Open Access Highly Accessed Research article

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

Magali Lescot19*, Pietro Piffanelli110, Ana Y Ciampi3, Manuel Ruiz1, Guillaume Blanc5, Jim Leebens-Mack6, Felipe R da Silva3, Candice MR Santos3, Angélique D'Hont1, Olivier Garsmeur1, Alberto D Vilarinhos17, Hiroyuki Kanamori8, Takashi Matsumoto8, Catherine M Ronning2, Foo Cheung2, Brian J Haas2, Ryan Althoff2, Tammy Arbogast2, Erin Hine2, Georgios J Pappas4, Takuji Sasaki8, Manoel T Souza3, Robert NG Miller4, Jean-Christophe Glaszmann1 and Christopher D Town2

Author Affiliations

1 French Agricultural Research Center for International Development (CIRAD), UMR 1096, Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France

2 The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville MD 20850, USA

3 Embrapa Genetic Resources and Biotechnology (CENARGEN), P B I., Final Av. W/5 Norte, Asa Norte 70770-900, Caixa-Postal: 02372, Brasília, Brazil

4 Genomic Sciences and Biotechnology program, Catholic University of Brasília (UCB), SGAN 916, Modulo B, Asa Norte 70790-160, Brasília DF, Brazil

5 Structural and Genomic Information Laboratory (IGS), C.N.R.S. UPR 2589, Institute of Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288 Marseille Cedex 9, France

6 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA

7 Brazilian Agricultural Research Corporation (EMBRAPA), National Research Center of Cassava and Fruit Crops (CNPMF), P.O Box 007, Zip Code 44380.000, Cruz das Almas BA, Brazil

8 Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan

9 Structural and Genomic Information Laboratory (IGS), C.N.R.S. UPR 2589, Institute of Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288 Marseille Cedex 9, France

10 Parco Tecnologico Padano, Via Einstein, Lodi 26900, Italy

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BMC Genomics 2008, 9:58  doi:10.1186/1471-2164-9-58

Published: 30 January 2008

Additional files

Additional file 1:

Supplementary Table 1. Additional list of probes used to identify the Musa BAC clones. Estimated copy numbers of these sequences in rice, Sorghum and Musa are indicated for SbRPG (Sorghum bicolor) sequences.

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Additional file 2:

Supplementary Table 2. Additional BAC clones analyzed to define Musa gene features and syntenic relationships with rice.

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Additional file 3:

Supplementary Table 3. Statistics of the 17 Musa BAC clones analyzed in the present study.

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Additional file 4:

Supplementary Table 4. Annotation overview of the Musa genes. The column «Pseudogene» indicates by [1] if the gene is a pseudogene and [0] if not. Closest sequence homolog is the first similar protein sequence found by BLASTP after the sequence itself.

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Additional file 5:

Supplementary Table 5. List of genes involved in synteny relationship between Musa and rice based on i-ADHoRE results. Multiplicon is a BAC genomic sequence on which the baseclusters are isolated and represents a cluster of 3 genes minima.

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Additional file 6:

Supplementary Figure 1. Musa-rice syntenic region between MuH9 BAC clone and rice chromosome 4. Homologous genes between Musa and rice are indicated by shaded areas. Genes annotated such as hypothetical genes are white.

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Additional file 7:

Supplementary Figure 2. The Musa-rice syntenic region around the highly conserved porphobilinogen deaminase gene. Shaded areas connect homologous genes conserved between chromosome 2 of rice and Musa MA4_42M13 BAC clone (isolated by SbRPG748 probe). Genes annotated such as hypothetical genes are white. In Musa, a recent local duplication of the porphobilinogen deaminase gene occurred (genes MA4_42M13.6 and MA4_42M13.8).

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Additional file 8:

Supplementary Figure 3. Phylogenetic analyses on the seven of the ten M. acuminata genes from MA4_25J11 BAC clone. These seven Musa genes have homologous genes in rice chromosomes 1 and 5 and the locus numbers are available on Figure 5B. MA4_25J11 BAC clone was isolated by SbRPG132 probe.

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Additional file 9:

Supplementary Figure 4. Musa-Arabidopsis syntenic region between Musa MA4_54B05 BAC clone and Arabidopsis chromosome 5. Homologous genes between Musa and Arabidopsis are indicated by shaded areas. Genes annotated such as hypothetical genes are white. MA4_54B05 BAC clone was isolated by SbRPG661 probe.

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Additional file 10:

Supplementary Figure 5. Collinearity between M. acuminata (MA4_54N07) and M. balbisiana (MBP_91N22) around the CIR560 marker. The shaded areas connecting the two genomic regions represent conserved genes. Predicted genes and their orientation in each Musa BAC clone are shown as boxed areas. The genes for which the name is in bold hybridize with the marker. Genes annotated such as hypothetical genes are white. (A) Dot plot analysis of the two pairs of homeologous BACs from M. acuminata and M. balbisiana. (B) Diagram of the syntenic regions between the two BAC clones.

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