Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs
- 378 Downloads
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.
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).
- Ben Amor B, Wirth S, Merchan F, Laporte P, d’Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19:57–69PubMedCrossRefGoogle Scholar
- Casu RE, Dimmock CM, Thomas M, Bower N, Knight D (2001) Genetic and expression profiling in sugarcane. Proc Int Soc Sugar Cane Technol 24:542–546Google Scholar
- D’Hont A, Glaszmann JC (2001) Sugarcane genome analysis with molecular markers, a first decade of research. Proc Int Soc Sugar Cane Technol 24:556–559Google Scholar
- Daniels J, Roach BT (1987) Taxonomy and evolution in sugarcane. In: Heinz D (ed) Sugarcane improvement through breeding. Elsevier Press, Amsterdam, pp 7–84Google Scholar
- Garcia AA, Kido EA, Meza AN, Souza HM, Pinto LR, Pastina MM, Leite CS, Silva JA, Ulian EC, Figueira A et al (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 112:298–314PubMedCrossRefGoogle Scholar
- Grivet L, Daniels C, Glaszmann JC, D’Hont A (2004) A review of recent molecular genetics evidence for sugarcane evolution and domestication. Ethnobot Res Appl 2:9–17Google Scholar
- Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682PubMedGoogle Scholar
- Pastina MM, Pinto LR, Oliveira KM, Souza KM, Garcia AAF (2010) Molecular mapping of complex traits. In: Henry (ed) Genetics, genomics and breeding of sugarcane. CRC Press, Science PublishersGoogle Scholar
- Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Development. 15; 19(18):2164–2175Google Scholar