Whole genome phylogeny for 21 drosophila species using predicted 2b-RAD fragments

PeerJ

Volumn 2013, Issue 1, 2013, Pages

  Seetharam, Arun S ^a   Stuart, Gary W ^b  

^a PURDUE UNIVERSITY   (United States)

^b INDIANA STATE UNIVERSITY   (United States)

Author keywords

Phylogenomics; Reduced genomic representation; Restriction site associated DNA (RAD) tags; Type IIB restriction enzymes

Indexed keywords

2B RAD FRAGMENT; DNA FRAGMENT; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; COMPUTER SIMULATION; DNA SEQUENCE; DROSOPHILA; ENZYME ACTIVITY; ENZYME ANALYSIS; INFORMATION PROCESSING; NONHUMAN; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENOMICS;

EID: 84891553161     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.226     Document Type: Article

References (44)

1. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, CreskoWA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376 DOI 10.1371/journal.pone.0003376.
2. Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML. 2011. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 6:e19315 DOI 10.1371/journal.pone.0019315.
3. Bourque G, Pevzner PA. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research 12:26-36.
4. Clark A, Eisen M, Smith D, Bergman C, Oliver B, Markow T, Kaufman T, Kellis M, Gelbart W, Iyer V, Pollard D, Sackton T, Larracuente A, Singh N, Abad J, Abt D, Adryan B, Aguade M, Akashi H, Anderson W, Aquadro C, Ardell D, Arguello R, Artieri C, Barbash D, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak S, Bradley R, Brand A, Brent M, Brooks A, Brown R, Butlin R, Caggese C, Calvi B, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker S, Chang J, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton S, Comeron J, Costello J, Coyne J, Daub J, David R, Delcher A, Delehaunty K, Do C, Ebling H, Edwards K, Eickbush T, Evans J, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia A, Gardiner A, Garfield D, Garvin B, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg A, Griffiths-Jones S, Gross S, Guigo R, Gustafson E, Haerty W, Hahn M, Halligan D, Halpern A, Halter G, Han M, Heger A, Hillier L, Hinrichs A, Holmes I, Hoskins R, Hubisz M, Hultmark D, Huntley M, Jaffe D, Jagadeeshan S, Jeck W, Johnson J, Jones C, Jordan W, Karpen G, Kataoka E, Keightley P, Kheradpour P, Kirkness E, Koerich L, Kristiansen K, Kudrna D, Kulathinal R, Kumar S, Kwok R, Lander E, Langley C, Lapoint R, Lazzaro B, Lee S, Levesque L, Li R, Lin C, Lin M, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado C, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride C, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer M, Montooth K, Mount S, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor M, O'Grady P, Pachter L, Papaceit M, Parisi M, Parisi M, Parts L, Pedersen J, Pesole G, Phillippy A, Ponting C, Pop M, Porcelli D, Powell J, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram K, Rand D, Rasmussen M, Reed L, Reenan R, Reily A, Remington K, Rieger T, Ritchie M, Robin C, Rogers Y, Rohde C, Rozas J, Rubenfield M, Ruiz A, Russo S, Salzberg S, Sanchez-Gracia A, Saranga D, Sato H, Schaeffer S, Schatz M, Schlenke T, Schwartz R, Segarra C, Singh R, Sirot L, Sirota M, Sisneros N, Smith C, Smith T, Spieth J, Stage D, Stark A, Stephan W, Strausberg R, Strempel S, Sturgill D, Sutton G, Sutton G, Tao W, Teichmann S, Tobari Y, Tomimura Y, Tsolas J, Valente V, Venter E, Venter J, Vicario S, Vieira F, Vilella A, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson R, Wing R, Wolfner M, Wong A, Wong G, Wu C, Wu G, Yamamoto D, Yang H, Yang S, Yorke J, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin A, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer S, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, BloomT, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley C, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin C, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard M, Hughes L, Hurhula B, Husby M, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono O, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Alvarez P, Brockman W, Butler J, Chin C, Grabherr M, Kleber M, Mauceli E, MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 DOI 10.1038/nature06341.
5. Da Lage JL, Kergoat GJ, Maczkowiak F, Silvain JF, Cariou ML, Lachaise D. 2007. A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries [Une phylogenie des Drosophilidae avec le gene Amyrel: remise en question des limites du groupe d'espèces Drosophila melanogaster]. Journal of Zoological Systematics and Evolutionary Research 45:47-63 DOI 10.1111/j.1439-0469.2006.00389.x.
6. Davey JW, Blaxter ML. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9:416-423 DOI 10.1093/bfgp/elq031.
7. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics 6:361-375 DOI 10.1038/nrg1603.
8. Dunn JJ, McCorkle SR, Praissman LA, Hind G, Van Der Lelie D, Bahou WF, Gnatenko DV, Krause MK. 2002. Genomic signature tags (GSTs): a system for profiling genomic DNA. Genome Research 12:1756-1765 DOI 10.1101/gr.306102.
9. Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, CreskoWA, Bradshaw WE, Holzapfel CM. 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America 107:16196-16200 DOI 10.1073/pnas.1006538107.
10. Etter PD, Bassham S, Hohenlohe PA, Johnson EA, CreskoWA. 2011. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods in Molecular Biology 772:157-178.
11. Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) In: author Db, editor. 3.6. ed. Hahn MW, Han MV, Han SG. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genetics 3:e197 DOI 10.1371/journal.pgen.0030197.
12. Haubold B, Pfaffelhuber P. 2012. Alignment-free population genomics: an efficient estimator of sequence diversity. G3 2:883-889 DOI 10.1534/g3.112.002527.
13. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, CreskoWA. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics 6:e1000862 DOI 10.1371/journal.pgen.1000862.
14. Huson DH, Steel M. 2004. Phylogenetic trees based on gene content. Bioinformatics 20:2044-2049 DOI 10.1093/bioinformatics/bth198.
15. Kopp A. 2006. Basal relationships in the Drosophila melanogaster species group. Molecular Phylogenetics and Evolution 39:787-798 DOI 10.1016/j.ympev.2006.01.029.
16. Kopp A, True JR. 2002. Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction. Systematic Biology 51:786-805 DOI 10.1080/10635150290102410.
17. Korbel JO, Snel B, Huynen MA, Bork P. 2002. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 18:158-162 DOI 10.1016/S0168-9525(01)02597-5.
18. Lin J, Gerstein M. 2000. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Research 10:808-818 DOI 10.1101/gr.10.6.808.
19. McQuilton P, St Pierre SE, Thurmond J. 2012. FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Research 40:D706-D714 DOI 10.1093/nar/gkr1030.
20. Pelandakis M, Solignac M. 1993. Molecular phylogeny of Drosophila based on ribosomal RNA sequences. Journal of Molecular Evolution 37:525-543 DOI 10.1007/BF00160433.
21. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135 DOI 10.1371/journal.pone.0037135.
22. Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh S-D, True JR, Carroll SB. 2006. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440:1050-1053 DOI 10.1038/nature04597.
23. Qi J, Luo H, Hao B. 2004. CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Research 32:45-47 DOI 10.1093/nar/gkh362.
24. Rebeiz M, Ramos-Womack M, Jeong S, Andolfatto P, Werner T, True J, Stern DL, Carroll SB. 2009. Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al. Cell 139:1189-1196 DOI 10.1016/j.cell.2009.11.004.
25. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY. 2003a. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Research 31:1805-1812 DOI 10.1093/nar/gkg274.
26. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY. 2003b. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Research 31:1805-1812 DOI 10.1093/nar/gkg274.
27. Roy SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proceedings of the National Academy of Sciences of the United States of America 102:4403-4408 DOI 10.1073/pnas.0409891102.
28. Rubin BE, Ree RH, Moreau CS. 2012. Inferring phylogenies from RAD sequence data. PLoS ONE 7:e33394 DOI 10.1371/journal.pone.0033394.
29. Schawaroch V. 2002. Phylogeny of a paradigm lineage: the Drosophila melanogaster species group (Diptera: Drosophilidae). Biological Journal of the Linnean Society 76:21-37 DOI 10.1111/j.1095-8312.2002.tb01711.x.
30. Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nature Genetics 21:108-110 DOI 10.1038/5052.
31. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-232 DOI 10.1038/nature06340.
32. Stebbins GL. 1950. Variation and evolution in plants. NY: Columbia University Press. Stuart GW, Moffett K, Leader JJ. 2002. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Molecular Biology and Evolution 19:554-562 DOI 10.1093/oxfordjournals.molbev.a004111.
33. Stuart GW, Moffett K, Leader JJ. 2002. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Molecular Biology and Evolution 19:554-562 DOI 10.1093/oxfordjournals.molbev.a004111
34. Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Research 9:550-557.
35. Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. 2004. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Research 32:e121 DOI 10.1093/nar/gnh120.
36. Toda MJ. 1991. Drosophilidae (Diptera) in Myanmar (Burma) VII. The Drosophila melanogaster species-group, excepting the D. montium species-subgroup. Oriental Insects 25:69-94 DOI 10.1080/00305316.1991.10432216.
37. van der Linde K, Houle D. 2008. A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae). Insect Systematics & Evolution 39:241-267 DOI 10.1163/187631208788784237.
38. van der Linde K, Houle D, Spicer GS, Steppan SJ. 2010. A supermatrix-based molecular phylogeny of the family Drosophilidae. Genome Research 92:25-38.
39. van Orsouw NJ, Hogers RC, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJ. 2007. Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172 DOI 10.1371/journal.pone.0001172.
40. Wang S, Meyer E, McKay JK, Matz MV. 2012. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nature Methods 9:808-810 DOI 10.1038/nmeth.2023.
41. Yang S, Doolittle RF, Bourne PE. 2005. Phylogeny determined by protein domain content. Proceedings of the National Academy of Sciences of the United States of America 102:373-378 DOI 10.1073/pnas.0408810102.
42. Yang Y, Hou ZC, Qian YH, Kang H, Zeng QT. 2012. Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera). Molecular Phylogenetics and Evolution 62:214-223 DOI 10.1016/j.ympev.2011.09.018.
43. Yang Y, Zhang YP, Qian YH, Zeng QT. 2004. Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B. Molecular Phylogenetics and Evolution 30:336-343 DOI 10.1016/S1055-7903(03)00212-4.
44. Yi H, Jin L. 2013. Co-phylog: an assembly-free phylogenomic approach for closely related organisms. Nucleic Acids Research 41:e75 DOI 10.1093/nar/gkt003. Seetharam