Comparative analysis of the Tribolium genome

Findings:

  • Phylogenetic tree (unrooted) relating 5 insect and 5 vertebrate species suggests more basal Hymenoptera radiation, rather than commonly believed Coleoptera. The tree was computed using maximum-likelihood method as implemented in PHYML and TREE-PUZZLE (JTT model with a gamma correction using 4 discrete classes, an estimated alpha parameter and proportion of invariable sites) on concatenated 336,069 aa positions extracted with Gblocks from Muscle alignment of 1,150 universal single-copy orthologs identified using our automatic procedure from the official gene sets (Ensembl for vertebrates). The shown values of statistical support were obtained from 500 replicates of bootstrap analyses. The species names are abbreviated from Latin names.
  • Comparison of gene repertoire of 5 insect and 5 vertebrate genomes , ranging from the metazoan core genes (dark fraction on the left) to the species-unique sequences (white band). The striped boxes correspond to insect- and vertebrate-specific orthologous genes. ‘N:N:N’ indicates orthologs present in multiple copies in all species (allowing one loss), and ‘Patchy’ indicates ancient orthologs differentially lost in some lineages (requiring at least two insect and two vertebrate genes).
  • Comparison of gene family size dynamics (see the table below) showed most prominent expansions of MSF small-solute-transporters and nucleases in Tribolium as compared to other insects (honey bee, fruit fly and two mosquitoes).
  • We are concentrating now on more detail analysis of orthologous gene losses and expansions.
    An example of an expansion is a subset of Cytochrome P450 genes thought to be involved in insecticide resistance, having 19 genes in Tribolium.
    The preliminary phylogenetic analysis confirms this Tribolium gene expansion and shows that these duplications are not very recent.
    DMEL AGAM AAED AMEL TCAS TNIG GGAL MDOM MMUS HSAP
    7 2 5 3 19 0 0 1 1 0
  • Cytochrome P450 genes in insects
    (maximum-likelihood majority-rule tree using phyml, in collaboration with David Nelson)
  • Data (T.cas, A.aeg, A.gam, D.mel, A.mel):

  • Orthologous groups (distribution of orthologs, distribution of phylogenetic patterns) computed using all_vs_all Smith-Waterman homology comparisons. 
  • The major gene families defined using InterPro 
  • Publication:

    The genome of the model beetle and pest Tribolium castaneum.

    Tribolium Genome Sequencing Consortium; Project leader, Richards S; Principal investigators, Gibbs RA, Weinstock GM; White paper, Brown SJ, Denell R, Beeman RW, Gibbs R; Analysis leaders, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM; DNA sequence and global analysis: DNA sequencing, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R; EST sequencing, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA; genome assembly, Liu Y, Worley K, Weinstock G; G+C content, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D; repetitive DNA, transposons and telomeres, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S; gene prediction and consensus gene set, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM; global gene content analysis, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P; Developmental processes and signalling pathways, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X; Pest biology, senses, Medea and RNAi: ligand gated ion channels, Jones AK, Sattelle DB; oxidative phosphorylation, Ebert PR; P450 genes, Nelson D, Scott JG, Beeman RW; chitin and cuticular proteins, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R; digestive proteinases, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C; immunity, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H; neurohormones and GPCRs, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P; neuropeptide processing enzymes, Raible F, Bork P; opsins, Friedrich M; odorant receptors and gustatory receptors, Walden KK, Robertson HM; odorant binding and chemosensory proteins, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA; Medea, Beeman RW, Lorenzen M; systemic RNAi, Tomoyasu Y, Miller SC, Grossmann D, Bucher G.
    Nature. 2008 Mar 23
    PMID: 18362917

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    InsVert-tree.pdf99.71 KB
    og12004-phyml-tree-1000bootstraps.pdf2.47 KB
    orthologous_groups.txt3.38 MB
    orthologs_tbl_dist.txt486.5 KB