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Tropical Plant Biology

, Volume 5, Issue 2, pp 199–205 | Cite as

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

  • R. VicentiniEmail author
  • L. E. V. Del BemEmail author
  • M. A. Van Sluys
  • F. T. S. Nogueira
  • M. Vincentz
Article

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.

Keywords ncRNAs Orthology Sorghum Sugarcane Transcriptome 

Notes

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).

Supplementary material

12042_2012_9103_MOESM1_ESM.xls (1.8 mb)
Table S1 List of unique sampled sugarcane protein-coding orthologs from sorghum or rice. (XLS 1882 kb)
12042_2012_9103_MOESM2_ESM.xls (266 kb)
Table S2 List of sugarcane putative ncRNAs (XLS 266 kb)
12042_2012_9103_MOESM3_ESM.xls (18 kb)
Table S3 Sugarcane putative ncRNAs showing positive hits against the TIGR Plant Repeat Databases (XLS 17 kb)
12042_2012_9103_MOESM4_ESM.xls (40 kb)
Table S4 Sugarcane putative ncRNAs with repetitive and/or low complexity sequences as indentified by RepeatMasker software (XLS 40 kb)
12042_2012_9103_MOESM5_ESM.fastq (5.3 mb)
File S1 Fastq file containing sRNAs sequences of 23 to 25 nucleotides showing perfect match against sugarcane putative ncRNAs. (FASTQ 5453 kb)
12042_2012_9103_Fig2_ESM.jpg (143 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)

12042_2012_9103_MOESM6_ESM.tif (1.4 mb)
High Resolution Image (TIFF 1470 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Systems Biology Laboratory, Center for Molecular Biology and Genetic EngineeringState University of CampinasCampinasBrazil
  2. 2.Plant Genetics Laboratory, Center for Molecular Biology and Genetic EngineeringState University of CampinasCampinasBrazil
  3. 3.Department of Genetics, Institute of BiosciencesSão Paulo State UniversityBotucatuBrazil
  4. 4.Genomes and Transposable Elements Laboratory, Department of Botany, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
  5. 5.Center for Molecular Biology and Genetic EngineeringState University of CampinasCampinasBrazil

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