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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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).
R. Vicentini and L. E. V. Del Bem are first authors.
Communicated by: Robert Henry
Electronic supplementary material
Below is the link to the electronic supplementary material.
List of unique sampled sugarcane protein-coding orthologs from sorghum or rice. (XLS 1882 kb)
List of sugarcane putative ncRNAs (XLS 266 kb)
Sugarcane putative ncRNAs showing positive hits against the TIGR Plant Repeat Databases (XLS 17 kb)
Sugarcane putative ncRNAs with repetitive and/or low complexity sequences as indentified by RepeatMasker software (XLS 40 kb)
Fastq file containing sRNAs sequences of 23 to 25 nucleotides showing perfect match against sugarcane putative ncRNAs. (FASTQ 5453 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