Open Access Highly Accessed Research article

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Jianping Wang1, Bruce Roe2, Simone Macmil2, Qingyi Yu3, Jan E Murray1, Haibao Tang4, Cuixia Chen1, Fares Najar2, Graham Wiley2, John Bowers4, Marie-Anne Van Sluys5, Daniel S Rokhsar6, Matthew E Hudson7, Stephen P Moose7, Andrew H Paterson4 and Ray Ming17*

Author Affiliations

1 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

2 Advanced Center for Genome Technology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-0370, USA

3 AgriLife Research Center, Texas A&M University, Weslaco, TX 78596-8344, USA

4 Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA

5 Department of Botany, University of Sao Paulo, 05508-090, Sao Paulo, SP, Brazil

6 Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA

7 Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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BMC Genomics 2010, 11:261  doi:10.1186/1471-2164-11-261

Published: 23 April 2010

Additional files

Additional file 1:

Selection of 20 sugarcane BACs using overgo hybridization.

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Additional file 2:

Row and column pools of sugarcane BACs for 454 sequencing.

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Additional file 3:

Gene and repeat distribution on sugarcane BACs.

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Additional file 4:

RT-PCR confirmation of 26 sugarcane genes inferred by sorghum ESTs.

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Additional file 5:

RT-PCR confirmation of 21 sugarcane genes predicted by sorghum gene models.

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Additional file 6:

List of 44 SSR markers developed from the sugarcane BAC sequences.

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Additional file 7:

Repetitive sequences in the expanded region of the sorghum genome. Alignment between sugarcane and sorghum homologous sequences showed DNA sequence expansion in the sorghum genome. The expanded DNA sequences are mostly transposable elements.

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Additional file 8:

Tandem duplication of putative genes in sugarcane genome. These genes were identified by aligning the genome sequences with sorghum annotated CDs. Gene B has two copies in sugarcane and one in sorghum. The putative function of genes A, B, C, D, and E are serine carboxypeptidase 2, receptor kinase, OSH15 protein, and homeobox transcription factor GNARLY1, respectively.

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Additional file 9:

Dot plot alignments between the 454 FLEX assembly, Sanger assembly and the corresponding sorghum regions for BAC SC118L15 and SC172L01. In both cases, the more complete assembly was put on the x-axis to represent the sugarcane BAC (FLEX assembly for SC118L15, Sanger assembly forSC172L01). The dot plot was based on a word size of 10, i.e. each dotrepresent a 10-mer hit. Green bands were used to visually separate individual contigs. Corresponding sorghum regions were identified as chromosome number: base range in megabase unit.

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Additional file 10:

Summary of repetitive sequences in sugarcane BACs, SC118L15 and SC172L01, and the orthologous euchromatic regions of sorghum.

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