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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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References

  • 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 19:57–69

    Article  PubMed  CAS  Google Scholar 

  • Bower NI, Casu RE, Maclean DJ, Reverter A, Chapman SC, Manners JM (2005) Transcriptional response of sugarcane roots tomethyl jasmonate. Plant Sci 168:761–772

    Article  CAS  Google Scholar 

  • Carson D, Botha F (2002) Genes expressed in sugarcane maturing internodal tissue. Plant Cell Rep 20:1075–1081

    Article  CAS  Google Scholar 

  • Carson DL, Huckett BI, Botha FC (2002) Sugarcane ESTs differentially expressed in immature and maturing intermodal tissue. Plant Sci 162:289–300

    Article  CAS  Google Scholar 

  • Casu RE, Dimmock CM, Thomas M, Bower N, Knight D (2001) Genetic and expression profiling in sugarcane. Proc Int Soc Sugar Cane Technol 24:542–546

    Google Scholar 

  • Casu RE, Grof CPL, Rae AL, McIntyre CL, Dimmock CM, Manners JM (2003) Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis. Plant Mol Biol 52:371–386

    Article  PubMed  CAS  Google Scholar 

  • De Lucia F, Dean C (2011) Long non-coding RNAs and chromatin regulation. Curr Opin Plant Biol 14(2):168–173

    Article  PubMed  Google Scholar 

  • D’Hont A (2005) Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res 109:27–33

    Article  PubMed  Google Scholar 

  • D’Hont A, Glaszmann JC (2001) Sugarcane genome analysis with molecular markers, a first decade of research. Proc Int Soc Sugar Cane Technol 24:556–559

    Google Scholar 

  • Daniels J, Roach BT (1987) Taxonomy and evolution in sugarcane. In: Heinz D (ed) Sugarcane improvement through breeding. Elsevier Press, Amsterdam, pp 7–84

    Google Scholar 

  • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8:967–974

    PubMed  CAS  Google 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 112:298–314

    Article  PubMed  CAS  Google Scholar 

  • Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann JC, Van Sluys MA et al (2011) High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytol 189:629–642

    Article  PubMed  CAS  Google Scholar 

  • Goldemberg J (2006) The ethanol program in Brazil. Environ Res Lett 1:014008

    Article  Google Scholar 

  • Grivet L, D’Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC (1996) RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid. Genetics 142:987–1000

    PubMed  CAS  Google Scholar 

  • Grivet L, Glaszmann JC, Vincentz M, da Silva F, Arruda P (2003) ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes. Theor Appl Genet 106(2):190–197

    PubMed  CAS  Google 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 2:9–17

    Google Scholar 

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    Article  PubMed  CAS  Google Scholar 

  • Gupta V, Raghuvanshi S, Gupta A, Saini N, Gaur A, Khan MS, Gupta RS, Singh J, Duttamajumder SK, Srtivastava S et al (2010) The water-deficit stress- and red-rot-related genes in sugarcane. Funct Integr Genomics 10:207–214

    Article  PubMed  CAS  Google Scholar 

  • Hoarau JY, Grivet L, Offmann B, Raboin LM, Diorflar JP, Payet J, Hellmann M, D’Hont A, Glaszmann JC (2002) Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). II. Detection of QTLs for yield components. Theor Appl Genet 105:1027–1037

    Article  PubMed  Google Scholar 

  • Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann J-C, Arruda P, D’Hont A (2007) Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J 50:574–585

    Article  PubMed  CAS  Google Scholar 

  • Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V, Sundaresan V, Vance V, Bowman LH (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 19:1429–1440

    Article  PubMed  CAS  Google Scholar 

  • Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518

    Article  PubMed  CAS  Google Scholar 

  • Lam E, Shine J, da Silva J, Lawton M, Bonos S, Calvino M, Carrer H, Silva-Filho MC, Glynn N, Helsel Z et al (2009) Improving sugarcane for biofuel: engineering for an even better feedstock. Glob Chang Biol Bioenergy 1:251–255

    Article  CAS  Google Scholar 

  • Ma HH, Schulze S, Lee S, Yang M, Mirkov E, Irvine J, Moore P, Paterson A (2004) An EST survey of the sugarcane transcriptome. Theor Appl Genet 108:851–863

    Article  PubMed  Google Scholar 

  • Mattick JS (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2:986–991

    Article  PubMed  CAS  Google Scholar 

  • Mattick JS (2005) The functional genomics of noncoding RNA. Science 309:1527–1528

    Article  PubMed  CAS  Google Scholar 

  • Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15:R17–R29

    Article  PubMed  CAS  Google Scholar 

  • Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJM (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21(3):367–376

    Article  PubMed  CAS  Google 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 150:1663–1682

    PubMed  CAS  Google Scholar 

  • Menossi M, Silva-Filho MC, Vincentz M, Van-Sluys M, Souza GM (2008) Sugarcane functional genomics: gene discovery for agronomic trait development. Int J Plant Genomics 2008:458732

    PubMed  CAS  Google Scholar 

  • Mercer TR, Dinger ME, Mattick JS (2009) Long noncoding RNAs: insights into function. Nat Rev Genet 10:155–159

    Article  PubMed  CAS  Google Scholar 

  • Moore PH (1995) Temporal and spatial regulation of sucrose accumulation in the sugarcane stem. Aust J Plant Physiol 22:661–679

    Article  CAS  Google Scholar 

  • Oliveira KM, Pinto LR, Marconi TG, Margarido GRA, Pastina MM, Teixeira LHM, Figueira AV, Ulian EC, Garcia AAF, Souza AP (2007) Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Mol Breed 20:189–208

    Article  CAS  Google Scholar 

  • Ouyang S, Buell CR (2004) The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 32:D360–D363

    Article  PubMed  CAS  Google 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 Publishers

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Article  PubMed  CAS  Google Scholar 

  • Piperidis G, Piperidis N, D’Hont A (2010) Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Mol Genet Genomics 284:65–73

    Article  PubMed  CAS  Google Scholar 

  • Somerville C, Youngs H, Taylor C, Davis SC, Long SP (2010) Feedstocks for lignocellulosic biofuels. Science 329:790–792

    Article  PubMed  CAS  Google Scholar 

  • Song X, Li P, Zhai J, Zhou M, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, Chu C, Wang XJ, Green PJ, Meyers BC, Cao X (2011) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J 69:462–474

    Article  PubMed  Google Scholar 

  • Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MIs, Henrique-Silva F, Giglioti EA, Lemos MVF, Coutinho LL et al (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 13:2725–2735

    Article  PubMed  Google 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):2164–2175

    Google Scholar 

  • Yu J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  PubMed  CAS  Google Scholar 

  • Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LEV, da Silva MJ, Vincentz M, Nogueira FTS (2010) Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biol 10:260

    Article  PubMed  Google Scholar 

  • Zhu QH, Wang MB (2012) Molecular functions of long non-coding RNAs in plants. Genes 3(1):176–190

    Article  Google Scholar 

Download references

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

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  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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Correspondence to R. Vicentini or L. 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)

High Resolution Image (TIFF 1470 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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