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Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs

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Abstract

Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we present a quantitative analysis of the gene content from publicly available sugarcane ESTs. The current sugarcane EST collection sampled orthologs for ~58 % of the closely-related sorghum proteome, suggesting that more than 10,000 sugarcane coding-genes remain undiscovered. Moreover the existence of more than 2,000 ncRNAs conserved between sugarcane and sorghum was revealed, among which over 500 are also detected in rice, supporting the existence of hundreds of conserved ncRNAs in grasses. New efforts towards sugarcane transcriptome sequencing were needed to sample the missing coding-genes as well as to expand the catalog of ncRNAs.

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Acknowledgments

This work was funded by grants 08/58031-0 (RV) and 08/52071-0 (MV) from FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) and LEVDB received a PhD scholarship from FAPESP (2008/09105-1).

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Authors and Affiliations

  1. Systems Biology Laboratory, Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil

    R. Vicentini

  2. Plant Genetics Laboratory, Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil

    L. E. V. Del Bem & M. Vincentz

  3. Department of Genetics, Institute of Biosciences, São Paulo State University, Botucatu, SP, Brazil

    F. T. S. Nogueira

  4. Genomes and Transposable Elements Laboratory, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil

    M. A. Van Sluys

  5. Center for Molecular Biology and Genetic Engineering, State University of Campinas, Av. Cândido Rondon, 400, Campinas, SP, Brazil, CEP: 13083-875

    R. Vicentini & L. E. V. Del Bem

Authors
  1. R. Vicentini

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  2. L. E. V. Del Bem

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  3. M. A. Van Sluys

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  4. F. T. S. Nogueira

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  5. M. Vincentz

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Corresponding authors

Correspondence toR. Vicentini orL. E. V. Del Bem.

Additional information

R. Vicentini and L. E. V. Del Bem are first authors.

Communicated by: Robert Henry

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Table S1

List of unique sampled sugarcane protein-coding orthologs from sorghum or rice. (XLS 1882 kb)

Table S2

List of sugarcane putative ncRNAs (XLS 266 kb)

Table S3

Sugarcane putative ncRNAs showing positive hits against the TIGR Plant Repeat Databases (XLS 17 kb)

Table S4

Sugarcane putative ncRNAs with repetitive and/or low complexity sequences as indentified by RepeatMasker software (XLS 40 kb)

File S1

Fastq file containing sRNAs sequences of 23 to 25 nucleotides showing perfect match against sugarcane putative ncRNAs. (FASTQ 5453 kb)

Figure S1

Schematic plot, using SeqMonk (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk), of the 13 sugarcane ncRNAs most enriched in perfectly matched sRNAs (>1,000 sRNAs) showing examples of phase-distributed sRNAs. In the top graph, red and blue lines represent sRNAs mapped in plus or minus strand of the sugarcane CSC, respectively. The middle graph shows the quantification by heat-map of the mapped sRNAs. Finally, the bottom graph shows mVISTA (http://genome.lbl.gov/vista) conservation plot between sugarcane’s CSC and sorghum possible orthologs. (JPEG 143 kb)

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Vicentini, R., Del Bem, L.E.V., Van Sluys, M.A.et al. Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs.Tropical Plant Biol.5, 199–205 (2012). https://doi.org/10.1007/s12042-012-9103-z

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