Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Zhou, Peng ^a   Silverstein, Kevin A T ^a   Gao, Liangliang ^a   Walton, Jonathan D ^b   Nallu, Sumitha ^c   Guhlin, Joseph ^a   Young, Nevin D ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

Gene prediction; Genome annotation; Homology search; Protein family

Indexed keywords

AB INITIO PREDICTION; ARABIDOPSIS THALIANA; COMPUTATIONAL STUDIES; GENE PREDICTION; GENOME ANNOTATION; HOMOLOGY SEARCH; PROTEIN FAMILY; SELF-INCOMPATIBILITY;

AMINO ACIDS; FORECASTING; PEPTIDES;

GENES;

PEPTIDE;

ALGORITHM; AMANITA; AMINO ACID SEQUENCE; ARABIDOPSIS; BARREL MEDIC; CHEMISTRY; COMPUTER PROGRAM; GENETICS; METABOLISM; PLANT GENOME; PREDICTIVE VALUE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ARTICLE;

ALGORITHMS; AMANITA; AMINO ACID SEQUENCE; ARABIDOPSIS; GENOME, PLANT; MEDICAGO TRUNCATULA; PEPTIDES; PREDICTIVE VALUE OF TESTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SOFTWARE;

EID: 84887661754     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-335     Document Type: Article

References (54)

1. Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2(7):493-503. http://www.ncbi.nlm.nih.gov/pubmed/11433356.
2. Yao H, Guo L, Fu Y, Borsuk L, Wen TJ, Skibbe DS, Cui X, Scheffler BE, Cao J, Emrich SJ, Ashlock D, Schnable PS. Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol 2005, 57(3):445-460. http://www.ncbi.nlm.nih.gov/pubmed/15830133.
3. Basrai M, Hieter P, Boeke J. Small open reading frames : beautiful needles in the haystack. Genome Res 1997, 768-771. http://genome.cshlp.org/content/7/8/768.short.
4. Lease K, Walker JC. The Arabidopsis unannotated secreted peptide database, a resource for plant peptidomics. Plant Physiol 2006, 142(3):831-838. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1630735&tool=pmcentrez&rendertype=abstract.
5. Hanada K, Zhang X, Borevitz J. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 2007, 517:632-640. http://genome.cshlp.org/content/17/5/632.short.
6. Yang X, Tschaplinski T, Hurst G. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 2011, 634-641. http://genome.cshlp.org/content/21/4/634.short.
7. Pan B, Sheng J, Sun W, Zhao Y, Hao P, Li X. OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. Nucleic Acids Res 2012, 15:1-7. http://www.ncbi.nlm.nih.gov/pubmed/23203890.
8. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database. Nucleic Acids Res 2012, 40(Database issue):D290-D301. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245129&tool=pmcentrez&rendertype=abstract.
9. 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, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 2012, 40(Database issue):D306-D312. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245097&tool=pmcentrez&rendertype=abstract.
10. Sigrist CJa D, Cerutti L, Cuche Ba H, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Res 2013, 41(Database issue):D344-D347. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3531220&tool=pmcentrez&rendertype=abstract.
11. Silverstein K, Moskal W, Wu H, Underwood B, Graham M, Town CD, VandenBosch KA. Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J 2007, 51(2):262-280. http://www.ncbi.nlm.nih.gov/pubmed/17565583.
12. Nallu S, Silverstein K, Samac D, Bucciarelli B, Vance CP, VandenBosch K. Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago Truncatula. PloS ONE 2013, 8(4):e60355. http://dx.plos.org/10.1371/journal.pone.0060355.
13. Tesfaye M, Silverstein KA, Nallu S, Wang L, Botanga CJ, Gomez SK, Costa LM, Harrison MJ, Samac DA, Glazebrook J, Katagiri F, Gutierrez-Marcos JF, Vandenbosch KA. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes. PloS ONE 2013, 8(3):e58992. http://scholar.google.com/scholar?hl=en&btnG=Search&q=intitle: Spatio-Temporal+Expression+Patterns+of+Arabidopsis+thaliana+and+Medicago+truncatula+Defensin-Like+Genes#0, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3601123&tool=pmcentrez&rendertype=abstract.
14. Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 2004, 20(16):2878-2879. http://www.ncbi.nlm.nih.gov/pubmed/15145805.
15. Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 2005, 33(20):6494-6506. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1298918&tool=pmcentrez&rendertype=abstract.
16. Blanco E, Parra G, Guigó R. Using geneid to identify genes. Curr Protoc Bioinformatics 2007, 1-28. http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0403s18/full.
17. Keller O, Kollmar M, Stanke M, Waack S. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 2011, 27(6):757-763. http://www.ncbi.nlm.nih.gov/pubmed/21216780.
18. Salamov AA. Ab initio gene finding in drosophila genomic DNA. Genome Res 2000, 10(516-522). http://www.genome.org/cgi/doi/10.1101/gr.10.4.516.
19. Birney E, Clamp M, Durbin R. GeneWise and genomewise. Genome Res 2004, 4:988-995. http://genome.cshlp.org/content/14/5/988.short.
20. Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=553969&tool=pmcentrez&rendertype=abstract.
21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. http://www.ncbi.nlm.nih.gov/pubmed/2231712.
22. Eddy S. Profile hidden Markov models. Bioinformatics Rev 1998, 14(9):755. http://bioinformatics.oxfordjournals.org/content/14/9/755.short.
23. Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 2004, 20(7):1157-1169. http://www.ncbi.nlm.nih.gov/pubmed/14764557.
24. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8(10):785-786. http://www.ncbi.nlm.nih.gov/pubmed/21959131.
25. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 2011, 7(539):539. http://www.ncbi.nlm.nih.gov/pubmed/21988835.
26. Capella-gutiérrez S, Silla-martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009, 25(15):1972-1973.
27. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7(10):e1002195. http://dx.plos.org/10.1371/journal.pcbi.1002195, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3197634&tool=pmcentrez&rendertype=abstract.
28. 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, et al. The, B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326(5956):1112-1115. http://www.ncbi.nlm.nih.gov/pubmed/19965430.
29. Rep M, Kistler HC. The genomic organization of plant pathogenicity in Fusarium species. Curr Opin Plant Biol 2010, 13(4):420-426. http://www.ncbi.nlm.nih.gov/pubmed/20471307.
30. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 1992, 89(22):10915-10919. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=50453&tool=pmcentrez&rendertype=abstract].
31. Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, et al. The, Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480(7378):520-524. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3272368&tool=pmcentrez&rendertype=abstract, http://www.ncbi.nlm.nih.gov/pubmed/22089132.
32. Leinonen R, Sugawara H, Shumway M. The sequence read archive. Nucleic Acids Res 2011, 39(Database issue):D19-D21. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013647&tool=pmcentrez&rendertype=abstract.
33. Burset M, Guigó R. Evaluation of gene structure prediction programs. Genomics 1996, 34(3):353-367. http://www.ncbi.nlm.nih.gov/pubmed/8786136.
34. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7(3):562-578. http://www.ncbi.nlm.nih.gov/pubmed/22383036.
35. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinformatics 2013, 14(2):178-192. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3603213&tool=pmcentrez&rendertype=abstract.
36. Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 2005, 3:7. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1082884&tool=pmcentrez&rendertype=abstract, http://www.biomedcentral.com/1741-7007/3/7.
37. Foote H, Ride J. Cloning and expression of a distinctive class of self-incompatibility (S) gene from Papaver rhoeas L. Proc Natl Acad Sci 1994, 91(6):2265-2269. http://www.pnas.org/content/91/6/2265.short.
38. 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. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2012, 40(Database issue):D1202-D1210. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3245047&tool=pmcentrez&rendertype=abstract.
39. Hallen HE, Luo H, Scott-Craig JS, Walton JD. Gene family encoding the major toxins of lethal Amanita mushrooms. Proc Natl Acad Sci 2007, 104(48):19097-19101. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2141914&tool=pmcentrez&rendertype=abstract.
40. Silverstein KAT, Graham MA, Paape TD, VandenBosch KA. Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol 2005, 138(2):600-610. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1150381&tool=pmcentrez&rendertype=abstract.
41. Jones-Rhoades MW, Borevitz JO, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PLoS Genet 2007, 3(10):1848-1861. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2014789&tool=pmcentrez&rendertype=abstract.
42. Takeuchi H, Higashiyama T. A species-specific cluster of defensin-like genes encodes diffusible pollen tube attractants in arabidopsis. PLoS Biol 2012, 10(12):e1001449. http://dx.plos.org/10.1371/journal.pbio.1001449.
43. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011, 1-5. http://www.nature.com/doifinder/10.1038/nature10414.
44. Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 2010, 6(5):e1000940. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2865524&tool=pmcentrez&rendertype=abstract.
45. Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 2011, 43(2):163-168. http://www.ncbi.nlm.nih.gov/pubmed/21217757.
46. Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P. Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula. PLoS ONE 2013, 8(5):e65688. http://dx.plos.org/10.1371/journal.pone.0065688.
47. Silverstein KAT, Graham MA, VandenBosch KA. Novel paralogous gene families with potential function in legume nodules and seeds. Curr Opin Plant Biol 2006, 9(2):142-146. http://www.ncbi.nlm.nih.gov/pubmed/16459131.
48. Wang D, Griffitts J, Starker C, Fedorova E, Limpens E, Ivanov S, Bisseling T, Long S. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science 2010, 327(5969):1126-1129. http://www.ncbi.nlm.nih.gov/pubmed/20185723.
49. Van de Velde W, Zehirov G, Szatmari A, Debreczeny M, Ishihara H, Kevei Z, Farkas A, Mikulass K, Nagy A, Tiricz H, Satiat-Jeunemaître B, Alunni B, Bourge M, Kucho Ki A, Kereszt A, Maroti G, Uchiumi T, Kondorosi E, Mergaert P. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 2010, 327(5969):1122-1126. http://www.ncbi.nlm.nih.gov/pubmed/20185722.
50. Mergaert P, Nikovics K, Kelemen Z, Maunoury N, Vaubert D, Kondorosi A, Kondorosi E. A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs. Plant Physiol 2003, 132:161-173. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=166962&tool=pmcentrez&rendertype=abstract.
51. Galagan JE, Henn MR, Ma LJ, Cuomo C, Birren B. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res 2005, 15(12):1620-1631. http://www.ncbi.nlm.nih.gov/pubmed/16339359.
52. Saxonov S, Daizadeh I, Fedorov A, Gilbert W. EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res 2000, 28:185-190. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=102483&tool=pmcentrez&rendertype=abstract.
53. Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AMV, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JIB, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, et al. Genome sequence and analysis of the, Irish potato famine pathogen Phytophthora infestans. Nature 2009, 461(7262):393-398. http://www.ncbi.nlm.nih.gov/pubmed/19741609.
54. Spanu PD, Abbott JC, Amselem J, Burgis T, Soanes DM, Stuber K, Loren van Themaat EV, Brown JKM, Butcher S, Gurr SJ, Lebrun MH, Ridout CJ, Schulze-Lefert P, Talbot NJ, Ahmadinejad N, Ametz C, Barton GR, Benjdia M, Bidzinski P, Bindschedler LV, Both M, Brewer MT, Cadle-Davidson L, Cadle-Davidson MM, Collemare J, Cramer R, Frenkel O, Godfrey D, Harriman J, Hoede C, et al. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 2010, 330(6010):1543-1546. http://www.sciencemag.org/cgi/doi/10.1126/science.1194573.