Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development

Plant Physiology

Volumn 156, Issue 4, 2011, Pages 1661-1678

  Garg, Rohini ^a   Patel, Ravi K ^a   Jhanwar, Shalu ^a   Priya, Pushp ^a   Bhattacharjee, Annapurna ^a   Yadav, Gitanjali ^a   Bhatia, Sabhyata ^a   Chattopadhyay, Debasis ^a   Tyagi, Akhilesh K ^a   Jain, Mukesh ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CICER ARIETINUM; FABACEAE;

EID: 79961197602     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.111.178616     Document Type: Article

References (68)

1. Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mandal MK, Chakraborty N, Datta A, Chakraborty S (2009) Comparative analyses of genotype dependent expressed sequence tags and stressresponsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 10: 415
2. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 5: 16
3. Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol 63: 1-11
4. Campbell MA, Zhu W, Jiang N, Lin H, Ouyang S, Childs KL, Haas BJ, Hamilton JP, Buell CR (2007) Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol 145: 1311-1322
5. Cannon SB, May GD, Jackson SA (2009) Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol 151: 970-977
6. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154: 1819-1825
7. Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP (2007) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res (Database issue) 35: D846-D851
8. Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118: 591-608
9. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619
10. Cloutier S, Niu Z, Datla R, Duguid S (2009) Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119: 53-63 Daubin V, Lerat E, Perriére G (2003) The source of laterally transferred genes in bacterial genomes. Genome Biol 4: R57
11. Daubin V, Lerat E, Perriére G (2003) The source of laterally transferred genes in bacterial genomes. Genome Biol 4: R57
12. Garg et al. Domazet-Loso T, Tautz D (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res 13: 2213-2219
13. Doyle JJ, Luckow MA (2003) The rest of the iceberg: legume diversity and evolution in a phylogenetic context. Plant Physiol 131: 900-910
14. Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol 11: 17
15. Galtier N, Piganeau G, Mouchiroud D, Duret L (2001) GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159: 907-911
16. Gao WR, Wang XS, Liu QY, Peng H, Chen C, Li JG, Zhang JS, Hu SN, Ma H (2008) Comparative analysis of ESTs in response to drought stress in chickpea (C. arietinum L.). Biochem Biophys Res Commun 376: 578-583
17. Garg R, Patel RK, Tyagi AK, Jain M(2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18: 53-63
18. Garg R, Sahoo A, Tyagi AK, Jain M (2010) Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem Biophys Res Commun 396: 283-288
19. Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12: 117
20. Graham MA, Silverstein KA, Cannon SB, VandenBosch KA (2004) Computational identification and characterization of novel genes from legumes. Plant Physiol 135: 1179-1197
21. Graham PH, Vance CP (2003) Legumes: importance and constraints to greater use. Plant Physiol 131: 872-877
22. Hale MC, McCormick CR, Jackson JR, Dewoody JA (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 10: 203
23. Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, et al (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14: 271-281
24. Hüttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinumL.). Genome 42: 210-217
25. Jain D, Chattopadhyay D (2010) Analysis of gene expression in response towater deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance. BMC Plant Biol 10: 24
26. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S,Tyagi AK, Khurana J P (2007) F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483
27. Jain M, Tyagi AK, Khurana JP (2008) Genome-wide identification, classification,evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J 275: 2845-2861
28. Kaur H, Shukla RK, Yadav G, Chattopadhyay D, Majee M (2008) Two divergent genes encoding L-myo-inositol 1-phosphate synthase1 (CaMIPS1) and 2 (CaMIPS2) are differentially expressed in chickpea. Plant Cell Environ 31: 1701-1716
29. Koski LB, Gray MW, Lang BF, Burger G (2005) AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 6: 151 Kristiansson E, Asker N, Fö rlin L, Larsson DG (2009) Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 10: 345
30. Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11: 571
31. La Rota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6: 23
32. Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ (2006) Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci USA 103: 9935-9939
33. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63: 86-99
34. Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G (2009) Legume transcription factor genes: what makes legumes so special? Plant Physiol 151: 991-1001
35. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110: 492-510
36. Lin H, Moghe G, Ouyang S, Iezzoni A, Shiu SH, Gu X, Buell CR (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol 10: 41
37. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21: 3448-3449
38. Mantri NL, Ford R, Coram TE, Pang EC (2007) Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. BMC Genomics 8: 303
39. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10: 72-80
40. Millan T, Clarke HJ, Siddique KHM, Buhariwalla HK, Gaur PM, Kumar J, Gil J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147: 81-103
41. Millan T,Winter P, Jüngling R, Gil J, Rubio J, Cho S, Cobos MJ, Iruela M, Rajesh PN, Tekeoglu M, et al (2010) A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations. Euphytica 175: 175-189.
42. Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, et al (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9: 553
43. Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, et al (2011) The saltresponsive transcriptome of chickpea roots and nodules via deep- SuperSAGE. BMC Plant Biol 11: 31
44. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30: 194-200
45. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10: 135-151
46. Nowick K, Stubbs L (2010) Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief Funct Genomics 9: 65-78
47. Pandey A, Chakraborty S, Datta A, Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol Cell Proteomics 7: 88-107
48. Pandey A, Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A, Chakraborty N (2006) The nuclear proteome of chickpea (Cicer arietinum L.) reveals predicted and unexpected proteins. J Proteome Res 5: 3301-3311
49. Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG (2009) Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinformatics 10: 447
50. Peng H, Yu X, Cheng H, Shi Q, Zhang H, Li J, Ma H (2010) Cloning and characterization of a novel NAC family gene CarNAC1 from chickpea (Cicer arietinum L.). Mol Biotechnol 44: 30-40
51. Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res (Database issue) 38: D822-D827
52. Radhika P, Gowda SJ, Kadoo NY, Mhase LB, Jamadagni BM, Sainani MN, Chandra S, Gupta VS (2007) Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115: 209-216
53. Rajesh PN, Coyne C, Meksem K, Sharma KD, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108: 663-669
54. Rajesh PN, O'Bleness M, Roe BA, Muehlbauer FJ (2008) Analysis of genome organization, composition and microsynteny using 500 kb BAC sequences in chickpea. Theor Appl Genet 117: 449-458
55. Schatz MC, Delcher AL, Salzberg SL (2010) Assembly of large genomes using second-generation sequencing. Genome Res 20: 1165-1173
56. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
57. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, et al (2010) RNA-Seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10: 160
58. Shukla RK, Tripathi V, Jain D, Yadav RK, Chattopadhyay D (2009) CAP2 enhances germination of transgenic tobacco seeds at high temperature and promotes heat stress tolerance in yeast. FEBS J 276: 5252-5262
59. Tripathi V, Parasuraman B, Laxmi A, Chattopadhyay D (2009) CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. Plant J 58: 778-790
60. Upadhyaya HD, Dwivedi SL, Baum M, Varshney RK, Udupa SM, Gowda CL, Hoisington D, Singh S (2008) Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol 8: 106
61. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55
62. Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, et al (2009) A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10: 523
63. Vinogradov AE (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Res 31: 1838-1844
64. Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32-42
65. Wilhelm BT, Landry JR (2009) RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48: 249-257
66. Xu G, Ma H, Nei M, Kong H (2009) Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci USA 106: 835-840
67. Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M (2010) Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 152: 1787-1795
68. Zhang X, Scheuring CF, Zhang M, Dong JJ, Zhang Y, Huang JJ, Lee MK, Abbo S, Sherman A, Shtienberg D, et al (2010) A BAC/BIBACbased physical map of chickpea, Cicer arietinum L. BMC Genomics 11: 501