Coverage-based consensus calling (CBCC) of short sequence reads and comparison of CBCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome

American Journal of Botany

Volumn 99, Issue 2, 2012, Pages 186-192

  Azam, Sarwar ^a   Thakur, Vivek ^a,b   Ruperao, Pradeep ^a,c   Shah, Trushar ^a   Balaji, Jayashree ^a   Amindala, Bhanu Prakash ^a   Farmer, Andrew D ^d   Studholme, David J ^e,f   May, Gregory D ^d   Edwards, David ^c   Jones, Jonathan D G ^e   Varshney, Rajeev K ^a,g  

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

^b INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^e SAINSBURY LABORATORY   (United Kingdom)

^f UNIVERSITY OF EXETER   (United Kingdom)

^g Theme Comparative and Applied Genomics   (Mexico)

Author keywords

Chickpea; Cicer arietinum; Fabaceae; Legumes; Molecular breeding; Next generation sequencing; SNP discovery

Indexed keywords

PLANT DNA; TRANSCRIPTOME;

ADVANCED TECHNOLOGY; GENOME; GENOTYPE; LEGUME; MODEL VALIDATION; POLYMORPHISM; PROBABILITY; REPRODUCTIVE STRATEGY;

ARTICLE; BIOLOGY; CHROMOSOME MAP; CICER; COMPARATIVE STUDY; CONSENSUS SEQUENCE; CROP; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT GENOME; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

BASE SEQUENCE; CHROMOSOME MAPPING; CICER; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; CROPS, AGRICULTURAL; DNA, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

CICER ARIETINUM; FABACEAE;

EID: 84863393432     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1100419     Document Type: Article

References (60)

1. AHN, S. M., T. H. KIM, S. LEE, D. KIM, H. GHANG, D. KIM, B. C. KIM, ET AL. 2009. The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Research 19: 1622-1629.
2. BARBAZUK, W. B., S. J. EMRICH, H. D. CHEN, L. LI, and P. S. SCHNABLE. 2007. SNP discovery via 454 transcriptome sequencing. Plant Journal 51: 910-918.
3. BARKER, G., J. BATLEY, H. O'sullivan, K. J. Edwards, and D. Edwards. 2003. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19: 421-422.
4. BATZOGLOU, S. 2005. The many faces of sequence alignment. Briefings in Bioinformatics 6: 6-22.
5. BENTLEY, D. R. 2006. Whole-genome re-sequencing. Current Opinion in Genetics & Development 16: 545-552.
6. COSTA, V., C. ANGELINI, I. DEFEIS, and A. CICCODICOLA. 2010. Uncovering the complexity of transcriptomes with RNA-Seq. Journal of Biomedicine & Biotechnology 2010: article ID 853916, 1-19.
7. DESCHAMPS, S., M. L. ROTA, J. P. RATASHAK, and P. BIDDLE. 2010. Rapid genome-wide single nucleotide polymorphism discovery in soybean and rice via deep resequencingof reduced representation libraries with the Illumina genome analyzer. Plant Genome 3: 53-68.
8. DUBEY, A., A. FARMER, J. SCHLUETER, S. B. CANNON, B. ABERNATHY, R. TUTEJA, J. WOODWARD, et al. 2011. De fining the transcriptome assembly and its use for genome dynamics and transcriptome pro filing studies in pigeonpea (Cajanus cajan L.). DNA Research 18: 153-164.
9. DURAN, C., N. APPLEBY, T. CLARK, D. WOOD, M. IMELFORT, J. BATLEY, and D. EDWARDS. 2009c. AutoSNPdb: An annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Research 37 (supplement 1): D951-D953.
10. DURAN, C., N. APPLEBY, D. EDWARDS, and J. BATLEY. 2009a. Molecular genetic markers: Discovery, applications, data storage and visualisation. Current Bioinformatics 4: 16-27.
11. DURAN, C., N. APPLEBY, M. VARDY, M. IMELFORT, D. EDWARDS, and J. BATLEY. 2009b. Single nucleotide polymorphism discovery in barley using AutoSNPdb. Plant Biotechnology Journal 7: 326-333.
12. DURAN, C., D. EALES, D. MARSHALL, M. IMELFORT, J. STILLER, P. J. BERKMAN, T. CLARK, et al. 2010. Future tools for association mapping in crop plants. Genome 53: 1017-1023.
13. EDWARDS, D., and J. BATLEY. 2010. Plant genome sequencing: Applications for crop improvement. Plant Biotechnology Journal 8: 2-9.
14. FLICEK, P., and E. BIRNEY. 2009. Sense from sequence reads: Methods for alignment and assembly. Nature Methods 6: S6-S12.
15. GARG, R., R. K. PATEL, A. K. TYAGI, and M. JAIN. 2011. De novo a ssembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Research 18: 53-63.
16. GUJARIA, N., A. KUMAR, P. DAUTHAL, A. DUBEY, P. HIREMATH, A. BHANUPRAKASH, A. FARMER, et al. 2011. Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 122: 1577-1589.
17. HERCUS, C. 2009. Novocraft short read alignment package. Website http://www.novocraft.com/.
18. HILLIER, L. W., G. T. MARTH, A. R. QUINLAN, D. DOOLING, G. FEWELL, D. BARNETT, P. FOX, et al. 2008. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 5: 183-188.
19. HIREMATH, P. J., A. FARMER, S. B. CANNON, J. WOODWARD, H. KUDAPA, R. TUTEJA, A. KUMAR, et al. 2011. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal 9: 922-931.
20. HUDSON, M. 2008. Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8: 3-17.
21. HYTEN, D. L., S. B. CANNON, Q. SONG, and N. WEEKS. 2010a. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.
22. HYTEN, D. L., Q. SONG, E. W. FICKUS, and C. V. QUIGLEY. 2010b. Highthroughput SNP discovery and assay development in common bean. BMC Genomics 11: 475.
23. IMELFORT, M., C. DURAN, J. BATLEY, and D. EDWARDS. 2009. Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnology Journal 7: 312-317.
24. IMELFORT, M., and D. EDWARDS. 2009. De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics 10: 609-618.
25. JAYASHREE, B., A. BHANUPRAKASH, A. JAMI, P. S. REDDY, S. NAYAK, and R. K. VARSHNEY. 2009. Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features. BMC Research Notes 2: 92.
26. LANGMEAD, B., C. TRAPNELL, M. POP, and S. L. SALZBERG. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
27. LI, B., V. RUOTTI, R. STEWART, J. THOMSON, and C. DEWEY. 2010. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
28. LI, H., and H. DURBIN. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
29. LI, H., and N. HOMER. 2010. A survey of sequence alignment algorithms for next generation sequencing. Briefings in Bioinformatics 11: 473-483.
30. LI, H., J. RUAN, and R. DURBIN. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
31. LI, R., C. YU, Y. LI, T. W. LAM, S. M. YIU, K. KRISTIANSEN, and J. WANG. 2009. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
32. LU, T., G. LU, D. FAN, C. ZHU, W. LI, Q. ZHAO, Q. FENG, et al. 2010. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Research 20: 1238-1249.
33. MACLEAN, D., J. D. G. JONES, and D. J. STUDHOLME. 2009. Application of 'next-generation' sequencing technologies to microbial genetics. Nature Reviews Microbiology 7: 287-296.
34. MARDIS, E. R. 2008. The impact of next-generation sequencing technology on genetics. Trends in Genetics 24: 133-141.
35. MARIONI, J., C. E. MASON, S. M. MANE, M. STEPHENS, and Y. GILADI. 2008. RNA-Seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18: 1509-1517.
36. MARSHALL, D. J., A. HAYWARD, D. EALES, M. IMELFORT, J. STILLER, P. J. BERKMAN, T. CLARK, et al. 2010. Targeted identification of genomic regions using TAGdb. Plant Methods 6: 19.
37. MARTH, G. T., I. KORF, M. D. YANDELL, R. T. YEH, Z. GU, H. ZAKERI, N. O. STITZIEL, et al. 1999. A general approach to single-nucleotide polymorphism discovery. Nature Genetics 23: 452-456.
38. METZKER, M. L. 2010. Sequencing technologies - The next generation. Nature Reviews Genetics 11: 31-46.
39. MILLER, N. A., S. F. KINGSMORE, and A. D. FARMER. 2008. Management of high-throughput DNA sequencing projects: Alpheus. Journal of Computer Science & Systems Biology 1: 132.
40. MORIN, R., M. BAINBRIDGE, A. FEJES, M. HIRST, M. KRZYWINSKI, T. PUGH, H. MCDONALD, et al. 2008. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 45: 81-94.
41. MORTAZAVI, A., B. A. WILLIAMS, K. MCCUE, L. SCHAEFFER, and B. WOLD. 2008. Mapping and quantifying mammalian transcriptomes by RNASeq. Nature Methods 5: 621-628.
42. NAYAK, S. N., H. ZHU, N. VARGHESE, S. DATTA, H. K. CHOI, R. HORRES, R. JÜNGLING, et al. 2010. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics 120: 1415-1441.
43. NOVAES, E., D. R. DROST, W. G. FARMERIE, G. J. JR. PAPPAS, D. GRATTAPAGLIA, R. R. SEDEROFF, and M. KIRST. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 312.
44. PARCHMAN, T. L., K. S. GEIST, J. A. GRAHNEN, C. W. BENKMAN, and C. A. BUERKLE. 2010. Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. BMC Genomics 11: 180.
45. PASANIUC, B., N. ZAITLEN, and E. HALPERIN. 2010. Accurate estimation of expression levels of homologous genes in RNA-seq experiments. In Proceedings of 14th Annual International Conference on Research in Computational Biology (RECOMB 2010), Lisbon, Portugal, 397-407. International Computer Science Institute, Berkeley, California, USA.
46. ROZEN, S., and H. SKALETSKY. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132: 365-386.
47. SMITH, A. D., Z. XUAN, and M. Q. ZHANG. 2008. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9: 128.
48. SOUCHE, E. L., B. HELLEMANS, H. J. K. J. VAN, and A. CANARIO. 2007. Mining for single nucleotide polymorphisms in expressed sequence tags of European sea bass. Journal of Integrative Bioinformatics 4: 73.
49. STEPHENS, M., J. S. SLOAN, P. D. ROBERTSON, P. SCHEET, and D. A. NICKERSON. 2006. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nature Genetics 38: 375-381.
50. SULTAN, M., M. H. SCHULZ, H. RICHARD, A. MAGEN, A. KLINGENHOFF, M. SCHERF, M. SEIFERT, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
51. TRICK, M., Y. LONG, J. MENG, and I. BANCROFT. 2009. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology Journal 7: 334-346.
52. UPADHYAYA, H. D., M. THUDI, N. DRONAVALLI, N. GUJARIA, S. SINGH, S. SHARMA, and R. K. V ARSHNEY. 2011. Genomic tools and germplasm diversity for chickpea improvement. Plant Genetic Resources 9: 45-58.
53. VARSHNEY, R. K., W. CHEN, Y. LI, A. K. BHARTI, R. K. SAXENA, J. A. SCHLUETER, M. A. DONOGHUE, et al. 2011. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30: 83-89.
54. VARSHNEY, R. K., S. N. NAYAK, G. D. MAY, and S. A. JACKSON. 2009. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27: 522-530.
55. WANG, J., W. WANG, R. LI, Y. LI, G. TIAN, L. GOODMAN, W. FAN, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456: 60-65.
56. WANG, Z., M. GERSTEIN, and M. SNYDER. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics 10: 57-63.
57. WHEELER, D. A., M. SRINIVASAN, M. E GHOLM, Y. SHEN, L. C HEN, A. MCGUIRE, W. HE, et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
58. XU, G., N. DENG, Z. ZHAO, T. JUDEH, E. FLEMINGTON, and D. ZHU. 2011. SAMMate: A GUI tool for processing short read alignments in SAM/BAM format. Source Code for Biology and Medicine 6: 2.
59. YU, X. 2011. How well do alignment programs perform on sequencing data with varying qualities and obtained from repeat regions? In Meeting of Sequencing Data Interest Group (SDIG), Cleveland, Ohio, USA; available as pdf at website http://cancer.case.edu/workinggroups/SDIG/index.html;cancer.case.edu/workinggroups/SDIG/2011/yu2-28-11.pdf.
60. ZHANG, J., D. A. WHEELER, I. Y AKUB, S. WEI, R. SOOD, W. ROWE, P. P. L IU, et al. 2005. SNPdetector: A software tool for sensitive and accurate SNP detection. PLoS Computational Biology 1: e53.