Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Luo, Chun ^a,b   Zhang, Qinglin ^a   Luo, Zhengrong ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF TROPICAL BIOSCIENCE AND BIOTECHNOLOGY   (China)

Author keywords

454 sequencing; Persimmon; Transcriptome analysis

Indexed keywords

ALCOHOL; ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; PROANTHOCYANIDIN; PYRUVATE DECARBOXYLASE;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; CHINA; DIOSPYROS; FRUIT; GENE LIBRARY; GENETIC ASSOCIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PLANT GENE; POLLINATION;

ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; CHINA; DIOSPYROS; ETHANOL; FRUIT; GENE LIBRARY; GENES, PLANT; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLLINATION; PROANTHOCYANIDINS; PYRUVATE DECARBOXYLASE;

EID: 84893690635     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-112     Document Type: Article

References (68)

1. Yonemori K, Sugiura A, Yamada M. Persimmon genetics and breeding. Plant Breeding Reviews. Volume 19 2010, Oxford, UK: Wiley & Sons, Inc, John JJ.
2. Akagi T, Katayama-Ikegami A, Yonemori K. Proanthocyanidin biosynthesis of persimmon (Diospyros kaki Thunb.) fruit. Sci Horti 2011, 130:373-380.
3. Ikeda I, Yamada M, Kurihara A. Inheritance of astringency in Japanese persimmon. J Jpn Soc Hortic Sci 1985, 54(1):39-45.
4. Yamada M, Sato A, Yakushiji H, Yoshinaga K, Yamane H, Endo M. Characteristics of "Luo Tian Tian Shi", a non-astringent cultivar of oriental persimmon (Diospyros kaki Thunb.) of Chinese origin in relation to non-astringent cultivars of Japanese origin. Bull Fruit Tree Res Sta 1993, 25:19-32.
5. Ikegami A, Yonemori K, Sugiura A, Sato A, Yamada M. Segregation of astringency in F1 progenies derived from crosses between pollination-constant, nonastringent persimmon cultivars. HortScience 2004, 39:371-374.
6. Ikegami A, Eguchi S, Yonemori K, Yamada M, Sato A, Mitani N, Kitajima A. Segregations of astringent progenies in the F1 populations derived from crosses between a Chinese pollination-constant nonastringent (PCNA) 'Luo Tian Tian Shi' and Japanese PCNA pollination-constant astringent (PCA) cultivars of Japanese origin. HortScience 2006, 41:561-563.
7. Luo Z, Wang R. Persimmon in China: domestication and traditional utilizations of genetic resources. Adv Hortic Sci 2008, 22:239-243.
8. Wang R. The origin of 'Luo Tian Tian Shi'. Chin Fruit Tree 1982, 2:16-19.
9. Porter LJ, Woodruffe J. Haemanalysis: the relative astringency of proanthocyanidin polymers. Phytochemistry 1984, 23:1255-1256.
10. Herrmann KM. The shikimate pathway as an entry to aromatic secondary metabolism. Plant Physiol 1995, 107:7-12. 10.1104/pp.107.1.7, 161158, 7870841.
11. Xie DY, Dixon RA. Proanthocyanidin biosynthesis-still more questions than answers?. Phytochemistry 2005, 66:2127-2144. 10.1016/j.phytochem.2005.01.008, 16153412.
12. Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M. Genetics and biochemistry of seed flavonids. Annu Rev Plant Biol 2006, 57:405-430. 10.1146/annurev.arplant.57.032905.105252, 16669768.
13. Ikegami A, Kitajima A, Yonemori K. Inhibition of flavonoid biosynthetic gene expression coincides with loss of astringency in pollination-constant, non-astringent (PCNA)-type persimmonfruit. J Hortic Sci Biotech 2005, 80:225-228.
14. Ikegami A, Eguchi S, Kitajima A, Inoue K, Yonemori K. Identification of genes involved in proanthocyanidin biosynthesis of persimmon (Diospyros kaki) fruit. Plant Sci 2007, 172:1037-1047.
15. Nakagawa T, Nakatsuka A, Yano K, Yasugahira S, Nakamura R, Sun N, Itai A, Suzuki T, Itamura H. Expressed sequence tags from persimmon at different developmental stages. Plant Cell Rep 2008, 27:931-938. 10.1007/s00299-008-0518-9, 18301901.
16. Akagi T, Ikegami A, Suzuki Y, Yoshida J, Yamada M, Sato A, Yonemori K. Expression balances of structural genes in shikimate and flavonoid biosynthesis cause a difference in proanthocyanidin accumulation in persimmon (Diospyros kaki Thunb.) fruit. Planta 2009, 230:899-915. 10.1007/s00425-009-0991-6, 19669159.
17. Akagi T, Ikegami A, Tsujimoto T, Kobayashi S, Sato A, Kono A, Yonemori K. DkMyb4 is a Myb transcription factor involved in proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol 2009, 151:2028-2045. 10.1104/pp.109.146985, 2785967, 19783643.
18. Akagi T, Ikegami A, Yonemori K. DkMyb2 wound-induced transcription factor of persimmon (Diospyros kaki Thunb.), contributes to proanthocyanidin regulation. Planta 2010, 232:1045-1059. 10.1007/s00425-010-1241-7, 20690029.
19. Akagi T, Tsujimoto T, Ikegami A, Yonemori K. Effects of seasonal temperature changes on DkMyb4 expression involved in proanthocyanidin regulation in two genotypes of persimmon (Diospyros kaki Thunb.) fruit. Planta 2011, 233:883-894. 10.1007/s00425-010-1346-z, 21225280.
20. Akagi T, Katayama-Ikegami A, Kobayashi S, Sato A, Kono A, Yonemori K. Seasonal abscisic acid signal and a basic leucine zipper transcription factor, DkbZIP5, regulate proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol 2012, 158:1089-1102. 10.1104/pp.111.191205, 3271745, 22190340.
21. Wang Y, Zhang Q, Luo Z. Isolation and expression of gene encoding leucoanthocyanidin reductase from Diospyros kaki during fruit development. Biol Plantarum 2010, 54:707-710.
22. Su F, Hu J, Zhang Q, Luo Z. Isolation and characterization of a basic Helix-Loop-Helix transcription factor gene potentially involved in proanthocyanidin biosynthesis regulation in persimmon (Diospyros kaki Thunb.). Sci Horti 2012, 136:115-121.
23. Hu Q, Luo C, Zhang Q, Luo Z. Isolation and characterization of a laccase gene potentially involved in proanthocyanidin polymerization in Oriental persimmon (Diospyros kaki Thunb.) fruit. Mol Biol Rep 2013, 40:2809-2820. 10.1007/s11033-012-2296-2, 23224657.
24. Brautigam A, Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol 2010, 12:831-841. 10.1111/j.1438-8677.2010.00373.x, 21040298.
25. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011, 11:759-769. 10.1111/j.1755-0998.2011.03024.x, 21592312.
26. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-D261. 10.1093/nar/gkh036, 308770, 14681407.
27. Tatusov RL. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
28. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280. 10.1093/nar/gkh063, 308797, 14681412.
29. Audic SCJ. The significance of digital gene expression profiles. Genome Res 1997, 7:986-995.
30. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
31. Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 2009, 9:51. 10.1186/1471-2229-9-51, 2688492, 19426529.
32. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 2009, 10:347. 10.1186/1471-2164-10-347, 2907694, 19646272.
33. Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z, Zhang Q, Liang X, Li Y. De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2012, 13:90. 10.1186/1471-2164-13-90, 3350410, 22409576.
34. Xie F, Burklew CE, Yang Y, Liu M, Xiao P, Zhang B, Qiu D. De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta 2012, 236:101-113. 10.1007/s00425-012-1591-4, 22270559.
35. Wheat CW. Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 2010, 138:433-451. 10.1007/s10709-008-9326-y, 18931921.
36. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
37. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
38. Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 2011, 12:99. 10.1186/1471-2164-12-99, 3042945, 21303537.
39. Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF, Yang CH. Characterization of Oncidium 'Gower Ramsey' transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol 2011, 52:1532-1545. 10.1093/pcp/pcr101, 21785129.
40. 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. 10.1186/1471-2164-11-180, 2851599, 20233449.
41. Bai XD, Rivera-Vega L, Mamidala P, Bonello P, Herms DA, Mittapalli O. Transcriptomic signatures of ash (Fraxinus spp.) phloem. PLoS ONE 2011, 6:e16368. 10.1371/journal.pone.0016368, 3025028, 21283712.
42. Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW. Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 2012, 13:104. 10.1186/1471-2164-13-104, 3352077, 22433453.
43. Edwards CE, Parchman TL, Weekley CW. Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. DNA Res 2012, 19:1-9. 10.1093/dnares/dsr037, 3276261, 22039173.
44. Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009, 10:399. 10.1186/1471-2164-10-399, 2748093, 19709400.
45. Liu G, Li W, Zheng P, Xu T, Chen L, Liu D, Hussain S, Teng Y. Transcriptomic analysis of 'Suli' pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq. BMC Genomics 2012, 13:700. 10.1186/1471-2164-13-700, 3562153, 23234335.
46. Peng Y, Abercrombie LL, Yuan JS, Riggins CW, Sammons RD, Tranel PJ, Stewart CN. Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes. Pest Manag Science 2010, 66:1053-1062.
47. Sui C, Zhang J, Wei J, Chen S, Li Y, Xu J, Jin Y, Xie C, Gao Z, Chen H, Yang C, Zhang Z, Xu Y. Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins. BMC Genomics 2011, 12:539. 10.1186/1471-2164-12-539, 3219613, 22047182.
48. Zhang XM, Zhao L, Larson-Rabin Z, Li DZ, Guo ZH. De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae). PLoS ONE 2012, 7:e42082. 10.1371/journal.pone.0042082, 3419236, 22916120.
49. Kaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 2011, 12:265. 10.1186/1471-2164-12-265, 3113791, 21609489.
50. Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EM, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262. 10.1186/1471-2164-11-262, 2873478, 20416102.
51. 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. 10.1186/1471-2164-12-30, 3027159, 21232141.
52. Wu Q, Sun C, Luo H, Li Y, Niu Y, Sun Y, Lu A, Chen S. Transcriptome analysis of Taxus cuspidata needles based on 454 pyrosequencing. Planta Med 2011, 77:394-400. 10.1055/s-0030-1250331, 20862637.
53. Lu FH, Yoon MY, Cho YI, Chung JW, Kim KT, Cho MC, Cheong SR, Park YJ. Transcriptome analysis and SNP/SSR marker information of red pepper variety YCM334 and Taean. Sci Horti 2011, 129:38-45.
54. Liu M, Qiao G, Jiang J, Yang H, Xie L, Xie J, Zhuo R. Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PLoS ONE 2012, 7:e46766. 10.1371/journal.pone.0046766, 3463524, 23056442.
55. Ness RW, Siol M, Barrett SC. De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genomics 2011, 12:298. 10.1186/1471-2164-12-298, 3128866, 21649902.
56. Sugiura A, Harada H, Tomana T. Studies on the removability of astringency in Japanese persimmon fruits, 1. J Jpn Soc Hortic Sci 1975, 44:265-272.
57. Tanaka T, Takahashi R, Kouno I, Nonaka G. Chemical evidence for the de-astringency (insolubilization of tannins) of persimmon fruit. J Chem Soc, Perkin Trans 1 1994, 20:3013-3022.
58. Strommer J. The plant ADH gene family. Plant J 2011, 66:128-142. 10.1111/j.1365-313X.2010.04458.x, 21443628.
59. Min T, Yin X, Shi YN, Luo ZR, Yao YC, Grierson D, Ferguson IB, Chen KS. Ethylene-responsive transcription factors interact with promoters of ADH and PDC involved in persimmon (Diospyros kaki) fruit de-astringency. J Exp Bot 2012, 63:6393-6405. 10.1093/jxb/ers296, 3504493, 23095993.
60. Oshida M, Yonemori K, Sugiura A. On the nature of coagulated tannins in astringent-type persimmon fruit after an artificial treatment of astringency removal. Postharvest Biol Tec 1996, 8:317-327.
61. Eaks I. Ripening and astringency removal in persimmon fruits. Proc Amer Soc Hort Sci 1967, 91:868-875.
62. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14:1147-1159. 10.1101/gr.1917404, 419793, 15140833.
63. Tatusov RL, Galperin M, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2008, 28:33-36.
64. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003, 31:315-318. 10.1093/nar/gkg046, 165493, 12520011.
65. Zdobnov EM, Apweiler R. InterProScan an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
66. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
67. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34:W293-W297. 10.1093/nar/gkl031, 1538768, 16845012.
68. Romualdi C, Bortoluzzi S, D'Alessi F, Danieli GA. IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 2003, 12:159-162.