De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
详细信息 查看全文
- 作者：Massimo Iorizzo (1)
Douglas A Senalik (1) (2)
Dariusz Grzebelus (3)
Megan Bowman (1)
Pablo F Cavagnaro (4)
Marta Matvienko (6) (7)
Hamid Ashrafi (5)
Allen Van Deynze (5)
Philipp W Simon (1) (2) - 刊名：BMC Genomics
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：12
- 期：1
- 全文大小：307KB
- 参考文献：1. Simon PW, Rubatzky VE, Bassett MJ, Strandberg JO, White JM: B7262, Purple carrot inbred. / HortScience 1997, 32:146-47.
2. Simon PW, Pollak LM, Clevidence BA, Holden JM, Haytowitz DB: Plant breeding for human nutritional quality. / Plant Breed Rev 2009, 31:325-92. CrossRef
3. Vilela NJ: Cenoura: un alimento nobre ne mesa popular. / Horticultura Brasileir 2004, 22:1-.
4. Arscott SA, Tanumihardjo SA: Carrots of many colors provide basic nutrition and bioavailable phytochemicals acting as a functional food. / Comprehensive reviews in Food Science and Food Safety 2010, 9:223-39. CrossRef
5. Bradeen JM, Bach IC, Briard M, le Clerc V, Grzebelus D, Senalik DA, Simon PW: Molecular diversity analysis of cultivated carrot ( Daucus carota L.) and wild Daucus populations reveals a genetically nonstructured composition. / J Amer Soc Hort Sci 2002, 127:383-91.
6. Bradeen JM, Simon PW: Carrot. In / Genome Mapping and Molecular Breeding in Plants. Edited by: Kole C. Berlin: Springer-Verlag; 2007:161-84.
7. Bradeen JM, Simon PW: Conversion of an AFLP fragment linked to the carrot Y2 locus to a simple, codominant, PCR-based marker form. / Theor Appl Genet 1998, 97:960-67. CrossRef
8. Yau YY, Simon PW: A 2.5-kb insert eliminates acid soluble invertase isozyme II transcript in carrot ( Daucus carota L.) roots, causing high sucrose accumulation. / Plant Mol Biol 2003, 53:151-62. CrossRef
9. Boiteux LS, Hyman JR, Bach IC, Fonseca MEN, Matthews WC, Roberts PA, Simon PW: Employment of flanking codominant STS markers to estimate allelic substitution effect in a nematode resistance locus in carrot. / Euphytica 2004, 136:37-4. CrossRef
10. Just BJ, Santos CAF, Fonseca MEN, Boiteux LS, Oloiza BB, Simon PW: Carotenoid biosynthesis structural genes in carrot ( Daucus carota ): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping. / Theor Appl Genet 2007, 114:693-04. CrossRef
11. Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H: Complete plastid genome of Daucus carota : implications for biotechnology and phylogeny of angiosperms. / BMC Genomics 2006, 7:222. CrossRef
12. Cavagnaro PF, Chung SM, Szklarczyk M, Grzebelus D, Senalik D, Atkins AE, Simon PW: Characterization of a deep-coverage carrot ( Daucus carota L.) BAC library and initial analysis of BAC-end sequences. / Mol Genet Genom 2009, 281:273-88. CrossRef
13. Bhasi A, Senalik D, Simon PW, Kumar B, Manikandan V, Philip P, Senapathy P: RoBuST: An integrated resource of genomics information for plants in the root and bulb crop families Apiaceae and Alliaceae. / BMC Plant Biol 2010, 10:161. CrossRef
14. Paszkiewicz K, Studholme DJ: De novo assembly of short sequence reads. / Briefings in bioinformatics 2010, 5:457-72. CrossRef
15. Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y: De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato ( Ipomoea batatas ). / BMC Genomics 2010b, 11:726. CrossRef
16. Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA: De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. / BMC Genomics 2010, 11:681. CrossRef
17. Garg R, Patel RK, Tyagi AK, Jain M: De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. / DNA Research 2011, 1:11.
18. Simon PW, Peterson CE, Gabelman WH: B493 and B9304, carrot inbreds for use in breeding, genetics and tissue culture. / HortScience 1990, 25:815.
19. Simon PW: Domestication, historical development, and modern breeding of carrot. / Plant Breed Rev 2000, 19:157-90.
20. Huang X, Madan A: CAP3: A DNA sequence assembly program. / Genome Res 1999, 9:868-77. CrossRef
21. Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. / Genome Res 2008, 18:821-29. CrossRef
22. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol ?: ABySS: A parallel assembler for short read sequence data. / Genome Res 2009, 19:1117-123. CrossRef
23. Kurilich AC, Clevidence BA, Britz SJ, Simon PW, Novotny JA: Plasma and urine responses are lower for acylated vs. non acylated anthocyanins from raw and cooked purple carrots. / J Agric Food Chem 2005, 53:6537-542. CrossRef
24. Grzebelus D, Yau YY, Simon PW: Master : a novel family of PIF/Harbinger-like transposable elements identified in carrot ( Daucus carota L.). / Mol Genet Genomics 2006, 275:450-59. CrossRef
25. Kohany O, Gentles AJ, Hankus L, Jurka J: Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. / BMC Bioinformatics 2006, 7:474. CrossRef
26. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavel A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH: A unified classification system for eukaryotic transposable elements. / Nature Rev Genet 2007, 8:973-82. CrossRef
27. Grzebelus D, Simon PW: Diversity of DcMaster -like elements of the PIF/Harbinger superfamily in the carrot genome. / Genetica 2009, 135:347-3. CrossRef
28. Itoh Y, Hasebe M, Davies E, Takeda J, Ozeki Y: Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome. / Mol Genet Genomics 2003, 269:49-9.
29. Santos CAF, Simon PW: QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. / Mol Genet Genom 2002, 268:122-29. CrossRef
30. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. / BMC Genomics 2010, 11:180. CrossRef
31. Oliver RE, Lazo GR, Lutz JD, Rubenfield MJ, Tinker NA, Anderson JM, Wisniewski Morehead NH, Adhikary D, Jellen EN, Maughan PJ, Brown Guedira GL, Chao S, Beattie AD, Carson ML, Rines HW, Obert DE, Bonman JM, Jackson EW: Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. / BMC Genomics 2011, 12:77. CrossRef
32. You FM, Huo N, Del KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OA: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. / BMC Genomics 2011, 12:59. CrossRef
33. Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA: De novo sequencing and characterization of floral transcriptome in two species of buckwheat ( Fagopyrum ). / BMC Genomics 2011, 12:30. CrossRef
34. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS: De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. / BMC Genomics 2010, 11:400. CrossRef
35. Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH: OrchidBase: A collection of sequences of transcriptome derived from orchids. / Plant and Cell Physiol 2011, 55:238-43. CrossRef
36. Ozeki Y, Davies E, Takeda J: Plant cell culture variation during long-term subculturing caused by insertion of a transposable element in a phenylalanine ammonia-lyase (PAL) gene. / Mol Gen Genet 1997, 254:407-16. CrossRef
37. Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, Datta S, Singh MN, Bachasab F, Kulwal P, Wanjari KB, Varchney RK, Cook DR, Singh NK: Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea ( Cajanus cajan (L.) Millspaugh). / BMC Plant Biol 2011, 11:17. CrossRef
38. Bureau TE, Wessler SR: Tourist: a large family of inverted-repeat elements frequently associated with maize genes. / Plant Cell 1992, 4:1283-294. CrossRef
39. Bureau TE, Wessler SR: Stowaway: a new family of inverted-repeat elements associated with genes of both monocotyledonous and dicotyledonous plants. / Plant Cell 1994, 6:907-16. CrossRef
40. Bureau TE, Ronald PC, Wessler SR: A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. / Proc Natl Acad Sci USA 1996, 93:8524-529. CrossRef
41. Tang S, Okashah RA, Cordonnier-Pratt MM, Pratt LH, Johnson VE, Taylor CA, Arnold ML, Knapp S: EST and EST-SSR marker resources for Iris. / BMC Plant Biology 2009, 9:72. CrossRef
42. Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y: Development of a EST dataset and characterization of EST-SSRs in a traditional Chenese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. / BMC Genomics 2010, 11:94. CrossRef
43. Ujino-Ihara T, Taguchi Y, Moriguchi Y, Tsumura Y: An efficient method for developing SNP markers based on EST data combined with high resolution melting (HRM) analysis. / BMC Research Notes 2010, 3:51. CrossRef
44. Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS: Development of a set of SNP markers present in expressed genes of the apple. / Genomics 2008, 92:353-58. CrossRef
45. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastros-Corrales M, Cregan PB: High-throughput SNP discovery and assay development in common bean. / BMC Genomics 2010, 11:475. CrossRef
46. Chang S, Pryear J, Cairney J: A simple and efficient method for isolating RNA from pine trees. / Plant Mol Biol Rep 1993, 11:113-16. CrossRef
47. / Illumina: mRNA sequencing sample preparation guide Illumina; 2009:24.
48. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. / Genome Res 1998, 8:175-85.
49. Chou HH, Holmes MH: DNA sequence quality trimming and vector removal. / Bioinformatics 2001, 17:1093-104. CrossRef
50. Rice P, Longden I, Bleasby A: EMBOSS: the European molecular biology open software suite. / Trends Genet 2000, 16:276-77. CrossRef
51. Thiel T, Michalek W, Varshney RK, Graner A: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley ( Hordeum vulgare L.). / Theor Appl Genet 2003, 106:411-22.
52. Hillier LW, Marth GT, Quinlan AR, Dooling D, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylle T, Schedl T, Wilson RK, Mardis ER: Whole genome sequencing and variant discovery in C. elegans . / Nat Methods 2008, 5:183-88. CrossRef
53. Rozen S, Skaletsky H: Primer3 on the www for general users and for biologist programmers. / Methods Mol Biol 2000, 132:365-6.
54. Schuelke M: An economic method for fluorescent labeling of PCR fragments. / Nature Biotechnology 2000, 18:233-34. CrossRef
55. Boss PK, Davies C, Robinson SP: Analysis of the expression of anthocyanin pathway genes in developing Vitis vinifera L. cv Shiraz grape barriers and the implications for pathway regulation. / Plant Physiol 1996,111(4):1059-066.
56. Hummer W, Schreier P: Analysis of proanthocyanidins. / Mol Nutr Food Res 2008,52(12):1382-398. CrossRef - 作者单位：Massimo Iorizzo (1)
Douglas A Senalik (1) (2)
Dariusz Grzebelus (3)
Megan Bowman (1)
Pablo F Cavagnaro (4)
Marta Matvienko (6) (7)
Hamid Ashrafi (5)
Allen Van Deynze (5)
Philipp W Simon (1) (2)
1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
2. USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
3. Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, Al. 29 Listopada 54, 31-425, Krakow, Poland
4. CONICET and INTA EEA La Consulta, CC8 La Consulta, (5567), Mendoza, Argentina
6. Genome Center, University of California, 1 Shields Ave, Davis, CA, USA
7. Life Technologies, 850 Lincoln Center Circle, Foster City, CA, USA
5. Seed Biotechnology Center, University of California, 1 Shields Ave, Davis, CA, USA
文摘
Background Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms. Results A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations. Conclusions This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.