De Novo Assembly, Gene Annotation and Marker Development Using Illumina Paired-End Transcriptome Sequences in Celery (Apium graveolens L.)

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Fu, Nan ^a   Wang, Qian ^a   Shen, Huo Lin ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MOLECULAR MARKER; TRANSCRIPTOME; GENETIC MARKER; MICROSATELLITE DNA;

ARTICLE; CELERY; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DNA POLYMORPHISM; EARLY FLOWERING 7 GENE; EARLY FLOWERING 8 GENE; FLOWERING TIME CONTROL GENE; GENE AMPLIFICATION; GENE FREQUENCY; GENE IDENTIFICATION; GENE MAPPING; GIBBERELLIN 1 OXIDASE 1 GENE; GIBBERELLIN 2 OXIDASE 2 GENE; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PETIOLE; PHOTOPERIOD INDEPENDENT EARLY FLOWERING GENE; PLANT GENE; PLANT ROOT; PLANT STEM; POLYMORPHIC LOCUS; PROTEIN DATABASE; RECEPTOR LIKE KINASE IN FLOWERS GENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMPLE SEQUENCE REPEAT; TERMINAL FLOWERING 2 GENE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC MARKER; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; PLANT STRUCTURES; PROCEDURES;

APIUM GRAVEOLENS; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENES, PLANT; GENETIC MARKERS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; PLANT STRUCTURES; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84874578930     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057686     Document Type: Article

References (77)

1. Muminovic J, Melchinger AE, Lubberstedt T, (2004) Prospects for celeriac (Apium graveolens var. rapaceum) improvement by using genetic resources of Apium, as determined by AFLP markers and morphological characterization. Plant Genetic Resources 2: 189-198.
2. Sampson S (2006) Chinese celery has robust taste. Toronto Star (Canada) ISSN:0319-0781.
3. Song XJ, Wang YT (2008) Research Progress in the Medicinal Function of Celery. Journal of Anhui Agricultural Sciences 36: 6360-6361, 6395.
4. TANG F, GUO J, ZHANG J, LI J, SU M, (2007) Study on Hypotensive and Vasodilatory Effects of Celery Juice. Food Science 28: 322-325.
5. Arus P, Ortan T, (1984) Inheritance patterns and linkage relationships of eight genes of celery. Journal of Heredity 75: 11-14.
6. Quiros CF, Douches D, D'Antonio V, (1987) Inheritance of annual habit in celery: cosegregation with isozyme and anthocyanin markers. TAG Theoretical and Applied Genetics 74: 203-208.
7. Huestis G, McGrath JM, Quiros CF, (1993) Development of genetic markers in celery based on restriction fragment length polymorphisms. TAG Theoretical and Applied Genetics 85: 889-896.
8. Yang X, Quiros C, (1993) Identification and classification of celery cultivars with RAPD markers. TAG Theoretical and Applied Genetics 86: 205-212.
9. Domblides A, Domblides H, Kharchenko V, (2008) Discrimination between celery cultivars with the use of RAPD markers. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences 62: 219-222.
10. Li G, Quiros CF, (2000) Use of amplified fragment length polymorphism markers for celery cultivar identification. HortScience 35: 726-728.
11. Ju J, (2007) An Analysis of Celery Genetic Diversity by AFLP. Chinese Agricultural Science Bulletin 23: 120-123.
12. Acquadro A, Magurno F, Portis E, Lanteri S, (2006) dbEST-derived microsatellite markers in celery (Apium graveolens L. var. dulce). Molecular Ecology Notes 6: 1080-1082.
13. Wang S, Yang W, Shen H, (2011) Genetic diversity in Apium graveolens and related species revealed by SRAP and SSR markers. Scientia Horticulturae 129: 1-8.
14. Andersen JR, Lubberstedt T, (2003) Functional markers in plants. Trends in plant science 8: 554-560.
15. Morozova O, Marra MA, (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264.
16. Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, et al. (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11: 384.
17. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular ecology 17: 1636-1647.
18. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA, (2012) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11: 180.
19. Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, et al. (2010) Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Proteomics 10: 2972-2981.
20. Shahin A, van Gurp T, Peters SA, Visser RGF, van Tuyl JM, et al. (2012) SNP markers retrieval for a non-model species: a practical approach. BMC Research Notes 5: 79.
21. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, 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.
22. Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA, (2010) De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 11: 681.
23. Crawford JE, Guelbeogo WM, Sanou A, Traore A, Vernick KD, et al. (2010) De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS one 5: e14202.
24. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29: 644-652.
25. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25: 3389-3402.
26. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic acids research 31: 315-318.
27. Zdobnov EM, Apweiler R, (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
28. Thiel T, Michalek W, Varshney RK, Graner A, (2003) Exploiting EST database for the development and characterization of gen-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
29. Kabelka E, Franchino B, Francis D, (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis. Phytopathology 92: 504-510.
30. Weir BS (1990) Genetic data analysis. Methods for discrete population genetic data. Sunderland, Massachusetts: Sinauer Associates, Inc. Publishers. 377 p.
31. Yeh FC, Yang R, Boyle T (1999) PopGene Version 1.31: Microsoft Window-based freeware for population genetic analysis. Available from http://www.ualberta.ca/~fyeh. University of Alberta and Center for International Forestry Research, Edmonton, Alberta, Canada.
32. Rohlf F J (2000). NTSYS-pc.Numerical Taxonomy and Multivariate Analysis System,Version 2.1. New York: Exeter Software.
33. Iorizzo M, Senalik DA, Grzebelus D, Bowman M, Cavagnaro PF, et al. (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12: 389.
34. Townsend G, Emerson R, Newhall A, (1946) Resistance to Cercospora-apii in celery. Phytopathology 36: 980-982.
35. Wang S, Shen H, Wu X, (2010) Studies on inheritance and phenotype of the yellow mutant of celery. Acta Agriculturae Boreali-Sinica 25: 119-122.
36. Yanmei G, Xingfang G, Chunzhen Z, Xiujuan F, Shengping Z, et al. (2003) Genetic mechanism of the cucumber leaf mutant. Acta Horticulturae Sinica 30: 409-412.
37. Xingfang G, Shengping Z, Xiurong C, (2005) Inheritance and linkage relationships among the genes of leaf mutant and bitterness with other five major genes in cucumber. Acta Horticulturae Sinica 32: 108-110.
38. Miao H, GU X, ZHANG S, WANG X, FANG Z, et al. (2010) Changes of the Photosynthetic Pigment and Differential Expression of the Correlated Genes in a Chlorophyll-Deficient Cucumber Mutant (Cucumis sativus L.). Scientia Agricultura Sinica 43: 4027-4035.
39. MA Z, WANG H, WEI W, YAN Y, (2011) Change of Photosynthetic Pigments and Enzyme Activities of Hot Pepper (Capsicum annuum) CMS Line Leaves with Yellow-green Marker. China Cucurbits and Vegetables 24: 20-24.
40. Nothnagel T, Straka P, (2003) Inheritance and mapping of a yellow leaf mutant of carrot (Daucus carota). Plant breeding 122: 339-342.
41. Shen H, Cheng J, Han Q, (2006) Studies on Inheritance and Phenotype of the Yellow Mutant of Carrot. Acta Horticulturae Sinica 33: 856-858.
42. Mouradov A, Cremer F, Coupland G, (2002) Control of flowering time interacting pathways as a basis for diversity. The Plant Cell Online 14: S111-S130.
43. Takahashi T, Mu JH, Gasch A, Chua NH, (1998) Identification by PCR of receptor-like protein kinases from Arabidopsis flowers. Plant molecular biology 37: 587-596.
44. Poupin MJ, Federici F, Medina C, Matus JT, Timmermann T, et al. (2007) Isolation of the three grape sub-lineages of B-class MADS-box TM6, PISTILLATA and APETALA3 genes which are differentially expressed during flower and fruit development. Gene 404: 10-24.
45. Latrasse D, Germann S, Houba-Herin N, Dubois E, Bui-Prodhomme D, et al. (2011) Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1. PloS one 6: e16592.
46. Noh YS, Amasino RM, (2003) PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. The Plant Cell Online 15: 1671-1682.
47. Mutasa-Gottgens ES, Qi A, Zhang W, Schulze-Buxloh G, Jennings A, et al. (2010) Bolting and flowering control in sugar beet: Relationships and effects of gibberellin, the bolting gene B and vernalization. AoB Plants 10.1093/aobpla/plq012.
48. Mutasa-Gottgens E, Qi A, Mathews A, Thomas S, Phillips A, et al. (2009) Modification of gibberellin signalling (metabolism & signal transduction) in sugar beet: analysis of potential targets for crop improvement. Transgenic research 18: 301-308.
49. Hirano K, Ueguchi-Tanaka M, Matsuoka M, (2008) GID1-mediated gibberellin signaling in plants. Trends in plant science 13: 192-199.
50. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, et al. (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. TAG Theoretical and Applied Genetics 114: 359-372.
51. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, et al. (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847-854.
52. Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, et al. (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC plant biology 11: 17.
53. Parra-Gonzalez LB, Aravena-Abarzua GA, Navarro-Navarro CS, Udall JA, Maugham PJ, et al. (2012) Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC genomics 13: 425.
54. Lesser MR, Parchman TL, Buerkle C, (2012) Cross-species transferability of SSR loci developed from transciptome sequencing in lodgepole pine. Molecular Ecology Resources 12: 448-455.
55. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
56. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
57. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
58. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis. Cell 133: 523-536.
59. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research 18: 821-829.
60. Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome research 17: 1697-1706.
61. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome research 18: 810-820.
62. Martin JA, Wang Z, (2011) Next-generation transcriptome assembly. Nature Reviews Genetics 12: 671-682.
63. Zhang J, Liang S, Duan J, Wang J, Chen S, et al. (2012) De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.). BMC Genomics 13: 90.
64. Wang Z, Fang B, Chen J, Zhang X, Luo Z, et al. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11: 726.
65. Wei W, Qi X, Wang L, Zhang Y, Hua W, et al. (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12: 451.
66. Chang L, Chen J, Xiao Y, Xia Y, (2011) De novo characterization of Lycoris sprengeri transcriptome using Illumina GA II. African Journal of Biotechnology 10: 12147-12155.
67. Zhou X, Fei Z, Thannhauser TW, Li L, (2011) Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis). BMC Plant Biology 11: 169.
68. Li D, Deng Z, Qin B, Liu X, 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.
69. Hao DC, Ma P, Mu J, Chen SL, Xiao PG, et al. (2012) De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Science China. Life sciences 55: 452-466.
70. He M, Wang Y, Hua W, Zhang Y, Wang Z, (2012) De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites. PloS one 7: e42081.
71. Huang L, Yang X, Sun P, Tong W, Hu S, (2012) The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers. PloS one 7: e38653.
72. Edwards CE, Parchman TL, Weekley CW, (2012) Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. DNA research 19: 1-9.
73. Li Y, Sun C, Luo H, Li X, Niu Y, et al. (2010) Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX. Acta pharmaceutica Sinica 45: 524-529.
74. Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, et al. (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12: 104.
75. Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, et al. (2011) Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA research 18: 471-482.
76. Lu FH, Cho MC, Park YJ, (2012) Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Molecular biology reports 39: 3327-3335.
77. 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.