Eukaryote DIRS1-like retrotransposons: An overview

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Piednoël, Mathieu ^a   Gonçalves, Isabelle R ^a   Higuet, Dominique ^a   Bonnivard, Eric ^a  

^a Université Pierre et Marie Curie Paris 6 ^*  (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MODEL; COPY NUMBER VARIATION; DIRS1 LIKE RETROPOSON; DNA TRANSPOSITION; EUKARYOTE; GENE FREQUENCY; GENETIC VARIABILITY; MATHEMATICAL COMPUTING; MOLECULAR PHYLOGENY; NEW SPECIES; NONHUMAN; RETROPOSON; SACCOGLOSSUS KOWALEVSKII; SEQUENCE ANALYSIS; SPECIES DIVERSITY; SPECIES IDENTIFICATION; ZEBRA FISH; EUKARYOTIC CELL; GENOME; METABOLISM; REVIEW;

CNIDARIA; DANIO RERIO; EUKARYOTA; MAMMALIA; SACCOGLOSSUS; SAUROPSIDA; STREPTOPHYTA; UNIKONTA;

EUKARYOTIC CELLS; GENOME; RETROELEMENTS;

EID: 83655183283     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-621     Document Type: Article

References (59)

1. Goodwin TJ, Poulter RT. The DIRS1 group of retrotransposons. Mol Biol Evol 2001, 18:2067-2082.
2. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8:973-982. 10.1038/nrg2165, 17984973.
3. Cappello J, Handelsman K, Lodish HF. Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence. Cell 1985, 43:105-15. 10.1016/0092-8674(85)90016-9, 2416457.
4. Curcio MJ, Derbyshire KM. The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol 2003, 4:865-877.
5. Poulter RTM, Goodwin TJD. DIRS-1 and the other tyrosine recombinase retrotransposons. Cytogenet Genome Res 2005, 110:575-588. 10.1159/000084991, 16093711.
6. Lorenzi HA, Robledo G, Levin MJ. The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol 2006, 145:184-194. 10.1016/j.molbiopara.2005.10.002, 16297462.
7. Llorens C, Muñoz-Pomer A, Bernad L, Botella H, Moya A. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct 2009, 4:41. 10.1186/1745-6150-4-41, 2774666, 19883502.
8. Goodwin TJD, Poulter RTM. A new group of tyrosine recombinase-encoding retrotransposons. Mol Biol Evol 2004, 21:746-759. 10.1093/molbev/msh072, 14963102.
9. Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005, 247:165-221.
10. Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res 2005, 110:475-490. 10.1159/000084981, 16093701.
11. Piskurek O, Jackson DJ. Tracking the Ancestry of a Deeply Conserved Eumetazoan SINE Domain. Mol Biol Evol 2011, 28:2727-2730. 10.1093/molbev/msr115, 21512106.
12. Arkhipova IR. Distribution and phylogeny of Penelope-like elements in eukaryotes. Syst Biol 2006, 55:875-885. 10.1080/10635150601077683, 17345670.
13. Pritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 2007, 390:3-17. 10.1016/j.gene.2006.08.008, 17034960.
14. Kapitonov VV, Jurka J. Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci USA 2006, 103:4540-4545. 10.1073/pnas.0600833103, 1450207, 16537396.
15. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 10.1159/000084979, 16093699.
16. Piednoël M, Bonnivard E. DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms. BMC Evol Biol 2009, 9:86. 10.1186/1471-2148-9-86, 2685390, 19400949.
17. Smit A, Hubley R, Green P. RepeatMasker Open-3.0 1996, , http://www.repeatmasker.org
18. Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity 2010, 104:520-533. 10.1038/hdy.2009.165, 19935826.
19. Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 2008, 9:18. 10.1186/1471-2105-9-18, 2253517, 18194517.
20. Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 2002, 12:1269-1276. 10.1101/gr.88502, 186642, 12176934.
21. Goodwin TJD, Poulter RTM, Lorenzen MD, Beeman RW. DIRS retroelements in arthropods: identification of the recently active TcDirs1 element in the red flour beetle Tribolium castaneum. Mol Genet Genomics 2004, 272:47-56.
22. Chung S, Zuker C, Lodish HF. A repetitive and apparently transposable DNA sequence in Dictyostelium discoideum associated with developmentally regulated RNAs. Nucleic Acids Res 1983, 11:4835-4852. 10.1093/nar/11.14.4835, 326089, 6308562.
23. Cappello J, Cohen SM, Lodish HF. Dictyostelium transposable element DIRS-1 preferentially inserts into DIRS-1 sequences. Mol Cell Biol 1984, 4:2207-2213. 369040, 6095047.
24. 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 J, 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. The ecoresponsive genome of Daphnia pulex. Science 2011, 331:555-561. 10.1126/science.1197761, 21292972.
25. Rho M, Schaack S, Gao X, Kim S, Lynch M, Tang H. LTR retroelements in the genome of Daphnia pulex. BMC Genomics 2010, 11:425. 10.1186/1471-2164-11-425, 2996953, 20618961.
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
27. Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, Donahue G, Yang P, Li Q, Li C, Zhang P, Huang Z, Berger SL, Reinberg D, Wang J, Liebig J. Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science 2010, 329:1068-1071. 10.1126/science.1192428, 20798317.
28. Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih C, Wu W, Yang C, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MAD, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D, Keller L. The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci USA 2011,
29. Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L, Keller L. Fourmidable: a database for ant genomics. BMC Genomics 2009, 10:5. 10.1186/1471-2164-10-5, 2639375, 19126223.
30. Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé M, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra ASI, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci USA 2011,
31. Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave M, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley J, Hu H, Viniegra ASI, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KKO, Wild AL, Yandell M, Yorke JA, Tsutsui ND. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci USA 2011,
32. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
33. Van Dongen S. Graph Clustering by Flow Simulation. 2000,
34. De Palmenaer D, Siguier P, Mahillon J. IS4 family goes genomic. BMC Evol Biol 2008, 8:18. 10.1186/1471-2148-8-18, 2266710, 18215304.
35. Siguier P, Gagnevin L, Chandler M. The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 2009, 160:232-241. 10.1016/j.resmic.2009.02.003, 19286454.
36. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
37. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552.
38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 21546353.
39. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
40. Milne I, Wright F, Rowe G, Marshall DF, Husmeier D, McGuire G. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 2004, 20:1806-1807. 10.1093/bioinformatics/bth155, 14988107.
41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
42. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai Y, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson K, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo J, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao Y, Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol Res 2007, 111:509-547. 10.1016/j.mycres.2007.03.004, 17572334.
43. Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, Roger AJ, Gray MW. The tree of eukaryotes. Trends Ecol Evol (Amst.) 2005, 20:670-676.
44. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749. 10.1038/nature06614, 18322464.
45. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Wörheide G, Manuel M. Phylogenomics revives traditional views on deep animal relationships. Curr Biol 2009, 19:706-712. 10.1016/j.cub.2009.02.052, 19345102.
46. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MDS, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJK, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297:1301-1310. 10.1126/science.1072104, 12142439.
47. Zuker C, Cappello J, Chisholm RL, Lodish HF. A repetitive Dictyostelium gene family that is induced during differentiation and by heat shock. Cell 1983, 34:997-1005. 10.1016/0092-8674(83)90557-3, 6194894.
48. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 2007, 317:86-94. 10.1126/science.1139158, 17615350.
49. Ruiz-Pérez VL, Murillo FJ, Torres-Martínez S. Prt1, an unusual retrotransposon-like sequence in the fungus Phycomyces blakesleeanus. Mol Gen Genet 1996, 253:324-333.
50. Volff J, Lehrach H, Reinhardt R, Chourrout D. Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. Mol Biol Evol 2004, 21:2022-2033. 10.1093/molbev/msh207, 15254255.
51. Eichinger L, Pachebat JA, Glöckner G, Rajandream M, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. The genome of the social amoeba Dictyostelium discoideum. Nature 2005, 435:43-57. 10.1038/nature03481, 1352341, 15875012.
52. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. The genome of the Western clawed frog Xenopus tropicalis. Science 2010, 328:633-636. 10.1126/science.1183670, 2994648, 20431018.
53. Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu J, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PWH, Satoh N, Rokhsar DS. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008, 453:1064-1071. 10.1038/nature06967, 18563158.
54. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu L, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen C, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral J, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen C, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WCA, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007, 318:245-250. 10.1126/science.1143609, 2875087, 17932292.
55. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 2010, 329:223-226. 10.1126/science.1188800, 2993248, 20616280.
56. 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 J, 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. The ecoresponsive genome of Daphnia pulex. Science 2011, 331:555-561. 10.1126/science.1197761, 21292972.
57. Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 2010, 140:631-642. 10.1016/j.cell.2010.01.032, 20211133.
58. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Li G, Su J, Wang X, Li G, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Xu J, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li C, Li D, Sun Y, Zhang Z, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Li J, Ye J, Chen H, Zhou Y, Liu B, Wang J, Ye J, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Li S, Wang J, Wong GK, Yang H. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 2004, 306:1937-1940.
59. Ma L, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim J, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen Y, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 2009, 5:e1000549. 10.1371/journal.pgen.1000549, 2699053, 19578406.