Draft whole-genome sequence of the biocontrol agent Trichoderma harzianum T6776

Genome Announcements

Volumn 3, Issue 3, 2015, Pages

  Baroncelli, Riccardo ^a   Piaggeschi, Giulia ^a   Fiorini, Lisa ^a   Bertolini, Edoardo ^b   Zapparata, Antonio ^a   Pè, Mario Enrico ^b   Sarrocco, Sabrina ^a   Vannacci, Giovanni ^a  

^a UNIVERSITY OF PISA   (Italy)

^b SCUOLA SUPERIORE SANT ANNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85008502154     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00647-15     Document Type: Article

References (19)

1. Whipps JM, Lumsden RD. 2001. Commercial use of fungi as plant disease biological control agents: status and prospects, p 9-22. In Butt TM, Jackson C, Magan N (ed), Fungi as biocontrol agents: progress, problems and potential. CAB International, Wallingford, United Kingdom.
2. Perotto S, Angelini P, Bianciotto V, Bonfante P, Girlanda M, Kull T, Mello A, Pecoraro L, Perini C, Persiani AM, Saitta A, Sarrocco S, Vannacci G, Venanzoni R, Venturella G, Selosse MA. 2013. Interactions of fungi with other organisms. Plant Biosyst 147:208-218. http://dx.doi.org/10.1080/11263504.2012.753136.
3. Jensen DF, Karlsson M, Sarrocco S, Vannacci G. Biological control using microorganisms as an alternative to disease resistance. In Collinge DB (ed), Biotechnology for plant disease control, in press. Wiley, New York, NY.
4. Sarrocco S, Moncini L, Pachetti G, Moretti A, Ritieni A, Vannacci G. 2013 Biological control of Fusarium head blight under field conditions. IOCB-WPRS Bull 86:95-100.
5. Fiorini L, Guglielminetti L, Mariotti L, Curadi M, Puntoni G, Scartazza A, Picciarelli P, Sarrocco S, Vannacci G. 2014. Trichoderma harzianum 6776 on tomato: a single beneficial isolate for two cultivation systems. J Plant Pathol 95(S4):61.
6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829. http://dx.doi.org/10.1101/gr.074492.107.
7. Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067. http://dx.doi.org/10.1093/bioinformatics/btm071.
8. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18:188-196. http://dx.doi.org/10.1101/gr.6743907.
9. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. 2007. WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585-W587. http://dx.doi.org/10.1093/nar/gkm259.
10. O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ. 2012. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 44:1060-1065. http://dx.doi.org/10.1038/ng.2372.
11. Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, Ver Loren van Themaat E, Brown JK, Butcher SA, 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, King BC, Klages S, Kleemann J, Knoll D, Koti PS, Kreplak J, López-Ruiz FJ, Lu X, Maekawa T, Mahanil S, Micali C, Milgroom MG, Montana G, Noir S, O'Connell RJ, Oberhaensli S, Parlange F, Pedersen C, Quesneville H, Reinhardt R, Rott M, Sacristán S, Schmidt SM, Schön M, Skamnioti P, Sommer H, Stephens A, Takahara H, Thordal-Christensen H, Vigouroux M, Wessling R, Wicker T, Panstruga R. 2010. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330:1543-1546. http://dx.doi.org/10.1126/science.1194573.
12. Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40. http://dx.doi.org/10.1186/gb-2011-12-4-r40.
13. Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367-373. http://dx.doi.org/10.1038/nature08850.
14. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868. http://dx.doi.org/10.1038/nature01554.
15. Baroncelli R, Sreenivasaprasad S, Sukno SA, Thon MR, Holub E. 2014. Draft genome sequence of Colletotrichum acutatum sensu lato (Colletotrichum fioriniae). Genome Announc 2(2):e00112-14. http://dx.doi.org/10.1128/genomeA.00112-14.
16. Baroncelli R, Sanz-Martín JM, Rech GE, Sukno SA, Thon MR. 2014. Draft genome sequence of Colletotrichum sublineola, a destructive pathogen of cultivated sorghum. Genome Announc 2(3):e00540-14. http://dx.doi.org/10.1128/genomeA.00540-14.
17. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun MH, Bohnert H, Coughlan S, Butler J, Calvo S, Ma LJ, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980-986. http://dx.doi.org/10.1038/nature03449.
18. Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee YH, Jensen DF. 2015. Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biol Evol 7:465-480. http://dx.doi.org/10.1093/gbe/evu292.
19. Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma LJ. 2011. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog 7:e1002137. http://dx.doi.org/10.1371/journal.ppat.1002137.