mustard, Rin Nakamura, Oliver Niehuis, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Garret Suen, Shu Tao, Candice W. Torres, Neil D. Tsutsui, Lumi Viljakainen, Florian Wolschin, and Jürgen Gadau
PNAS April 5, 2011 108 (14) 5667-5672; https://doi.org/10.1073/pnas.1007901108
Chris R. Smith
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Christopher D. Smith
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Hugh M. Robertson
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Martin Helmkampf
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Aleksey Zimin
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Mark Yandell
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Carson Holt
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Hao Hu
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Ehab Abouheif
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Richard Benton
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Elizabeth Cash
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Vincent Croset
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Cameron R. Currie
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Eran Elhaik
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Christine G. Elsik
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Marie-Julie Favé
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Vilaiwan Fernandes
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Joshua D. Gibson
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Dan Graur
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Wulfila Gronenberg
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Kirk J. Grubbs
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Darren E. Hagen
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Ana Sofia Ibarraran Viniegra
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Brian R. Johnson
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Reed M. Johnson
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Abderrahman Khila
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Jay W. Kim
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Kaitlyn A. Mathis
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Monica C. Munoz-Torres
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Marguerite C. Murphy
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Julie A. Mustard
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Rin Nakamura
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Oliver Niehuis
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Surabhi Nigam
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Rick P. Overson
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Jennifer E. Placek
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Rajendhran Rajakumar
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Justin T. Reese
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Garret Suen
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Shu Tao
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Candice W. Torres
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Neil D. Tsutsui
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Lumi Viljakainen
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Florian Wolschin
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Jürgen Gadau
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  • For correspondence: jgadau@asu.edu
  1. Edited* by Gene E. Robinson, University of Illinois at Urbana–Champaign, Urbana, IL, and approved November 9, 2010 (received for review June 5, 2010)

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    Fig. 1.

    A pictorial description of the phylogenetic position of the samples used for the genome and transcriptome sequencing, with each put in the context of environmental and genetic caste determination (for a more complete phylogenetic tree, see SI Appendix, Chapter 1). The dependent lineages (H1/H2 or J1/J2) obligately co-occur because hybridization between them is necessary to produce workers, although within either J or H, the constituent lineages are reproductively isolated because interlineage hybrids cannot become queens (red/blue box). In the boxes to the right, workers are represented by “horned” female symbols. In all P. barbatus, the queen mates multiply; polyandry in genetic caste determining (GCD) colonies is obligate to produce both female castes (queens originate from intralineage matings and workers from interlineage matings). In environmental caste determination (ECD), alleles from any father have an equal chance to be in queens or workers (black box). Photo of gyne and worker P. barbatus by C. R. Smith.

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    Fig. 2.

    Genome-wide analyses of nucleotide and relative gene content. (A) Synopsis of GC and CpG(o/e) content of the P. barbatus genome. (Upper panels) Comparison of genome regions with the same GC composition. (Lower panels) Comparison of the same features for exons. These distributions are similar to those found in other hymenopterans, except that P. barbatus shows no evidence of bimodality in CpG(o/e) for either exons (like A. mellifera) or introns (like N. vitripennis) (for comparisons, see SI Appendix, Chapter 4). (B) A Venn diagram displaying overlap in orthologous genes in three hymenopteran and one dipteran insect (for a detailed description of the method, see SI Appendix, Chapter 5). A subset of gene ontology terms significantly enriched in P. barbatus are displayed at the right. (*) Hymenoptera-specific genes; (+) social Hymenoptera-specific genes.

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    Fig. 3.

    Evolutionary rate and the accumulation of pseudogene-causing (“pseudogenizing”) mutations in three gene families in the ant P. barbatus (green), the honey bee A. mellifera (red), and the jewel wasp N. vitripennis (blue). (A) The relationships among analyzed taxa. (B) A comparison of the evolutionary rates based amino acid substitutions in a set of 4,774 orthologs shared among the three species and D. melanogaster (the outgroup). (C) The accumulation of pseudogenizing mutations in three ecologically relevant gene families (Gr, Or, and cytochrome P450s). The number of pseudogenes found in each species is below the gene family name in each panel. Only one gene represents the Grs in A. mellifera; all other A. mellifera Gr pseudogenes had accrued a very high number of mutations and most are fragments. Of those analyzed here, the pseudogenes in P. barbatus tend to be much older than those in A. mellifera and N. vitripennis (ANOVA: F2,156 = 4.7, P = 0.01).

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    Table 1.

    Comparison of metrics for recently sequenced insect genomes

    SpeciesOrder/nameFold coverageN50 scaffold (kb)No. of genesGene setSource
    Pogonomyrmex barbatusHymenoptera (red harvester ant)1279317,177OGS1.1This study
    Nasonia vitripennisHymenoptera (jewel wasp)6.870918,822OGS1.2(6)
    Apis melliferaHymenoptera (honey bee)7.536210,156/21,001OGS1/OGS2(5)
    Acyrthosiphon pisumSternorrhyncha (pea aphid)6.288.534,604OGS1(37)
    Tribolium castaneumColeoptera (red flower beetle)7.399016,404Consensus set(38)

Data supplements

  • Supporting Information

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    • Download Dataset_S02 (XLS)
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Draft genome of the red harvester ant Pogonomyrmex barbatus
Chris R. Smith, Christopher D. Smith, Hugh M. Robertson, Martin Helmkampf, Aleksey Zimin, Mark Yandell, Carson Holt, Hao Hu, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Favé, Vilaiwan Fernandes, Joshua D. Gibson, Dan Graur, Wulfila Gronenberg, Kirk J. Grubbs, Darren E. Hagen, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Kaitlyn A. Mathis, Monica C. Munoz-Torres, Marguerite C. Murphy, Julie A. Mustard, Rin Nakamura, Oliver Niehuis, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Garret Suen, Shu Tao, Candice W. Torres, Neil D. Tsutsui, Lumi Viljakainen, Florian Wolschin, Jürgen Gadau
Proceedings of the National Academy of Sciences Apr 2011, 108 (14) 5667-5672; DOI: 10.1073/pnas.1007901108

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Draft genome of the red harvester ant Pogonomyrmex barbatus
Chris R. Smith, Christopher D. Smith, Hugh M. Robertson, Martin Helmkampf, Aleksey Zimin, Mark Yandell, Carson Holt, Hao Hu, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Favé, Vilaiwan Fernandes, Joshua D. Gibson, Dan Graur, Wulfila Gronenberg, Kirk J. Grubbs, Darren E. Hagen, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Kaitlyn A. Mathis, Monica C. Munoz-Torres, Marguerite C. Murphy, Julie A. Mustard, Rin Nakamura, Oliver Niehuis, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Garret Suen, Shu Tao, Candice W. Torres, Neil D. Tsutsui, Lumi Viljakainen, Florian Wolschin, Jürgen Gadau
Proceedings of the National Academy of Sciences Apr 2011, 108 (14) 5667-5672; DOI: 10.1073/pnas.1007901108
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