A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) Using sanger and second-generation sequencing platforms

Molecular Plant

Volumn 5, Issue 5, 2012, Pages 1020-1028

  Kudapa, Himabindu ^a   Bharti, Arvind K ^b   Cannon, Steven B ^c,d   Farmer, Andrew D ^b   Mulaosmanovic, Benjamin ^c   Kramer, Robin ^b   Bohra, Abhishek ^a   Weeks, Nathan T ^c   Crow, John A ^b   Tuteja, Reetu ^a   Shah, Trushar ^a   Dutta, Sutapa ^e   Gupta, Deepak K ^e   Singh, Archana ^e   Gaikwad, Kishor ^e   Sharma, Tilak R ^e   May, Gregory D ^b   Singh, Nagendra K ^e   Varshney, Rajeev K ^a,f  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d IOWA STATE UNIVERSITY   (United States)

^e NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^f Generation Challenge Programme   (Mexico)

Author keywords

Cajanus cajan (L.); intron spanning region (ISR) markers; second generation sequencing; transcriptome assembly

Indexed keywords

CAJANUS CAJAN; GLYCINE MAX;

EID: 84863135476     PISSN: 16742052     EISSN: 17529867     Source Type: Journal    
DOI: 10.1093/mp/ssr111     Document Type: Article

References (31)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller,W., and Lipman, D.J. (1997). Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-402.
2. Bohra, A., et al. (2011a). Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea, (Cajanus spp.). BMC Plant Biol. 11, 56.
3. Bohra, A., Saxena, R.K., Gnanesh, B.N., Saxena, K.B., Byregowda, M., Rathore, A., Kavi Kishor, P.B., Cook, D.R., and Varshney, R.K. (2011b). An intra-specific consensus genetic map of pigeonpea (Cajanus cajan (L.) Millspaugh) derived from six mapping populations. BMC Genomics (submitted revised version).
4. Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A.J., Müller, W.E., Wetter, T., and Suhai, S. (2004). Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147-1159.
5. Dubey, A., et al. (2011). Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Res. 18, 153-164.
6. Duke, J.A. (1981). Handbook of Legumes ofWorld Economic Importance (New York: Plenum Press), p. 345.
7. Dutta, S., et al. (2011). Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea (Cajanus cajan (L.) Millspaugh). BMC Plant Biol. 11, 17.
8. Galeano, C.H., Fernández, A.C., Gó mez, M., and Blair, M.W. (2009). Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genomics. 10, 629.
9. Garg, R., Patel, R.K., Jhanwar, S., Priya, P., Bhattacharjee, A., Yadav, G., Bhatia, S., Chattopadhyay, D., Tyagi, A.K., and Jain, M. (2011). Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 156, 1661-1678.
10. Gnanesh, B.N., Bohra, A., Sharma, M., Byregowda, M., Pandey, S., Wesley, V., Saxena, R.K., Saxena, K.B., Kavi Kishor, P.B., and Varshney, R.K. (2011). Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea (Cajanus cajan (L.) Millsp.). Field Crops Res. 123, 53-61.
11. Greilhuber, J., and Obermayer, R. (1998). Genome size variation in Cajanus cajan (Fabaceae): a reconsideration. Plant Syst. Evol. 212, 135-141.
12. Gujaria, N., et al. (2011). Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor. Appl. Genet. 122, 1577-1589.
13. Raju, N.L., Gananesh, B.N., Lekha, P., Jayashree, B., Pande, S., Hiremath, P.J., Byregowda, M., Singh, N.K., and Varshney, R.K. (2010). The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol. 10, 45.
14. Reddy, B.V.S., Green, J.M., and Bise, S.S. (1978). Genetic male sterility in pigeonpea. Crop Sci. 18, 362-364.
15. Rosen, S., and Skaletsky, H.J. (2000). Primer 3 on theWWWfor general users and for biologist programmers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology, Krawetz, S., Misener, S., eds (Totowa, NJ: Humana Press), pp. 365-386.
16. Saxena, K.B. (2008). Genetic improvement of pigeonpea: a review. Tropical Plant Biol. 1, 159-178.
17. Saxena, K.B., Wallis, E.S., and Byth, D.E. (1983). A new gene for male sterility in pigeonpea (Cajanus cajan (L.) Millsp). Heredity. 51, 419-421.
18. Schatz, M.C., Delcher, A.L., and Salzberg, S.L. (2010). Assembly of large genomes using second generation sequencing. Genome Res. 20, 1165-1173.
19. Schmutz, J., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature. 463, 178-183.
20. Schuler, G.D. (1997). Sequence mapping by electronic PCR. Genome Res. 7, 541-750.
21. 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, 1117-1123.
22. Slater, G.C., and Birney, E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 6, 31.
23. Stefanovic, S., Pfeil, B.E., Palmer, J.D., and Doyle, J.J. (2009). Relationships among phaseolid legumes based on sequences from eight chloroplast regions. Syst. Bot. 34, 115-125.
24. Thudi, M., Senthilvel, S., Bottley, A., Hash, C.T., Reddy, A.R., Feltus, A.F., Paterson, A.H., Hoisington, D.A., and Varshney, R.K. (2010). A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica. 174, 253-260.
25. van der Maesen, L.J.G. (1990). Pigeonpea: origin, history, evolution and taxonomy, In Pigeonpea, Nene Y.L., Hall, S.D., and Sheila V.K., eds (Wallingford: CAB International), pp. 15-46.
26. Varshney, R.K., Close, T.J., Singh, N.K., Hoisington, D.A., and Cook, D.R. (2009a). Orphan legume crops enter the genomics era. Curr. Opin. Plant Biol. 12, 202-210.
27. Varshney, R.K., et al. (2010). Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol. Breeding. 26, 393-408.
28. Varshney, R.K., Nayak, S.N., May, G.D., and Jackson, S.A. (2009b). Next generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27, 522-530.
29. Wanjari, K.B., and Patel, M.C. (2003). Fertility restorers isolated from germplasm for cytoplasmic male sterility in pigeonpea. PKV Res. J. 27, 111-113.
30. Yang, S., Pang, W., Ash, G., Harper, J., Carling, J., Wenzl, P., Huttner, E., Zong, X., and Kilian, A. (2006). A Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor. Appl. Genet. 113, 585-595.
31. You, F.M., Huo, N., Gu, Y.Q., Luo, M., Ma, Y., Hane, D., Lazo, G.R., Dvorak, J., and Anderson, O.D. (2008). BatchPrimer3: a high throughput web application for PCR and sequencing primer designing. BMC Bioinformatics. 9, 253.