Genomics and bioinformatics resources for translational science in Rosaceae

Plant Biotechnology Reports

Volumn 8, Issue 2, 2014, Pages 49-64

  Jung, Sook ^a   Main, Dorrie ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Breeding; Database; Genetics; Genomics; Rosaceae

Indexed keywords

ROSACEAE;

EID: 84926289766     PISSN: 18635466     EISSN: 18635474     Source Type: Journal    
DOI: 10.1007/s11816-013-0282-3     Document Type: Review

References (116)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656
2. Aharoni A, Keizer LC, Van Den Broeck HC, Blanco-Portales R, Muñoz-Blanco J, Bois G, Smit P, De Vos RC, O’Connell AP (2002) Novel insight into vascular, stress, and auxin-dependent and -independent gene expression programs in strawberry, a non-climacteric fruit. Plant Physiol 129:1019–1031
3. Aharoni A, Giri AP, Verstappen FW, Bertea CM, Sevenier R, Sun Z, Jongsma MA, Schwab W, Bouwmeester HJ (2004) Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16:3110–3131
4. Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TA, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH (2011) Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics 12:569
5. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, Chothia C, Murzin AG (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36:D419–D425
6. Aoki KF, Kanehisa M (2005) Using the KEGG database resource. Curr Protoc Bioinforma Chapter 1:Unit 1.12
7. Audergon JM, Ruiz D, Bachellez A, Blanc A, Corre MN, Croset C, Ferréol AM, Lambert P, Pascal T, Poëssel JL, Signoret V, Quilot B, Gouble B, Grotte M, Bogé M, Reiling P, Reich M, Bureau S, Boudehri K, Renaud C, Dirlewanger E, Deborde C, Maucourt M, Moing A, Monllor S, Dondini L, Arús P (2009) ISAFRUIT: study of the genetic basis of Prunus fruit quality in two peach and two apricot populations. Acta Hortic 814:523–528
8. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320:938–941
9. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES (2002) ARACHNE: a whole genome shotgun assembler. Genome Res 13:91–96
10. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic Acids Res 41:D36–D42
11. Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301–D303
12. Bink MC, van Eeuwijk FA (2009) A Bayesian QTL linkage analysis of the common dataset from the 12th QTLMAS workshop. BMC Proc 3(Suppl 1):S4
13. Bombarely A, Merchante C, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, Blanco-Portales R, Botella MA, Muñoz-Blanco J, Sánchez-Sevilla JF, Valpuesta V (2010) Generation and analysis of ESTs from strawberry (Fragaria × ananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC Genomics 11:503
14. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The sol genomics network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39:D1149–D1155
15. Botton A, Eccher G, Forcato C, Ferrarini A, Begheldo M, Zermiani M, Moscatello S, Battistelli A, Velasco R, Ruperti B, Ramina A (2011) Signaling pathways mediating the induction of apple fruitlet abscission. Plant Physiol 155:185–208
16. Cabrera A, Kozik A, Howad W, Arus P, Iezzoni AF, van der Knaap E (2009) Development and bin mapping of a Rosaceae conserved ortholog set (COS) of markers. BMC Genomics 10:562
17. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci USA 105:21034–21038
18. Chagne D, Crowhurst R, Troggio M, Davey M, Gilmore B, Lawley C, Vanderzante S, Hellens R, Kumar S, Cestaro A, Velasco R, Main D, Rees J, Iezzoni A, Mockler T, Wilhelm L, van de Weg E, Gardiner S, Bassil N, Peace C (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7(2):e31745. doi:10.1371/journal.pone.0031745
19. Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V (2013) Facing growth in the European nucleotide archive. Nucleic Acids Res 41:D30–D35
20. Costa F, Alba R, Schouten H, Soglio V, Gianfranceschi L, Serra S, Musacchi S, Sansavini S, Costa G, Fei Z, Giovannoni J (2010) Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biol 10:229
21. Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res 39:D420–D426
22. Dardick CD, Callahan AM, Chiozzotto R, Schaffer RJ, Piagnani MC, Scorza R (2010) Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. BMC Biol 8:13
23. Dewey CN (2007) Aligning multiple whole genomes with Mercator and MAVID. Methods Mol Biol 395:221–236
24. Diamant J, Sguigna V, Mezzetti B, Faedi W, Maltoni ML, Denoyes B, Chartier P, Petit A (2012) European small berries genetic resources, GENBERRY: testing a protocol for detecting fruit nutritional quality in EU strawberry germplasm collections. Acta Hortic 926:33–37
25. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101:9891–9896
26. Donlin MJ (2007) Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinforma Chapter 9:Unit 9.9
27. Filichkin SA, Priest HD, Givan SA, Shen RK, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Gen Res 20:45–58
28. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222
29. Geisler-Lee J, O’Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317–329
30. Georgi LL, Wang Y, Yverggniaux D, Ormsbee T, Inigo M, Reighard GL, Abbott AG (2002) Construction of a BAC library and its application to the identification of simple sequence repeats in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105:1151–1158
31. Gianfranceschi L, Soglio V (2004) The European project HiDRAS: innovative multidisciplinary approaches to breeding high quality disease resistant apples. Acta Hortic 663:327–330
32. Gibney G, Baxevanis AD (2011) Searching NCBI databases using Entrez. Curr Protoc Bioinforma Chapter 1:Unit 1.3
33. Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20:3643–3646
34. Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35:D213–D218
35. Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arús P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419–1428
36. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171:1305–1309
37. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan WuZ, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281
38. Hummel J, Selbig J, Walther D, Kopka J (2007) The Golm metabolome database: a database for GC–MS based metabolite profiling. In: Nielsen J, Jewett MC (eds) Metabolomics. Springer, Berlin, pp 75–96
39. Hummel J, Strehmel N, Selbig J, Walther D, Kopka J (2010) Decision tree supported substructure prediction of metabolites from GC–MS profiles. Metabolomics 6:322–333
40. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40:D306–D312
41. Iezzoni A, Weebadde C, Luby J, Yue C, Peace C, Bassil N, McFerson J (2010) RosBREED: enabling marker-assisted breeding in Rosaceae. Acta Hortic 859:389–394
42. Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol 143:587–599
43. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
44. Isserlin R, El-Badrawi RA, Bader GD (2011) The biomolecular interaction network database in PSI-MI 2.5. Database 2011:baq037
45. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P, French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
46. Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Bowen JH, Crowhurst RN, Gleave AP, Ledger S, McArtney S, Pichler FB, Snowden KC, Ward S (2008) Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 8:16
47. Jensen PJ, Halbrendt N, Fazio G, Makalowska I, Altman N, Praul C, Maximova SN, Ngugi HK, Crassweller RM, Travis JW, McNellis TW (2012) Rootstock-regulated gene expression patterns associated with fire blight resistance in apple. BMC Genomics 13:9
48. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36:D1034–D1040
49. Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, Velasco R, Sargent DJ (2012) Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics 13:129
50. Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y (2011) DDJB progress report. Nucleic Acids Res 39:D22–D27
51. Khan MA, Han Y, Zhao YF, Korban SS (2012) A high-throughput apple SNP genotyping platform using the GoldenGate™ assay. Gene 492:196–201
52. Krost C, Petersen R, Lokan S, Brauksiepe B, Braun P, Schmidt ER (2013) Evaluation of the hormonal state of columnar apple trees (Malus × domestica) based on high throughput gene expression studies. Plant Mol Biol 81:211–220
53. Lalli DA, Decroocq V, Blenda AV, Schurdi-Levraud V, Garay L, Le Gall O, Damsteegt V, Reighard GL, Abbott AG (2005) Identification and mapping of resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus. Theor Appl Genet 111:1504–1513
54. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210
55. Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C (2008) Version VI of the ESTree db: an improved tool for peach transcriptome analysis. BMC Bioinforma 9(Suppl 2):S9
56. Lee YP, Yu GH, Seo YS, Han SE, Choi YO, Kim D, Mok IG, Kim WT, Sung SK (2007) Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 26:917–926
57. Lee T, Cho I, Peace C, Jung S, Zheng P, Main D (2011) Development approach and architecture of GenSAS BIOCOMP’11, July 2011, Las Vegas
58. Lee TH, Tang H, Wang X, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41:D1152–D1158
59. Li Y, Wu B, Yu Y, Yang G, Wu C, Zheng C (2011) Genome-wide analysis of the RING finger gene family in apple. Mol Genet Genomics 286:81–94
60. Li X, Korir NK, Liu L, Shangguan L, Wang Y, Han J, Chen M, Fang J (2012) Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca. J Plant Physiol 169:1776–1788
61. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
62. Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53:661–673
63. Martínez-Gómez P, Crisosto CH, Bonghi C, Rubio M (2011) New approaches to Prunus transcriptome analysis. Genetica 139:755–769
64. Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K (2010) AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol 152:566–578
65. McKay SJ, Vergara IA, Stajich JE (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinforma Chapter 9:Unit 9.12
66. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38:D204–D210
67. Mihara M, Itoh T, Izawa T (2010) SALAD database: a motif-based database of protein annotations for plant comparative genomics. Nucleic Acids Res 38:D835–D842
68. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ et al (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147–166
69. Ogundiwin EA, Martí C, Forment J, Pons C, Granell A, Gradziel TM, Peace CP, Crisosto CH (2008) Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit. Plant Mol Biol 68:379–397
70. Pampanwar V, Engler F, Hatfield J, Blundy S, Gupta G, Soderlund C (2005) FPC web tools for rice, maize, and distribution. Plant Physiol 138:116–126
71. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
72. Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A (2012) Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS ONE 7:e48305
73. Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP (2007) Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci USA 104:4730–4735
74. Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP (2009) MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev 23:80–92
75. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61–D65
76. Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 39:D1095–D1102
77. Santos AM, Oliver MJ, Sánchez AM, Payton PR, Gomes JP, Miguel C, Oliveira MM (2009) An integrated strategy to identify key genes in almond adventitious shoot regeneration. J Exp Bot 60:4159–4173
78. Sargent DJ, Kuchta P, Lopez Girona E, Zhang H, Davis TM, Celton JM, Marchese A, Korbin M, Folta KM, Shulaev V, Simpson DW (2011) Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence. Plant Genome 4:165–177
79. Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ (2011) MaizeGDB: curation and outreach go hand-in-hand. Database 2011:bar022
80. Schaffer RJ, Friel EN, Souleyre EJ, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma JH, Nain B, Cohen D, Gleave AP, Crowhurst RN, Janssen BJ, Yao JL, Newcomb RD (2007) A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway. Plant Physiol 144:1899–1912
81. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–83. Erratum in: Nature 465:120
82. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
83. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flügge UI, Kunze R (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol 131:16–26
84. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797
85. Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arús P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003
86. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116
87. Simillion C, Janssens K, Sterck L, Van de Peer Y (2008) i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24:127–128
88. Spiller M, Linde M, Hibrand-Saint Oyant L, Tsai CJ, Byrne DH, Smulders MJ, Foucher F, Debener T (2011) Towards a unified genetic map for diploid roses. Theor Appl Genet 122:489–500
89. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002) The Generic Genome Browser: a building block for a model organism system database. Genome Res 12:1599–1610
90. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320:486–488
91. Tatsuki M, Nakajima N, Fujii H, Shimada T, Nakano M, Hayashi KI, Hayama H, Yoshioka H, Nakamura Y (2013) Increased levels of IAA are required for system 2 ethylene synthesis causing fruit softening in peach (Prunus persica L. Batsch). J Exp Bot 64(4):1049–1059. doi:10.1093/jxb/ers381
92. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinforma 4:41
93. The Gene Ontology Consortium (2013) Gene ontology annotations and resources. Nucleic Acids Res 41:D530–D535
94. The UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:D71–D75
95. Trainotti L, Zanin D, Casadoro G (2003) A cell wall-oriented genomic approach reveals a new and unexpected complexity of the softening in peaches. J Exp Bot 54:1821–1831
96. Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol 158:590–600
97. Vecchietti A, Lazzari B, Ortugno C, Bianchi F, Malinverni R, Caprera A, Mignani I, Pozzi C (2009) Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch). Tree Genet Genome 5:377–391
98. Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ (2011) PDBe: Protein Data Bank in Europe. Nucleic Acids Res 39(Suppl 1):D402–D410
99. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839
100. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C (2012) Development and evaluation of a 9 K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS ONE 7(4):e35668. doi:10.1371/journal.pone.0035668
101. Vizoso P, Meisel LA, Tittarelli A, Latorre M, Saba J, Caroca R, Maldonado J, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Silva H (2009) Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality. BMC Genomics 10:423
102. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu S (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098–1103
103. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequecing. Plant Physiol 144:32–42
104. Wegrzyn JL, Lee JM, Tearse BR, Neale DB (2008) TreeGenes: a forest tree genome database. Intl J Plant Genomics 2008:412875. doi:10.1155/2008/412875
105. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35:D5–D12
106. Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J (2009) SUPERFAMILY: sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res 37:D380–D386
107. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408
108. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y (2012) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66
109. Yao Q, Bollinger C, Gao J, Xu D, Thelen JJ (2012) P3DB: an integrated database for plant protein phosphorylation. Front Plant Sci 3:206
110. Yi G, Sze SH, Thon MR (2007) Identifying clusters of functionally related genes in genome. Bioinformatics 23:1053–1060
111. Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094
112. Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z, Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z, Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of Prunus mume. Nat Commun 3:1318
113. Zhebentyayeva T, Swire-Clark G, Georgi L, Garay L, Juns S, Forrest S, Blenda A, Blackmon B, Mook J, Horn R, Howad W, Arus P, Main D, Tomkins J, Sosinski B, Baird W, Reighard G, Abbott A (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genome 4:745–756
114. Zhu Y, Varanasi V, Zheng P, Main D, Curry E, Mattheis J (2012) Multiple plant hormones and cell wall metabolism regulate apple fruit maturation patterns and texture attributes. Tree Genet Genome 8:1389–1406
115. Ziliotto F, Begheldo M, Rasori A, Bonghi C, Tonutti P (2008) Transcriptome profiling of ripening nectarine (Prunus persica L. Batsch) fruit treated with 1-MCP. J Exp Bot 59:2781–2791
116. Ziosi V, Bonghi C, Bregoli AM, Trainotti L, Biondi S, Sutthiwal S, Kondo S, Costa G, Torrigiani P (2008) Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit. J Exp Bot 59:563–573