Open Access Highly Accessed Research article

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

Marco A N Passos1, Viviane Oliveira de Cruz1, Flavia L Emediato1, Cristiane Camargo de Teixeira2, Vânia C Rennó Azevedo3, Ana C M Brasileiro3, Edson P Amorim4, Claudia F Ferreira4, Natalia F Martins3, Roberto C Togawa3, Georgios J Pappas1, Orzenil Bonfim da Silva3 and Robert NG Miller1*

Author Affiliations

1 Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil

2 Universidade Católica de Brasília, SGAN 916, Módulo B, CEP 70.790-160, Brasília, D.F, Brazil

3 EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil

4 EMBRAPA Mandioca e Fruticultura Tropical, Rua Embrapa, CEP 44.380-000, Cruz das Almas, BA, Brazil

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BMC Genomics 2013, 14:78  doi:10.1186/1471-2164-14-78

Published: 5 February 2013

Additional files

Additional file 1:

Mapping data for M. acuminata Calcutta 4 and Cavendish Grande Naine unigene contigs aligned to M. acuminata DH Pahang all gene models. Data shows all assembled contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine generated through de novo assembly mapping to M. acuminata ssp. malaccensis var. Pahang (DH Pahang) whole genome sequence. Specific data is also presented for contigs mapped to cytoplasmic nucleotide binding site-leucine-rich repeat proteins, together with TBLASTX scoring hits obtained by comparison of all unmapped contigs against EST (others) database of GenBank at an E value < e-5.

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Additional file 2:

Example of M. acuminata Calcutta 4 unigene contigs mapping to single M. acuminata DH Pahang gene models.

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Additional file 3:

Venn diagram showing the overlap between transcriptome unigene datasets (contigs and singletons) for the M. acuminata genotypes Calcutta 4 and Cavendish Grande Naine. All gene models in the reference M. acuminata DH Pahang genome were used as a base for identification of common mapped genes.

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Additional file 4:

Consensus sequences and BLASTX analysis of assembled unigene contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine. Data represent the consensus sequences of assembled contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine generated through de novo assembly, together with the three best BLASTX scoring hits obtained by comparison against nr database of GenBank at an E value < e-5.

Format: XLSX Size: 16.7MB Download file

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Additional file 5:

The most representative InterPro domains (IPR) observed across the assembled unigene contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine.

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Additional file 6:

Analysis of assembled unigene contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine for Gene Ontology (GO) terms related to defense response. Assembled contigs of M. acuminata Calcutta 4 and Cavendish Grande Naine were assigned to GO terms related to defense.

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Additional file 7:

Mapping data for M. acuminata Calcutta 4 and Cavendish Grande Naine pre-processed 454 sequence reads aligned to Mycosphaerella fijiensis v2.0 All Gene Models.

Format: XLSX Size: 26KB Download file

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Additional file 8:

Sequence information of all the SSR primer pairs designed with Mreps and Primer3 for M. acuminata Calcutta 4 and Cavendish Grande Naine unigenes. Data represent all the identified SSR loci, together with supporting information (SSR motif, primer sequences, PCR amplification information, predicted gene function and in silico expression data).

Format: XLSX Size: 2.4MB Download file

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