Arthropod Genomics

Arthropod Genomics

The Drosophila melanogaster genome played a pioneering role in insect genomics providing a logical framework for building a comprehensive biological knowledgebase. As the prime human malaria vector in Africa, the Anopheles gambiae mosquito was prioritised for sequencing creating the first opportunity for comparative analysis of two insect genomes. Agricultural, economic or health impacts drove subsequent sequencing of the silk moth, honey bee, Aedes mosquito, and beetle genomes, facilitating initial large-scale quantitative analyses that revealed strikingly faster rates of evolution compared to vertebrates. The comparative analyses of 12 drosophilid genomes demonstrated how evolutionary sequence signature characterisation can accurately define encoded functional elements, improving protein-coding gene prediction and discovering novel genes such as microRNAs. Indeed, discovery of functional elements through evolutionary signature analysis across multiple drosophilids represents a methodological milestone. More recent insect genome projects also reflect their impact on human agriculture - the parasitoid Nasonia wasps and the pea aphid pest - or health - the human body louse and the Culex mosquito disease-vectors.

Selected Publications in Arthropod Genomics

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

Li J, Waterhouse RM and Zdobnov EM
BMC Evolutionary Biology 2011, 11:337 (18 November 2011)
PMID: 22098672

The ecoresponsive genome of Daphnia pulex

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.
Science
PMID: 21292972

Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi.

Waterhouse RM, Zdobnov EM, Kriventseva EV.
Genome Biol Evol
PMID: 21148284

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.
Science
PMID: 20929810

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens

Bartholomay LC, Waterhouse RM, Mayhew GF, Campbell CL, Michel K, Zou Z, Ramirez JL, Das S, Alvarez K, Arensburger P, Bryant B, Chapman SB, Dong Y, Erickson SM, Karunaratne SH, Kokoza V, Kodira CD, Pignatelli P, Shin SW, Vanlandingham DL, Atkinson PW, Birren B, Christophides GK, Clem RJ, Hemingway J, Higgs S, Megy K, Ranson H, Zdobnov EM, Raikhel AS, Christensen BM, Dimopoulos G, Muskavitch MA.
Science
PMID: 20929811

Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins

Waterhouse RM, Povelones M, Christophides GK.
BMC Genomics
PMID: 20920294

A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Zhao C, Escalante LN, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM, Wheeler D, Andersson MN, Bao R, Batterton M, Behura SK, Blankenburg KP, Caragea D, Carolan JC, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen CJ, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani SN, Johnson AJ, Kalra D, Korchina V, Kovar CL, Lara F, Lee SL, Liu X, Löfstedt C, Mata R, Mathew T, Muzny DM, Nagar S, Nazareth LV, Okwuonu G, Ongeri F, Perales L, Peterson BF, Pu LL, Robertson HM, Schemerhorn BJ, Scherer SE, Shreve JT, Simmons D, Subramanyam S, Thornton RL, Xue K, Weissenberger GM, Williams CE, Worley KC, Zhu D, Zhu Y, Harris MO, Shukle RH, Werren JH, Zdobnov EM, Chen MS, Brown SJ, Stuart JJ, Richards S.
Curr Biol.
PMID: 25660540

Extensive introgression in a malaria vector species complex revealed by phylogenomics

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ.
Science
PMID: 25431491

Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ.
Science
PMID: 25554792

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Krause E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR
Proc Natl Acad Sci U S A. 2010 Jun 21. [Epub ahead of print]
PMID: 20566863

A caspase-like decoy molecule enhances the activity of a paralogous caspase in the yellow fever mosquito, Aedes aegypti.

Bryant B, Ungerer MC, Liu Q, Waterhouse RM, Clem RJ.
Insect Biochem Mol Biol.
PMID: 20417712

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S
PLoS Computational Biology 6(1):e1000652
PMID: 20126523

Sociality is linked to rates of protein evolution in a highly social insect

Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SY, Goodisman MAD
Journal of Molecular Biology and Evolution 27(3):497-500
PMID: 20110264

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

The Nasonia Genome Working Group (incl. Junier T, Gerlach D, Waterhouse RM, Kriventseva EV, Wyder S, Zdobnov EM)
Science. 2010 Jan 15;327(5963):343-8.
PMID: 20075255

Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae.

Pinto SB, Lombardo F, Koutsos AC, Waterhouse RM, McKay K, An C, Ramakrishnan C, Kafatos FC, Michel K.
Proc Natl Acad Sci U S A.
PMID: 19940242

Leucine-Rich Repeat Protein Complex Activates Mosquito Complement in Defense Against Plasmodium Parasites

Povelones M, Waterhouse RM, Kafatos FC, Christophides GK
Science
PMID: 19264986

Expression profiles of Urbilaterian genes uniquely shared between honey bee and vertebrates

Matsui T, Yamamoto T, Wyder S, Zdobnov EM, Kadowaki T
BMC Genomics 2009, 10:17
PMID: 19138430

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

The Aedes aegypti genome: a comparative perspective

Waterhouse RM, Wyder S, Zdobnov EM
Insect Mol Biol. 2008 Feb;17(1):1-8
PMID: 18237279

Insect Immunity

Evolution of genes and genomes on the Drosophila phylogeny

Drosophila 12 Genomes Consortium (Zdobnov EM)
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Koutsos AC, Blass C, Meister S, Schmidt S, Maccallum RM, Soares MB, Collins FH, Benes V, Zdobnov EM, Kafatos FC, Christophides GK
Proc Natl Acad Sci USA. 2007 Jun 11
PMID: 17563388