The banana genome hub

Database

Volumn 2013, Issue , 2013, Pages

  Droc, Gaëtan ^a   Larivière, Delphine ^a   Guignon, Valentin ^b   Yahiaoui, Nabila ^a   This, Dominique ^a   Garsmeur, Olivier ^a   Dereeper, Alexis ^c   Hamelin, Chantal ^a   Argout, Xavier ^a   Dufayard, Jean François ^a   Lengelle, Juliette ^a,d   Baurens, Franc Christophe ^a   Cenci, Alberto ^b   Pitollat, Bertrand ^a   D'Hont, Angélique ^a   Ruiz, Manuel ^a   Rouard, Mathieu ^b   Bocs, Stéphanie ^a  

^a UMR AGAP   (France)

^b BIOVERSITY INTERNATIONAL   (Italy)

^c INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^d Centre National de la Recherche Scientifique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CHROMOSOME MAP; GENE DUPLICATION; GENETIC DATABASE; GENETICS; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; MUSA; PHYLOGENY; PLANT GENE; PLANT GENOME; RICE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; TRANSPOSON;

CHROMOSOME MAPPING; DATABASES, GENETIC; DNA TRANSPOSABLE ELEMENTS; GENE DUPLICATION; GENES, PLANT; GENOME, PLANT; LIKELIHOOD FUNCTIONS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; MUSA; ORYZA SATIVA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTOME;

EID: 84885904157     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat035     Document Type: Article

References (68)

1. D'Hont,A., Denoeud,F., Aury,J.M. et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488, 213-217.
2. Howe,K.L., Chothia,T. and Durbin,R. (2002) GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res., 12, 1418-1427.
3. Flutre,T., Duprat,E., Feuillet,C. et al. (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One, 6, e16526.
4. Argout,X., Fouet,O., Wincker,P. et al. (2008) Towards the understanding of the cocoa transcriptome: production and analysis of an exhaustive dataset of ESTs of Theobroma cacao generated from various tissues and under various conditions. BMC Genomics, 9, 512.
5. Rouard,M., Guignon,V., Aluome,C. et al. (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res., 39, D1095-D1102.
6. SouthGreen Bioinformatics Platform. http://southgreen.cirad.fr/ (6 May 2013, date last accessed).
7. Jaiswal,P., Ni,J., Yap,I. et al. (2006) Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res., 34, D717-D723.
8. Bombarely,A., Menda,N., Tecle,IY. et al. (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res., 39, D1149-D1155.
9. Kersey,P.J., Staines,D.M., Lawson,D. et al. (2012) Ensembl genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res., 40, D91-D97.
10. Mungall,C.J. and Emmert,D.B. (2007) A chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
11. Guignon,V., Droc,G., Alaux,M. et al. (2012) Chado controller: advanced annotation management with a community annotation system. Bioinformatics, 28, 1054-1056.
12. Carver,T., Berriman,M., Tivey,A. et al. (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics, 24, 2672-2676.
13. Ficklin,S.P., Sanderson,L.A., Cheng,C.H. et al. (2011) Tripal: a construction toolkit for online genome databases. Database (Oxford), 2011, bar044.
14. Goecks,J., Nekrutenko,A., Taylor,J. et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
15. Yandell,M. and Ence,D. (2012) A beginner's guide to eukaryotic genome annotation. Nature Rev., 13, 329-342.
16. GNPAnnot portal. http://www.gnpannot.org (6 May 2013, date last accessed).
17. Legeai,F., Shigenobu,S., Gauthier,J.P. et al. (2010) AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. Insect Mol. Biol., 19, 5-12.
18. Amselem,J., Cuomo,C.A., van Kan,J.A. et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet., 7, e1002230.
19. Genome Model Organism Database project (GMOD). National Science Foundation (DBI-0849896); 2008. http://gmod.org (6 May 2013, date last accessed).
20. Parra,G., Blanco,E. and Guigó,R. (2000) Geneid in Drosophila. Genome Res., 10, 511-515.
21. Korf,I. (2004) Gene finding in novel genomes. BMC Bioinformatics, 5, 59.
22. Salamov,A.A. and Solovyev,V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res., 2000; 10:516-522.
23. Birney,E., Clamp,M. and and Durbin,R. (2004) Gene wise and genomewise. Genome Res., 14, 988-995.
24. Mott,R. (1997) EST-GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
25. Denoeud,F., Aury,J.M., Da Silva,C. et al. (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol., 9, R175.
26. Zdobnov,E.M. and Apweiler,R. (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
27. Gene Ontology Consortium. (2013) Gene ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
28. Mbéguié-A-Mbéguié,D., Hubert,O., Baurens,F.C. et al. (2009) Expression patterns of cell wall-modifying genes from banana during fruit ripening and in relationship with finger drop. J. Exp. Bot., 60, 2021-2034.
29. Bocs,S., Baurens,F.C., Rouard,M. et al. (2010) Mechanisms of haplo-type divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC Plant Biol., 10, 149.
30. Garsmeur,O., Charron,C., Bocs,S. et al. (2011) High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytol., 189, 629-642.
31. Conte,M., Gaillard,S., Lanau,N. et al. (2008) GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res., 36 (Suppl. 1), D991-D998.
32. Plant Genome Duplication Database. National Science Foundation (DBI-0849896); 2008. http://chibba.agtec.uga.edu/duplication/index/home (6 May 2013, date last accessed).
33. Tang,H., Lyons,E., Pedersen,B. et al. (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics, 12, 102.
34. Tang,H.synonymous-calc.py https://github.com/tanghaibao/biopipeline/tree/ master/synonymous-calculation/. 2011 (6 May 2013, date last accessed).
35. Karp,P.D., Paley,S.M., Krummenacker,M. et al . (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform., 11, 40-79.
36. Claudel-Renard,C., Chevalet,C., Faraut,T. et al. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res., 31, 6633-6639.
37. Rudd,S. (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci., 8, 321-329.
38. Li,H. and Durbin,R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
39. Li,H., Handsaker,B., Wysoker,A. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
40. Dereeper,A., Nicolas,S., Le Cunff,L. et al. (2011) SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. BMC Bioinformatics, 12, 134.
41. Hamelin,C., Sempere,G., Jouffe,V. et al. TropGeneDB, the multi-tropical crop information system updated and extended. Nucleic Acids Res., 41, D1172-D1175.
42. Hippolyte,I., Jenny,C., Gardes,L. et al. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers. Ann. Bot., 109, 937-951.
43. Droc,G., Perin,C., Fromentin,S. et al. OryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucleic Acids Res., 37, D992-D995.
44. Maillol,V., Roberto B., Sidibe Bocs,S. et al. (eds). (2012) In: Role of Galaxy in a bioinformatic plant breeding platform. Galaxy Community Conference. University of Illinois Chicago.
45. Blankenberg,D., Coraor,N., Von Kuster,G. et al. (2011) Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database, 2011, bar011.
46. Agopian,R.G.D., Peroni-Okita,F.H.G., Soares,C.A. et al. (2011) Low temperature induced changes in activity and protein levels of the enzymes associated to conversion of starch to sucrose in banana fruit. Postharvest. Biol. Technol., 62, 133-140.
47. Fung,R.W.M., Langenkamper,G., Gardner,R.C. et al . (2003) Differential expression within an SPS gene family. Plant Sci., 164, 459-470.
48. Whittaker,A., Martinelli,T., Farrant,J.M. et al. (2007) Sucrose phosphate synthase activity and the co-ordination of carbon partitioning during sucrose and amino acid accumulation in desiccation-tolerant leaf material of the C4 resurrection plant Sporobolus stapfianus during dehydration. J. Exp. Bot., 58, 3775-3787.
49. Choudhury,S.R., Roy,S., Singh,S.K. et al. (2010) Understanding the molecular mechanism of transcriptional regulation of banana Sucrose phosphate synthase (SPS) gene during fruit ripening: an insight into the functions of various cis-acting regulatory elements. Plant Signal. Behav., 5.
50. Li,M., Feng,F. and Cheng,L. (2012) Expression patterns of genes involved in sugar metabolism and accumulation during apple fruit development. PloS One, 7, e33055.
51. Huber,S.C. and Huber,J.L. (1996) Role and regulation of sucrose-phosphate synthase in higher plants. Annu. Rev. Plant Physiol. Plant. Mol. Biol., 47, 431-444.
52. Castleden,C.K., Aoki,N., Gillespie,V.J. et al. (2004) Evolution and function of the sucrose-phosphate synthase gene families in wheat and other grasses. Plant Physiol., 135, 1753-1764.
53. Lutfiyya,L.L., Xu,N., D'Ordine,R.L. et al. (2007) Phylogenetic and expression analysis of sucrose phosphate synthase isozymes in plants. J. Plant Physiol., 164, 923-933.
54. Carpita,N.C. and Gibeaut,D.M. (1993) Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Plant J., 3, 1-30.
55. Harris,P.J., Kelderman,M.R., Kendon,M.F. et al. (xxxx) Monosaccharide compositions of unlignified cell walls of monocotyledons in relation to the occurrence of wall-bound ferulic acid. Biochem. System. Ecol., 25, 167-179.
56. Carpita,N.C. (2011) Update on mechanisms of plant cell wall biosynthesis: how plants make cellulose and other (1->4)-beta-D-glycans. Plant Physiol., 155, 171-184.
57. Richmond,T.A. and Somerville,C.R. (2000) The cellulose synthase superfamily. Plant Physiol., 124, 495-498.
58. Hazen,S.P., Scott-Craig,J.S. and Walton,J.D. (2002) Cellulose synthase-like genes of rice. Plant Physiol., 128, 336-340.
59. Penning,B.W., Hunter,C.T. 3rd, Tayengwa,R. et al. (2009) Genetic resources for maize cell wall biology. Plant Physiol., 151, 1703-1728.
60. Fincher,G.B. (2009) Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses. Plant Physiol., 149, 27-37.
61. Yin,Y., Huang,J. and Xu,Y. (2009) The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biol., 9, 99.
62. Katoh,K., Asimenos,G. and Toh,H. (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol., 537, 39-64.
63. Gascuel,O., Guindon,S., Dufayard,J.F. et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
64. Burton,R.A., Wilson,S.M., Hrmova,M. et al . (2006) Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1,3;1,4)-beta-D- glucans. Science, 311, 1940-1942.
65. Lee,S.C. and Luan,S. (2012) ABA signal transduction at the cross-road of biotic and abiotic stress responses. Plant Cell Environ., 35, 53-60.
66. Payasi,A. and Sanwal,G.G. (2010) Ripening of climacteric fruits and their control. J. Food Chem., 34, 679-710.
67. Zhang,Y.M., Tan,J.L., Guo,Z.F. et al . Increased abscisic acid levels in transgenic tobacco over-expressing 9 cis-epoxycarotenoid dioxygenase influence H(2)O(2) and NO production and antioxidant defences. Plant Cell Environ, 2009 May;32(5):509-19.
68. Hobo,T., Kobayashi,M. and Shinozaki,K. (2002) Characterization of the AtNCED2 gene, encoding 9-cis-epoxycarotenoid dioxygenase, a key enzyme in ABA biosynthesis in Arabidopsis seed maturation. Plant Cell Physiol., 43, S93-S93S.