A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

Plant Journal

Volumn 74, Issue 5, 2013, Pages 715-729

  Jain, Mukesh ^a   Misra, Gopal ^a   Patel, Ravi K ^a   Priya, Pushp ^a   Jhanwar, Shalu ^a   Khan, Aamir W ^a   Shah, Niraj ^a   Singh, Vikas K ^a   Garg, Rohini ^a   Jeena, Ganga ^a   Yadav, Manju ^a   Kant, Chandra ^a   Sharma, Priyanka ^a   Yadav, Gitanjali ^a   Bhatia, Sabhyata ^a   Tyagi, Akhilesh K ^a   Chattopadhyay, Debasis ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

chickpea; Cicer arietinum; desi type; gene expression; genome sequence; ICC4958; marker resource; technical advance

Indexed keywords

CHICKPEA; CICER ARIETINUM; DESI-TYPE; GENOME SEQUENCES; ICC4958; MARKER RESOURCE; TECHNICAL ADVANCES;

CROPS; CULTIVATION; GENE EXPRESSION; PLANTS (BOTANY); RNA; TISSUE;

GENETIC ENGINEERING;

MICROSATELLITE DNA; TRANSCRIPTOME; VEGETABLE PROTEIN;

ARTICLE; CHROMOSOME MAP; CICER; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; FABACEAE; GENETIC VARIABILITY; GENETICS; GENOTYPE; METHODOLOGY; PHYLOGENY; PLANT CHROMOSOME; PLANT GENOME; SYNTENY;

BASE COMPOSITION; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CICER; FABACEAE; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; MICROSATELLITE REPEATS; PHYLOGENY; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA; SYNTENY; TRANSCRIPTOME;

BACTERIA (MICROORGANISMS); CICER ARIETINUM;

EID: 84878341271     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12173     Document Type: Article

References (79)

1. Abbo, S., Berger, J., and, Turner, N.C., (2003a) Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct. Plant Biol. 30, 1081-1087.
2. Abbo, S., Shtienberg, D., Lichtenzveig, J., Lev-Yadun, S., and, Gopher, A., (2003b) The chickpea, summer cropping, and a new model for pulse domestication in the ancient near East. Quant. Rev. Biol. 78, 435-448.
3. Agarwal, G., Jhanwar, S., Priya, P., Singh, V.K., Saxena, M.S., Parida, S.K., Garg, R., Tyagi, A.K., and, Jain, M., (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS ONE, 7, e52443.
4. Al-Dous, E.K., George, B., Al-Mahmoud, M.E., et al,. (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat. Biotechnol. 29, 521-527.
5. Anders, S., and, Huber, W., (2010) Differential expression analysis for sequence count data. Genome Biol. 11, R106.
6. Argout, X., Salse., J., Aury, J.M., et al,. (2011) The genome of Theobroma cacao. Nat. Genet. 43, 101-108.
7. Arnon, I., (1972) Crop Production in Dry Regions, Vol. I. London: Leonard Hill, pp. 460-462.
8. Arumuganathan, K., and, Earle, E.D., (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218.
9. Benedito, V.A., Torres-Jerez, I., Murray, J.D., et al,. (2008) A gene expression atlas of the model legume Medicago truncatula. Plant J. 55, 504-513.
10. Birney, E., Clamp, M., and, Durbin, R., (2004) Genewise and genomewise. Genome Res. 14, 988-995.
11. Bonnin, I., Ronfort, J., Wozniak, F., and, Olivieri, I., (2010) Spatial effects and rare outcrossing events in Medicago truncatula (Fabaceae). Mol. Ecol. 10, 1371-1383.
12. Branca, A., Paape, T.D., Zhou, P., et al,. (2011) Whole-genome nucleotide diversity, recombination, and linkage disquilibrium in the model legume Medicago truncatula. Proc. Natl Acad. Sci. USA, 108, E864-E870.
13. Caicedo, A.L., Williamson, S.H., Hernandez, R.D., et al,. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3, e163.
14. Campbell, M.A., Haas, B.J., Hamilton, J.P., Mount, S.M., and, Buell, C.R., (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics, 7, 327.
15. 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, 1311-1322.
16. Cannon, S.B., Sterck, L., Rombauts, S., et al,. (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl Acad. Sci. USA, 103, 14959-14964.
17. Chen, N., (2004) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics, 25, 4.10.1-4.10.14.
18. Choi, H.K., Mun, J.H., Kim, D.J., et al,. (2004) Estimating genome conservation between crop and model legume species. Proc. Natl Acad. Sci. USA, 101, 15289-15294.
19. Comal, L., (2005) The advantages and disadvantages of being polyploidy. Nat. Rev. Genet. 6, 836-846.
20. Conesa, A., Götz, S., García-Gõmez, J.M., Terol, J., Talõn, M., and, Robles, M., (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
21. Delcher, A.L., Phillippy, A., Carlton, J., and, Salzberg, S.L., (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478-2483.
22. Edgar, R.C., and, Myers, E.W., (2005) PILER: identification and classification of genomic repeats. Bioinformatics, 21 (Suppl), i152-i158.
23. Elsik, C.G., Mackey, A.J., Reese, J.T., Milshina, N.V., Roos, D.S., and, Weinstock, G.M., (2007) Creating a honey bee consensus gene set. Genome Biol. 8, R13.
24. Enright, A.J., Van Dongen, S., and, Ouzounis, C.A., (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584.
25. FAOSTAT (2009) Faostat.fao.org/site/567/DesktopDefault.aspx?PageID= 567anchor.
26. Fawcett, J.A., Maere, S., and, van de Peer, Y., (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl Acad. Sci. USA, 106, 5737-5742.
27. 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.
28. Gaur, R., Azam, S., Jeena, G., Khan, A.W., Choudhary, S., Jain, M., Yadav, G., Tyagi, A.K., Chattopadhyay, D., and, Bhatia, S., (2012a) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res. 19, 357-373.
29. Gaur, P.M., Jukanti, A.K., and, Varshney, R.K., (2012b) Impact of genomic technologies on chickpea breeding strategies. Agronomy, 2, 199-221.
30. Gore, M.A., Chia, J.M., Elshire, R.J., et al,. (2009) A first-generation haplotype map of maize. Science, 326, 1115-1117.
31. Graham, P.H., and, Vance, C.P., (2003) Legumes: importance and constraints to greater use. Plant Physiol. 131, 872-877.
32. Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Buell, C.R., and, Wortman, J.R., (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7.
33. Huang, S., Li, R., Zhang, Z., et al,. (2009) The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41, 1275-1281.
34. Hunter, S., Apweiler, R., Attwood, T.K., et al,. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211-D215.
35. Jaillon, O., Aury, J.M., Noel, B., et al,. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463-467.
36. Jhanwar, S., Priya, P., Garg, R., Parida, S.K., Tyagi, A.K., and, Jain, M., (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J. 10, 690-702.
37. Koski, L.B., Gray, M.W., Lang, B.F., and, Burger, G., (2005) AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics, 6, 151.
38. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., and, Marra, M.A., (2009) Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.
39. Lam, H.M., Xun, X., Liu, X., et al,. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053-1059.
40. Lavin, M., Herendeen, P.S., and, Wojciechowski, M.F., (2005) Evolutionary rates analysis of leguminosae implicates a rapid diversification of lineages during the tertiary. Syst. Biol. 54, 575-594.
41. Libault, M., Joshi, T., Benedito, V.A., Xu, D., Udvardi, M.K., and, Stacey, G., (2009) Legume transcription factor genes: what makes legumes so special? Plant Physiol. 151, 991-1001.
42. 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, 86-99.
43. Lin, H., Moghe, G., Ouyang, S., Iezzoni, A., Shiu, S.H., Gu, X., and, Buell, C.R., (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol. Biol. 10, 41.
44. Lowe, T.M., and, Eddy, S.R., (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.
45. Lynch, M., and, Conery, J.S., (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
46. Maere, S., Heymans, K., and, Kuiper, M., (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
47. Margulies, M., Egholm, M., Altman, W.E., et al,. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
48. Nawrocki, E.P., Kolbe, D.L., and, Eddy, S.R., (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
49. Otto, S.P., and, Whitton, J., (2000) Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401-437.
50. Parra, G., Bradnam, K., and, Korf, I., (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23, 1061-1067.
51. Patel, R.K., and, Jain, M., (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE, 7, e30619.
52. Paterson, A.H., Bowers, J.E., and, Chapman, B.A., (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl Acad. Sci. USA, 101, 9903-9908.
53. Pfeil, B.E., Schlueter, J.A., Shoemaker, R.C., and, Doyle, J.J., (2005) Placing paleoploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst. Biol. 54, 441-454.
54. Price, A.L., Jones, N.C., and, Pevzner, P.A., (2005) De novo identification of repeat families in large genomes. Bioinformatics, 21 (Suppl), i351-i358.
55. Proost, S., Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., Van de Peer, Y., and, Vandepoele, K., (2012) i-Adhore 3.0-fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. 40, e11.
56. Rozen, S., and, Skaletsky, H., (2000) Primer 3 on WWW for general users and for biologists programmers. Methods Mol. Biol. 132, 365-386.
57. Salamov, A.A., and, Solovyev, V.V., (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522.
58. Sanseverino, W., Roma, G., De Simone, M., Faino, L., Melito, S., Stupka, E., Frusciante, L., and, Ercolano, M.R., (2010) PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res. 38, D814-D821.
59. Sato, S., Nakamura, Y., Kaneko, T., et al,. (2008) Genome structure of the legume, Lotus japonicus. DNA Res. 15, 227-239.
60. Schmutz, J., Cannon, S.B., Schlueter, J., et al,. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183.
61. 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.
62. Singh, K.B., Malhotra, R.S., Saxena, M.C., and, Bejiga, G., (1997) Superiority of winter sowing over traditional spring sowing of chickpea in the Mediterranean region. Agron. J. 89, 112-118.
63. Siol, M., Prosperi, J.M., Bonnin, I., and, Ronfort, J., (2008) How multilocus genotypic pattern helps to understand the history of selfing populations: a case study in Medicago truncatula. Heredity, 100, 517-525.
64. Stanke, M., and, Waack, S., (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19 (Suppl), ii215-ii225.
65. Summerfield, R.J., Ellis, R.H., and, Roberts, E.H., (1989) Vernalization in chickpea (Cicer arietinum): fact or artefact? Ann. Bot. 64, 599-604.
66. Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M., and, Paterson, A.H., (2008) Unraveling ancient hexaploidity through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944-1954.
67. Taylor, J.S., and, Raes, J., (2004) Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38, 615-643.
68. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
69. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635-641.
70. Thudi, M., Bohra, A., Nayak, S.N., et al,. (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE, 6, e27275.
71. Varshney, R.K., Chen, W., Li, Y., et al,. (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83-89.
72. Varshney, R.K., Song, C., Saxena, R.K., et al,. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240-246.
73. Wilf, P., and, Johnson, K.R., (2004) Land plant extinction at the end of the Cretaceous: a quantitative analysis of the North Dakota megafloral record. Paleobiology, 30, 347-368.
74. Wojciechowski, M.F., Lavin, M., and, Sanderson, M.J., (2004) A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am. J. Bot. 91, 1846-1862.
75. Xu, Z., and, Wang, H., (2007) LTR-FINDER: an efficient tool for the prediction of full- length LTR retrotransposons. Nucleic Acids Res. 35, W265-W268.
76. Yang, Z., (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.
77. Young, N., and, Bharti, A., (2012) Genome-enabled insights into legume biology. Annu. Rev. Plant Biol. 63, 283-305.
78. Young, N.D., Debellé, F., Oldroyd, G.E., et al,. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480, 520-524.
79. Zohary, D., and, Hopf, M., (2000) Pulse. Domestication of plants in the old world. New York: Oxford University Press, pp. 108-111.