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  • Alagna, F., D'Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., Chiusano, M.L., Baldoni, L. and Perrotta, G. (2009) Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics, 10, 399.
  • Alo, F., Furman, J.B., Akhunov, E., Dvorak, J. and Gepts, P. (2011) Leveraging genomic resources of model species for the assessment of diversity and phylogeny in wild and domesticated lentil. J. Hered. 102, 315329.
  • Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D. and Sorrells, M.E. (1993) Optimizing parental selection for genetic linkage maps. Genome, 36, 181186.
  • Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208218.
  • Barakat, A., DiLoreto, D.S., Zhang, Y., Smith, C., Baier, K., Powell, W.A., Wheeler, N., Sederoff, R. and Carlson, J.E. (2009) Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol. 9, 51.
  • Blanca, J., Canizares, J., Roig, C., Ziarsolo, P., Nuez, F. and Picó, B. (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics, 12, 104.
  • Campbell, M.A., Zhu, W., Jiang, N., Lin, H., Ouyang, S., Childs, K.L., Haas, B.J., Hamilton, J.P. and Buell, C.R. (2007) Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol. 145, 13111322.
  • Chen, X., Zhu, W., Azam, S., Li, H., Zhu, F., Li, H., Hong, Y., Liu, H., Zhang, E., Wu, H., Yu, S., Zhou, G., Li, S., Zhong, N., Wen, S., Li, X., Knapp, S.J., Ozias-Akins, P., Varshney, R. and Liang, X. (2013) Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biot. J. 11, 115127.
  • Cho, Y.G., Ishii, T., Temnykh, S., Chen, X., Lipovich, L., McCouch, S.R., Park, W.D., Ayres, N. and Cartinhour, S. (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 713722.
  • Choudhary, S., Sethy, N.K., Shokeen, B. and Bhatia, S. (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet. 118, 591608.
  • Cordeiro, G.M., Casu, R., McIntyre, C.L., Manners, J.M. and Henry, R.J. (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs across transferable to Erianthus and Sorghum. Plant Sci. 160, 11151123.
  • Duan, J., Xia, C., Zhao, G., Jia, J. and Kong, X. (2012) Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics, 13, 392.
  • Dubey, A., Farmer, A., Schlueter, J., Cannon, S.B., Abernathy, B., Tuteja, R., Woodward, J., Shah, T., Mulasmanovic, B., Kudapa, H., Raju, N.L., Gothalwal, R., Pande, S., Xiao, Y., Town, C.D., Singh, N.K., May, G.D., Jackson, S. and Varshney, R.K. (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in Pigeonpea (Cajanus cajan L.). DNA Res. 18, 153164.
  • Durán, Y., Fratini, R., Gracía, P. and Pérez de la Vega, M. (2004) An intersubspecific genetic map of Lens. Theor. Appl. Genet. 108, 12651273.
  • Eujayl, I., Sorrells, M.E., Baum, M., Wolters, P. and Powell, W. (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor. Appl. Genet. 104, 399407.
  • Feldmeyer, B., Wheat, C.W., Krezdorn, N., Rotter, B. and Pfenninger, M. (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics, 12, 317.
  • Franssen, S.U., Shrestha, R.P., Bräutigam, A., Bornberg-Bauer, E. and Weber, A.P.M. (2011) Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics, 12, 227.
  • Fu, B. and He, S. (2012) Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. DNA Res. 19, 131142.
  • Gao, X., Han, J., Lu, Z., Li, Y. and He, C. (2012) Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers. Com. Biochem. Physiol. 7, 277284.
  • Garg, R., Patel, R.K., Tyagi, A.K. and Jain, M. (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18, 5363.
  • Graham, M.A., Silverstein, K.A., Cannon, S.B. and VandenBosch, K.A. (2004) Computational identification and characterization of novel genes from legumes. Plant Physiol. 135, 11791197.
  • Gupta, M., Verma, B., Kumar, N., Chahota, R.K., Rathour, R., Sharma, S.K., Bhatia, S. and Sharma, T.R. (2012) Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. J. Genet. 91, 279287.
  • Hamwieh, A., Udupa, S.M., Choumane, W., Sarkar, A., Dreyer, F., Jung, C. and Baum, M. (2005) A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance. Theor. Appl. Genet. 110, 669677.
  • Iorizzo, M., Senalik, D.A., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., VanDeynze, A. and Simon, P.W. (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics, 12, 389.
  • Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 2730.
  • Kaur, S., Cogan, O.N., Pembleton, L.W., Shinozuka, M., Savin, K.W., Materne, M. and Forster, J.W. (2011) Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 12, 265.
  • Khanuja, S.P.S., Shasany, A.K., Darokar, M.P. and Kumar, S. (1999) Rapid isolation of DNA from dry and fresh samples of plant producing large amounts of secondary metabolites and essential oils. Plant Mol. Biol. Rep. 17, 17.
  • Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Mulaosmanovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K. and Varshney, R.K. (2012) A comprehensive transcriptome assembly of Pigeonpea (Cajanus cajan L.) using sanger and second-generation sequencing platforms. Mol. Plant, 5, 10201028.
  • Li, Y.C., Korol, A.B., Fahima, T. and Nevo, E. (2004) Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21, 9911007.
  • Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B. and Bai, Y. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311317.
  • Li, Y.J., Fu, Y.R., Huang, J.G., Wu, C.A. and Zheng, C.C. (2011) Transcript profiling during the early development of the maize brace root via Solexa sequencing. FEBS J. 278, 156166.
  • Li, D., Deng, Z., Qin, B., Liu, X. and Men, Z. (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics, 13, 192.
  • Liang, X., Chen, X., Hong, Y., Liu, H., Zhou, G., Li, S. and Guo, B. (2009) Utility of EST-derived SSR in cultivated peanut (Arachis hypogea L.) and Arachis wild species. BMC Plant Biol. 9, 35.
  • Libault, M., Joshi, T., Benedito, V.A., Xu, D., Udvardi, M.K. and Stacy, G. (2009) Legume transcription factor genes: what makes legumes so special. Plant Physiol. 151, 9911001.
  • Libault, M., Farmer, A., Joshi, T., Takahashi, K., Langley, R.J., Franklin, L.D., He, J., Xu, D., May, G. and Stacey, G. (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 63, 8699.
  • Lulin, H., Xiao, Y., Pei, S., Wen, T. and Shangqin, H. (2012) The first Illumina based de novo transcriptome sequencing and analysis of Safflower flowers. PLoS ONE, 7, e38653.
  • Metzker, M.L. (2010) Sequencing technologies —the next generation. Nat. Reviews, 11, 3146.
  • Meyer, E., Aglyamova, G., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J., Willis, B. and Matz, M. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-FLX. BMC Genomics, 10, 219.
  • Muehlbauer, F.J., Slinkard, A.E. and Wilson, V.E. (1980) Lentil. In Hybridization of Crop Plants (Fehr, W.R. and Hadley, H.H., eds), pp. 417426. Madison: Alliance of Crop, Soil and Environmental Science Societies Publications.
  • Muehlbauer, F.J., Cho, S., Sarker, A., McPhee, K.E., Coyne, C.J., Rajesh, P.N. and Ford, R. (2006) Application of biotechnology in breeding lentil for resistance to biotic and abiotic stress. Euphytica, 147, 149165.
  • Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 13441349.
  • Ness, R.W., Siol, M. and Barrett, S.C.H. (2011) De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genomics, 12, 298.
  • Novaes, E., Drost, D.R., Farmerie, W.G., Pappas, G.J. Jr, Grattapaglia, D., Sederoff, R.R. and Kirst, M. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomic, 9, 312.
  • Parchman, T.L., Geist, K.S., Grahnen, J.A., Benkman, C.W. and Buerkle, C.A. (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11, 180.
  • Patel, R.K. and Jain, M. (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE, 7, e30619.
  • Perez-Rodriguez, P., Riano-Pachon, D.M., Correa, L.G.G., Rensing, S.A., Kersten, B. and Mueller-Roeber, B. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38, 822827.
  • Rohlf, F.J. (1998) NTSYS: numerical taxonomy and multivariate analysis system, Version 2.1. NewYork: Applied Biostastistics Setauket 1998.
  • Rosenkranz, R., Borodina, T., Lehrach, H. and Himmelbauer, H. (2008) Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics, 92, 187194.
  • Rubeena., Ford, R. and Taylor P.W.J. (2003) Construction of an interaspecific linkage map of lentil (Lens culinaris ssp. culinaris). Theor. Appl. Genet. 107, 910916.
  • Sharpe, A.G., Ramsay, L., Sanderson, L.-A., Fedoruk, M.J., Clarke, W.E., Li, R., Kagale, S., Vijayan, P., Vandenberg, A. and Bett, K.E. (2013) Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil. BMC Genomics, 14, 192. doi:10.1186/1471-2164-14-192.
  • Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. and Birol, I. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 11171123.
  • Surget-Groba, Y. and Montoya-Burgos, J.I. (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 20, 14321440.
  • Tao, X., Gu, Y.H., Wang, H.Y., Zheng, W., Li, X., Zhao, C.W. and Zhang, Y.Z. (2012) Digital gene expression analysis based on integrated De novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam.]. PLoS ONE, 7, e36234.
  • Thiel, T., Michalek, W., Varshney, R.K. and Graner, A. (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411422.
  • Toth, G., Gaspari, Z. and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10, 967981.
  • Triwitayakorn, K., Chatkulkawin, P., Kanjanawattanawong, S., Sraphet, S., Yoocha, T., Sangsrakru, D., Chanprasert, J., Ngamphiw, C., Jomchai, N., Therawattanasuk, K. and Tangphatsornruang, S. (2011) Transcriptome sequencing of H. brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res. 18, 471482.
  • Varshney, R.K., Thiel, T., Stein, N., Langridge, P. and Graner, A. (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell. Mol. Biol. Lett. 7, 537546.
  • Varshney, R.K., Graner, A. and Sorrells, M.E. (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23, 4855.
  • Wang, X.W., Luan, J.B., Li, J.M., Bao, Y.Y., Zhang, C.X. and Liu, S.S. (2010a) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics, 11, 400410.
  • Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X. and Li, Y. (2010b) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics, 11, 726.
  • Wang, S., Wang, X., He, Q., Liu, X., Xu, W., Li, L., Gao, J. and Wang, F. (2012a) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep. 31, 14371447.
  • Wang, Y., Zeng, X., Iyer, N.J., Bryant, D.W., Mockler, T.C. and Mahalingam, R. (2012b) Exploring the Switchgrass transcriptome using second-generation sequencing technology. PLoS ONE, 7, 34225.
  • Wei, W.L., Qi, X.Q., Wang, L.H., Zhang, Y.X., Hua, W., Li, D.H., Lv, H.X. and Zhang, X.R. (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12, 451463.
  • Xia, Z., Xu, H., Zhai, J., Li, D., Luo, H., He, C. and Huang, X. (2011) RNA-Seq analysis and de novo transcriptome assembly of H. brasiliensis. Plant Mol. Biol. 77, 299308.
  • Xie, F., Burklew, C.E., Yang, Y., Liu, M., Xiao, P., Zhang, B. and Qiu, D. (2012) De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta, 236, 101113.
  • Yang, X., Xu, Y., Shah, T., Li, H., Han, Z., Li, J. and Yan, J. (2011) Comparison of SSRs and SNPs in assessment of genetic relatedness in maize. Genetica, 139, 10451054.
  • Yao, B., Zhao, Y., Zhang, H., Zhang, M., Liu, M., Liu, H. and Li, J. (2012) Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology. Biotechnol. Lett. 34, 813822.
  • Yeh, F.C. and Boyle, T.J.B. (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian J. Bot. 129, 157.
  • Zeng, S., Xiao, G., Guo, J., Fei, Z., Xu, Y., Roe, B.A. and Wang, Y. (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics, 11, 94.
  • Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821829.
  • Zhang, J., Liang, S., Duan, J., Wang, J., Chen, S., Cheng, Z., Zhang, Q., Liang, X. and Li, Y. (2012a) De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in Peanut (L.). BMC Genomics, 13, 90.
  • Zhang, X.M., Zhao, L., Larson-Rabin, Z., Li, D.Z. and Guo, Z.H. (2012b) De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae). PLoS ONE, 7, e42082.