Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: Gene assembly, annotation and marker development

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Passos, Marco A N ^a   de Cruz, Viviane Oliveira ^a   Emediato, Flavia L ^a   de Teixeira, Cristiane Camargo ^b   Azevedo, Vânia C Rennó ^c   Brasileiro, Ana C M ^c   Amorim, Edson P ^d   Ferreira, Claudia F ^d   Martins, Natalia F ^c   Togawa, Roberto C ^c   Pappas, Georgios J ^a   da Silva, Orzenil Bonfim ^c   Miller, Robert N G ^a  

^a UNIVERSITY OF BRASILIA   (Brazil)

^b UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^c EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^d EMBRAPA CERRADOS   (Brazil)

Author keywords

454 pyrosequencing; Biotic stress; Musa acuminata; Mycosphaerella musicola; SSR; Transcriptome

Indexed keywords

BIOLOGICAL MARKER; TRANSCRIPTOME;

ARTICLE; BANANA; BIOTIC STRESS; CONIDIUM; CONTROLLED STUDY; DNA LIBRARY; EXON; FUNGUS; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC POLYMORPHISM; HOST RESISTANCE; MYCOSPHAERELLA MUSICOLA; NONHUMAN; PLANT DEFENSE; PLANT FUNGUS INTERACTION; PLANT GENE; PLANT IMMUNITY; PLANT LEAF; RNA ANALYSIS; SEQUENCE HOMOLOGY; SIMPLE SEQUENCE REPEAT; TRANSCRIPTION REGULATION;

ASCOMYCOTA; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; MUSA; PLANT DISEASES; PLANT LEAVES; TRANSCRIPTOME;

MUSA; MUSA ACUMINATA; MUSA SP.; MYCOSPHAERELLA MUSICOLA;

EID: 84873248067     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-78     Document Type: Article

References (92)

1. FAOSTAT Food and agricultural commodities production. Food and Agricultural organization Statistics 2012, http://faostat.fao.org/, FAOSTAT.
2. Jones DR. Diseases of banana, abacá and enset 1999, Wallingford, Oxon: CABI Publishing.
3. Jones DR. Disease and pest constraints to banana production. Acta Hort 2009, 828:21-36.
4. Mouliom-Pefoura A, Lassoudière A, Foko J, Fontem DA. Comparison of development of Mycosphaerella fijiensis and Mycosphaerella musicola on banana and plantain in the various ecological zones in Cameroon. Plant Dis 1996, 80:950-954.
5. James AC, Arzanlou M, Canto-Canche B, Jorge HR, Ferraez CL, Echeverria PS. Fungal Diseases of Banana. Bananas: Nutrition, Diseases and Trade Issues 2011, 65-122. Nova Science Publishers Inc, Cohen AE.
6. Cordeiro ZJM, Matos AP, Meissner Filho PE. Doenças e métodos de controle. O Cultivo da Bananeira 2004, 146-182. Cruz das Almas: Nova Civilização, Cruz das Almas: Nova Civilização, Borges AL, Souza LS, 1st.
7. Cordeiro ZJM, Matos AP, Kimati H. Doenças Da Bananeira (Musa Spp.). Manual de Fitopatologia 2005, 99-117. São Paulo: Agronômica Ceres, Kimati H, Amorin L, Rezende JAM, Bergamin Filho A, Camargo LEA, 4th.
8. Marín DH, Romero RA, Guzmán M, Sutton TB. Black Sigatoka: an increasing threat to banana cultivation. Plant Dis 2003, 87:208-222.
9. Sierotzki H, Parisi S, Steinfeld U, Tenzer I, Poirey S, Gisi U. Mode of resistance to respiration inhibitors at the cytochrome bc1 enzyme complex of Mycosphaerella fijiensis field isolates. Pest Manag Sci 2000, 56:833-841.
10. Heslop-Harrison JS, Schwarzacher T. Domestication, genomics and the future for banana. Ann Bot 2007, 100:1073-1084. 10.1093/aob/mcm191, 2759213, 17766312.
11. Ortiz R. Secondary polyploids, heterosis, and evolutionary crop breeding for further improvement of the plantain and banana (Musa spp. L.) genome. Theor Appl Genet 1997, 94:1113-1120.
12. Horry JP. The use of Molecular Markers in the CIRAD Banana Breeding Programme. Acta Hort 2011, 897:237-243.
13. Bakry F, Carreel F, Jenny C, Horry JP. Genetic Improvement of Banana. Breeding Plantain Tree Crops: Tropical Species 2009, 3-46. New York: Springer Verlag Publisher, Jain SM, Priyadarshan PM.
14. Lysak MA, Dolezelova M, Horry JP, Swennen R, Dolezel J. Flow cytometric analysis of nuclear DNA content in Musa. Theor Appl Genet 1999, 98:1344-1350.
15. D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012,
16. Roux N, Baurens FC, Dolezel J, Hribova E, Heslop-Harrison P, Town C, Sasaki T, Matsumoto T, Aert R, Remy S, Souza M, Lagoda P. Genomics of Banana and Plantain (Musa spp.), Major Staple Crops in the Tropics. Genomics of Tropical Crop Plants 2008, 83-111. New York: Springer, Moore PH, Ming R.
17. Manrique-Trujillo SM, Ramírez-López AC, Ibarra-Laclette E, Gómez-Lim MA. Identification of genes differentially expressed during ripening of banana. J Plant Physiol 2007, 164:1037-1050. 10.1016/j.jplph.2006.07.007, 16934912.
18. Jin ZQ, Xu BY, Liu JH, Zhang ZB, Jia CH. Combination of suppression-subtractive hybridization with cDNA microarray, a novel Way to identify genes from banana involved in fruit ripening. Acta Hort 2011, 897:195-206.
19. Santos CMR, Martins NF, Horberg HM, de Almeida ERP, Coelho MCF, Togawa RC, da Silva FR, Caetano AR, Miller RNG, Souza MT. Analysis of expressed sequence tags from Musa acuminata ssp. burmannicoides, var. Calcutta 4 (AA) leaves submitted to temperature stresses. Theor Appl Genet 2005, 110:1517-1522. 10.1007/s00122-005-1989-5, 15841358.
20. Ravishankar KV, Rekha A, Laxman RH, Savitha G, Swarupa V. Gene Expression Analysis in Leaves of 'Bee Hee Kela' a drought-Tolerant Musa balbisiana Genotype from Northeast India. Acta Hort 2011, 897:279-280.
21. Nyine M, Nanteza A, Chan A, Town C, Lorenzen J. Insights from a 454-based Reference Transcriptome for Banana From Drought Stressed and Control Tissues. Proceedings of the XX International Plant and Animal Genome Conference (PAG) 2012, 14-18. San Diego, W070.
22. Van den Berg N, Berger DK, Hein I, Birch PR, Wingfield MJ, Viljoen A. Tolerance in banana to Fusarium wilt is associated with early up-regulation of cell wall strengthening genes in the roots. Mol Plant Pathol 2007, 8:333-341. 10.1111/j.1364-3703.2007.00389.x, 20507503.
23. Portal O, Izquierdo Y, De Vleesschauwer D, Sánchez-Rodríguez A, Mendoza-Rodríguez M, Acosta-Suárez M, Ocaña B, Jiménez E, Höfte M. Analysis of expressed sequence tags derived from a compatible Mycosphaerella fijiensis-banana interaction. Plant Cell Rep 2011, 30:913-928. 10.1007/s00299-011-1008-z, 21279642.
24. Passos MAN, de Oliveira Cruz V, Emediato FL, de Camargo Teixeira C, Souza MT, Matsumoto T, Rennó Azevedo VC, Ferreira CF, Amorim EP, de Alencar Figueiredo LF, Martins NF, de Jesus Barbosa Cavalcante M, Baurens FC, da Bonfim Silva O, Pappas GJ, Pignolet L, Abadie C, Ciampi AY, Piffanelli P, Miller RNG. Development of expressed sequence tag and EST-SSR marker resources for Musa acuminata. AoB Plants 2012, pls030.
25. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 2007, 144:32-42. 10.1104/pp.107.096677, 1913805, 17351049.
26. Yang H, Hu L, Hurek T, Reinhold-Hurek B. Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing. BMC Genomics 2010, 11:705. 10.1186/1471-2164-11-705, 3016420, 21159186.
27. Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JFS, Jung HJG, Vance CP, Gronwald JW. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 2011, 12:199. 10.1186/1471-2164-12-199, 3112146, 21504589.
28. Liu Z, Crampton M, Todd A, Kalavacharla V. Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.). BMC Plant Biol 2012, 12:42. 10.1186/1471-2229-12-42, 3353201, 22443214.
29. Mahomed W, Van den Berg N. EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi. BMC Plant Biol 2011, 11:167. 10.1186/1471-2229-11-167, 3233532, 22108245.
30. Danielsson M, Lundén K, Elfstrand M, Hu J, Zhao T, Arnerup J, Ihrmark K, Swedjemark G, Borg-Karlson AK, Stenlid J. Chemical and transcriptional responses of Norway spruce genotypes with different susceptibility to Heterobasidion spp. infection. BMC Plant Biol 2011, 11:154. 10.1186/1471-2229-11-154, 3240162, 22067529.
31. Narina SS, Buyyarapu R, Kottapalli KR, Sartie AM, Ali MI, Robert A, Hodeba MJ, Sayre BL, Scheffler BE. Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.). BMC Genomics 2011, 12:100. 10.1186/1471-2164-12-100, 3047301, 21303556.
32. Fernandez D, Tisserant E, Talhinhas P, Azinheira H, Vieira A, Petitot AS, Loureiro A, Poulain J, da Silva C, Silva MD, Duplessis S. 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction. Mol Plant Pathol 2011, 13:17-37.
33. Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 2009, 9:11. 10.1186/1471-2229-9-11, 2639587, 19161628.
34. Uma S, Mustaffa MM, Saraswathi MS, Durai P. Exploitation of diploids in Indian breeding programmes. Acta Hort 2011, 897:215-223.
35. Cheung F, Town CD. A BAC end view of the Musa Accuminata genome. BMC Plant Biol 2007, 7:29. 10.1186/1471-2229-7-29, 1904220, 17562019.
36. Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ, Sasaki MT, Souza MT, Miller RNG, Glaszmann JC, Town CD. Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 2008, 9:58. 10.1186/1471-2164-9-58, 2270835, 18234080.
37. Azhar M, Heslop-Harrison JS. Genomes, diversity and resistance gene analogues in Musa species. Cytogenet Genome Res 2008, 121:59-66. 10.1159/000124383, 18544928.
38. Miller RNG, Bertioli DJ, Baurens FC, Santos CM, Alves PC, Martins NF, Togawa RC, Souza MT, Pappas GJ. Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping. BMC Plant Biol 2008, 8:15. 10.1186/1471-2229-8-15, 2262081, 18234103.
39. Beveraggi A, Mourichon X, Salle G. Etude des interactions hôte-parasite chez des bananiers sensibles et résistants inoculés par Cercospora fijiensis (Mycosphaerella fijiensis) responsable de la maladie des raies noires. Can J Bot 1995, 73:1328-1337.
40. Arzanlou M, Abeln ECA, Kema GHJ, Waalwijk C, Carlier J, de Vries I, Guzman M, Crous PW. Molecular diagnostics for the Sigatoka disease complex of banana. Phytopathology 2007, 97:1112-1118. 10.1094/PHYTO-97-9-1112, 18944176.
41. Donzelli BGG, Churchill ACL. A quantitative assay using mycelial fragments to assess virulence of Mycosphaerella fijiensis. Phytopathology 2007, 97:916-929. 10.1094/PHYTO-97-8-0916, 18943631.
42. Churchill ACL. Mycosphaerella fijiensis, the black leaf streak pathogen of banana: progress towards understanding pathogen biology and detection, disease development, and the challenges of control. Mol Plant Path 2011, 12:307-328.
43. Liu G, Kennedy R, Greenshields DL, Peng G, Forseille L, Selvaraj G, Wei Y. Detached and attached Arabidopsis leaf assays reveal distinctive defense responses against hemibiotrophic Colletotrichum spp. Mol Plant Microbe Interact 2007, 20:1308-1319. 10.1094/MPMI-20-10-1308, 17918632.
44. Nürnberger T, Kemmerling B. PAMP-triggered basal immunity in plants. Adv Bot Res 2009, 51:1-38.
45. Jones JDG, Dangl JL. The plant immune system. Nature 2006, 444:323-329. 10.1038/nature05286, 17108957.
46. Morel JB, Dangl JL. The hypersensitive response and the induction of cell death in plants. Cell Death Differ 1997, 4:671-683. 10.1038/sj.cdd.4400309, 16465279.
47. Choi D, Kim HM, Yun HK, Park JA, Kim WT, Bok SH. Molecular cloning of a metallothionein-like gene from Nicotiana glutinosa L. and its induction by wounding and tobacco mosaic virus infection. Plant Physiol 1996, 112:353-359. 10.1104/pp.112.1.353, 157956, 8819331.
48. Hamer DH. Metallothionein. Annu Rev Biochem 1986, 55:913-951. 10.1146/annurev.bi.55.070186.004405, 3527054.
49. Liu P, Goh CJ, Loh CS, Pua EC. Differential expression and characterization of three metallothionein-like genes in Cavendish banana (Musa acuminata). Physiol Plant 2002, 114:241-250. 10.1034/j.1399-3054.2002.1140210.x, 11903971.
50. Cavalcante MJB, Escoute J, Madeira JP, Romero RE, Nicole M, Oliveira LC, Hamelin C, Lartaud M, Verdeil JL. Reactive oxygen species and cellular interactions between mycosphaerella fijiensis and banana. Trop Plant Biol 2011, 4:134-143.
51. Hammond-Kosack KE, Jones JDG. Plant disease resistance genes. Annu Rev Plant Physiol Plant Mol Biol 1997, 48:573-605.
52. McHale L, Tan X, Koehl P, Michelmore RW. Plant NBS-LRR proteins: adaptable guards. Genome Biol 2006, 7:212. 1-212 · 11, 1557992, 16677430.
53. Mohamad A, Heslop-Harrison JS. Genomes, diversity and resistance gene analogs in Musa species. Cytogenet Genome Res 2008, 121:59-66. 10.1159/000124383, 18544928.
54. Shiu SH, Bleecker AB. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases 2001, 10763-10768. Proceedings of the National Academy of Science of the United States of America.
55. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 1995, 270:1804-1806. 10.1126/science.270.5243.1804, 8525370.
56. Gómez-Gómez L, Boller T. FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol Cell 2000, 5:1003-1011. 10.1016/S1097-2765(00)80265-8, 10911994.
57. Mohr TJ, Mammarella ND, Hoff T, Woffenden BJ, Jelesko JG, McDowell JM. The Arabidopsis Downy Mildew Resistance Gene RPP8 Is Induced by Pathogens and Salicylic Acid and Is Regulated by W Box cis Elements. MPMI 2010, 23:1303-1315. 10.1094/MPMI-01-10-0022, 20831409.
58. Goodwin SB, Dunkle LD, Zismann VL. Phylogenetic Analysis of Cercospora and Mycosphaerella Based on the Internal Transcribed Spacer Region of Ribosomal DNA. Phytopathology 2001, 91:648-658. 10.1094/PHYTO.2001.91.7.648, 18942994.
59. Bolton MD, van Esse HP, Vossen JH, de Jonge R, Stergiopoulos I, Stulemeijer IJE, van den Berg GCM, Borrás-Hidalgo O, Dekker HL, de Koster CG, de Wit PJGM, Joosten MHAJ, Thomma BPHJ. The novel Cladosporium fulvum lysine motif effector Ecp6 is a virulence factor with orthologs in other fungal species. Mol Microbiol 2008, 69:119-136. 10.1111/j.1365-2958.2008.06270.x, 18452583.
60. de Jonge R, van Esse HP, Kombrink A, Shinya T, Desaki Y, Bours R, van der Krol S, Shibuya N, Joosten MH, Thomma BP. Conserved fungal LysMeffector Ecp6 prevents chitin-triggered immunity in plants. Science 2010, 329:953-955. 10.1126/science.1190859, 20724636.
61. Marshall R, Kombrink A, Motteram J, Loza-Reyes E, Lucas J, Hammond-Kosack KE, Thomma BP, Rudd JJ. Analysis of two in planta expressed LysM effector homologs from the fungus Mycosphaerella graminicola reveals novel functional properties and varying contributions to virulence on wheat. Plant Physiol 2011, 156:756-769. 10.1104/pp.111.176347, 3177273, 21467214.
62. Cho Y, Hou S, Zhong S. Analysis of expressed sequence tags from the fungal banana pathogen Mycosphaerella fijiensis. Open Mycol J 2008, 2:61-73.
63. Lagoda PJL, Noyer JL, Dambier D, Baurens FC, Grapin A, Lanaud C. Sequence tagged microsatellite site (STMS) markers in the Musaceae. Mol Ecol 1998, 7:657-666.
64. Christelová P, Valárik M, Hřibová E, Van den Houwe I, Channelière S, Roux N, Dolezě l J. A platform for efficient genotyping in Musa using microsatellite markers. AoB Plants 2011, plr024.
65. Hippolyte I, Bakry F, Seguin M, Gardes L, Rivallan R, Risterucci AM, Jenny C, Perrier X, Carreel F, Argout X, Piffanelli P, Khan I, Miller RNG, Pappas GJ, Mbeguie-a-mbeguie D, Matsumoto T, De Bernardinis V, Huttner E, Kilian A, Baurens FC, D'Hont A, Cote F, Courtois B, Glaszmann JC. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas. BMC Plant Biol 2010, 10:65. 10.1186/1471-2229-10-65, 2923539, 20388207.
66. Tranbarger TJ, Kluabmongkol W, Sangsrakru D, Morcillo F, Tregear JW, Tragoonrung S, Billotte N. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis. BMC Plant Biol 2012, 12:1. 10.1186/1471-2229-12-1, 3282652, 22214433.
67. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 2003, 270:315-323. 10.1007/s00438-003-0921-4, 14508680.
68. Kaemmer D, Fisher D, Jarret RL, Baurens FC, Grapin A, Dambier D, Noyer JL, Lanaud C, Kahl G, Lagoda PJL. Molecular breeding in genusMusa: a strong case for SSR marker technology. Euphytica 1997, 96:49-62.
69. Buhariwalla HK, Jarret RL, Jayashree B, Crouch JH, Ortiz R. Isolation and characterization of microsatellite markers from Musa balbisiana. Mol Ecol Notes 2005, 5:327-330.
70. Miller RN, Passos MA, Menezes NN, Souza MT, Costa MMC, Azevedo VCR, Amorim EP, Pappas GJ, Ciampi AY. Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides, var. Calcutta 4. BMC Res Notes 2010, 3:148. 10.1186/1756-0500-3-148, 2893197, 20507605.
71. Ravishankar KV, Vidhya L, Cyriac A, Rekha A, Goel R, Singh NK, Sharma TR. Development of SSR markers based on a survey of genomic sequences and their molecular analysis in banana (Musa spp.). J Hortic Sci Biotech 2012, 87:84-88.
72. Wang JY, Chen YY, Liu WL, Wu YT. Development and application of EST-derived SSR markers for bananas (Musa nana Lour.). Hereditas 2008, 30:933-940.
73. Amorim EP, Silva PH, Ferreira CF, Amorim VBO, Santos VJ, Vilarinhos AD, Santos CMR, Souza Júnior MT, Miller RNG. New microsatellite markers for bananas (Musa spp). Genet Mol Res 2012, 11:1093-1098. 10.4238/2012.April.27.8, 22614278.
74. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106:411-422.
75. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol 2005, 23:48-55. 10.1016/j.tibtech.2004.11.005, 15629858.
76. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ. Analysis of SSRs derived from grape ESTs. Theor Appl Genet 2000, 100:723-726.
77. Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol 2010, 10:4. 10.1186/1471-2229-10-4, 2827423, 20056000.
78. Amorim EP, Lessa LS, da Silva Ledo CA, de Oliveira Amorim VB, Viana dos Reis R, Santos-Serejo JA, de Oliveira e Silva S. Caracterização agronômica e molecular de genótipos diplóides melhorados de bananeira. Rev Bras Frutic 2009, 31:154-161.
79. Dochez C, Tenkouano A, Ortiz R, Whyte J, De Waele D. Host plant resistance to Radopholus similis in a diploid banana hybrid population. Nematology 2009, 11:329-335.
80. Rekha A, Ravishankar KV, Ambika DS. Generation of segregating F1 populations for mapping the Musa genome. Acta Hort 2011, 897:277-278.
81. Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG. Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinforma 2009, 10:447.
82. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11:1725-1729. 10.1101/gr.194201, 311141, 11591649.
83. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
84. Hazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R. An overview of the wcd EST clustering tool. Bioinformatics 2008, 24:1542-1546. 10.1093/bioinformatics/btn203, 2718666, 18480101.
85. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14:1147-1159. 10.1101/gr.1917404, 419793, 15140833.
86. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875. 10.1093/bioinformatics/bti310, 15728110.
87. Zdobnov EM, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
88. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676. 10.1093/bioinformatics/bti610, 16081474.
89. Gene Ontology Consortium The Gene Ontology project in 2008. Nucleic Acids Res 2008, 36:D440-D444. 2238979, 17984083, Gene Ontology Consortium.
90. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
91. Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols; Methods in Molecular Biology 2000, 365-386. New Jersey: Humana Press, Krawetz S, Misener S.
92. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 2007, 35:W71-W74. 10.1093/nar/gkm306, 1933133, 17485472.