Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Li, Xiaobai ^a   Luo, Jie ^a   Yan, Tianlian ^b   Xiang, Lin ^a   Jin, Feng ^c   Qin, Dehui ^a   Sun, Chongbo ^a   Xie, Ming ^a  

^a INSTITUTE OF PLANT PROTECTION AND MICROBIOLOGY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c HUBEI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; FLOWER; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; ORCHIDACEAE; PLANT GENE; SINGLE NUCLEOTIDE POLYMORPHISM;

FLOWERS; GENE EXPRESSION PROFILING; GENES, PLANT; GENETIC MARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; ORCHIDACEAE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84893633147     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085480     Document Type: Article

References (97)

1. Leitch IJ, Kahandawala I, Suda J, Hanson L, Ingrouille MJ et al. (2009) Genome size diversity in orchids: consequences and evolution. Ann Bot 104: 469-481. doi:10.1093/aob/mcp003. PubMed: 19168860.
2. Fukai S, Hasegawa A, Goi M (2002) Polysomaty in Cymbidium. Hortscience 37: 1088-1091. (Pubitemid 36087426)
3. Liu ZJ, Chen SC, Ru ZZ, Chen LJ, editors (2006) Chinese Cymbidium plants. Beijing: Science Press.
4. Du Puy D, Cribb P, Tibbs M, Royal Botanic Gardens K (2007) The Genus Cymbidium: Kew Pub.
5. Nash (1996) Flavar of the month, Cymbidium ensifolium. Orchids 9: 972-974.
6. Coen ES, Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353: 31-37. doi:10.1038/353031a0. PubMed: 1715520. (Pubitemid 21912446)
7. Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: an armchair guide. Nat Rev Genet 6: 688-698. doi:10.1038/nrg1675. PubMed: 16151374. (Pubitemid 41192320)
8. Aceto S, Gaudio L (2011) The mads and the beauty: genes involved in the development of orchid flowers. Curr Genomics 12: 342-356. doi:10.2174/ 138920211796429754. PubMed: 22294877.
9. Glover BJ (2007) Understanding flowers and flowering: an integrated approach. Oxford University Press Oxford.
10. Komeda Y (2004) Genetic regulation of time to flower in Arabidopsis thaliana. Annu Rev Plant Biol 55: 521-535. doi:10.1146/annurev.arplant.55. 031903.141644. PubMed: 15377230.
11. Xiang L, Li B, Qin D, Guo F, Wu C et al. (2011) Cloning and Real-time Expression Analysis of GLO Gene from Cymbidium goeringii. Acta Agriculturae Zhejiang ensis 23: 517-522.
12. Xiang I, D Q, Li X, Li B, Guo F, et al. (2011) Cloning and expression analysis of b class mads-box genes from Cymbidium faberi. Acta Horticulturae Sinica 38: 143-147.
13. Wang SY, Lee PF, Lee YI, Hsiao YY, Chen YY et al. (2011) Duplicated C-Class MADS-Box genes reveal distinct roles in gynostemium development in Cymbidium ensifolium (Orchidaceae). Plant Cell Physiol 52: 563-577. doi:10.1093/pcp/pcr015. PubMed: 21278368.
14. Hsu CC, Chung YL, Chen TC, Lee YL, Kuo YT et al. (2011) An overview of the Phalaenopsis orchid genome through BAC end sequence analysis. BMC Plant Biol 11: 3. doi:10.1186/1471-2229-11-3. PubMed: 21208460.
15. Hsiao YY, Tsai WC, Kuoh CS, Huang TH, Wang HC et al. (2006) Comparison of transcripts in Phalaenopsis bellina and Phalaenopsis equestris (Orchidaceae) flowers to deduce the monoterpene biosynthesis pathway. BMC Plant Biol 6: 14. doi:10.1186/1471-2229-6-14. PubMed: 16836766.
16. Tsai W, Hsiao Y, Lee S, Tung C, Wang D et al. (2006) Expression analysis of the ESTs derived from the flower buds of Phalaenopsis equestris. Plant Sci 170: 426-432. doi:10.1016/j.plantsci.2005.08.029. (Pubitemid 43116935)
17. Tan J, Wang HL, Yeh KW (2005) Analysis of organ-specific, expressed genes in Oncidium orchid by subtractive expressed sequence tags library. Biotechnol Lett 27: 1517-1528. doi:10.1007/s10529-005-1468-8. PubMed: 16231226. (Pubitemid 41464552)
18. Teh SL, Chan WS, Abdullah JO, Namasivayam P (2011) Development of expressed sequence tag resources for Vanda Mimi Palmer and data mining for EST-SSR. Mol Biol Rep 38: 3903-3909. doi:10.1007/s11033-010-0506-3. PubMed: 21116862.
19. Hsiao YY, Chen YW, Huang SC, Pan ZJ, Fu CH et al. (2011) Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids. BMC Genomics 12: 360. doi: 10.1186/1471-2164-12-360. PubMed: 21749684.
20. Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF et al. (2011) 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 52: 1532-1545. doi:10.1093/pcp/pcr101. PubMed: 21785129.
21. Sedeek KE, Qi W, Schauer MA, Gupta AK, Poveda L et al. (2013) Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PLOS ONE 8: e64621. doi:10.1371/journal.pone. 0064621. PubMed: 23734209.
22. Górniak M, Paun O, Chase MW (2010) Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results. Mol Phylogenet Evol 56: 784-795. doi:10.1016/j.ympev.2010.03.003. PubMed: 20211743.
23. Bouck A, Vision T (2007) The molecular ecologist's guide to expressed sequence tags. Mol Ecol 16: 907-924. PubMed: 17305850.
24. Emrich SJ, Barbazuk WB, Li L, Schnable PS (2006) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 16: 1-5. PubMed: 16344566.
25. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17: 1636-1647. doi:10.1111/j.1365-294X.2008.03666.x. PubMed: 18266620. (Pubitemid 351441703)
26. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918. doi: 10.1111/j.1365-313X. 2007.03193.x. PubMed: 17662031. (Pubitemid 47301664)
27. Novaes E, Drost DR, Farmerie WG, Pappas JG, Grattapaglia D et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 312. doi:10.1186/1471-2164-9-312. PubMed: 18590545.
28. Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol 17: 3599-3613. PubMed: 18662225.
29. Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot 99: 257-266. doi:10.3732/ajb.1100292. PubMed: 22268224.
30. Liu L, Li Y, Li S, Hu N, He Y et al. (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 11: 251-364. PubMed: 22829749.
31. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159. doi:10.1101/gr.1917404. PubMed: 15140833. (Pubitemid 38811551)
32. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. doi:10.1101/gr.074492. 107. PubMed: 18349386. (Pubitemid 351645072)
33. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092. doi:10.1093/bioinformatics/ bts094. PubMed: 22368243.
34. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics 25: 2872-2877. doi:10.1093/bioinformatics/btp367. PubMed: 19528083.
35. Robertson G, Schein J, Chiu R, Corbett R, Field M et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7: 909-912. doi:10.1038/nmeth.1517. PubMed: 20935650.
36. Li R, Yu C, Li Y, Lam TW, Yiu SM et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967. doi:10.1093/bioinformatics/btp336. PubMed: 19497933.
37. 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. Nat Biotechnol 29: 644-652. doi:10.1038/nbt.1883. PubMed: 21572440.
38. 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
39. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. doi:10.1093/ bioinformatics/bti610. PubMed: 16081474. (Pubitemid 41264107)
40. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res 40: 109-114. doi:10.1093/nar/gkr988.
41. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30. doi:10.1093/nar/28.7.e27. PubMed: 10592173.
42. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM et al. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5: R7. doi:10.1186/gb-2004-5-3-p7. PubMed: 14759257.
43. Tsai WC, Fu CH, Hsiao YY, Huang YM, Chen LJ, et al. (2013) OrchidBase 2.0: comprehensive collection of Orchidaceae floral transcriptomes. Plant Cell Physiol 54: e7.
44. Faircloth BC (2008) msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 8: 92-94. doi:10.1111/j.1471-8286.2007.01884.x. PubMed: 21585724.
45. Rozen S, Skaletsky HJ (2000) Primer3 on the www for general users and for biologist programmers. In: S KrawetzS MisenerNJ Totowa. In Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press.
46. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/ bioinformatics/btp324. PubMed: 19451168.
47. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352. PubMed: 19505943.
48. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 11: 41. PubMed: 12969510.
49. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-D484. PubMed: 18077471. (Pubitemid 351149770)
50. Mondragón-Palomino M, Theissen G (2008) MADS about the evolution of orchid flowers. Trends Plant Sci 13: 51-59. doi:10.1016/j.tplants. 2007.11.007. PubMed: 18262819.
51. Mondragon-Palomino M, Theissen G (2009) Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes. Ann Bot (Lond) 104: 583- 594. doi:10.1093/aob/mcn258.
52. Mondragon-Palomino M, Theissen G (2011) Conserved differential expression of paralogous DEFICIENS- and GLOBOSA-like MADS-box genes in the flowers of Orchidaceae: refining the 'orchid code'. Plant J 66: 1008-1019. doi:10.1111/j.1365-313X.2011.04560.x. PubMed: 21435045.
53. Kim DH, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 25: 277-299. doi:10.1146/annurev.cellbio.042308.113411. PubMed: 19575660.
54. Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by thePHDfinger protein VIN3. Nature 427: 159-164. doi:10.1038/ nature02195. PubMed: 14712276. (Pubitemid 38094956)
55. Xiang L, Li X, Qin D, Guo F, Wu C et al. (2012) Functional analysis of FLOWERING LOCUS T orthologs from spring orchid (Cymbidium goeringii Rchb. f.) that regulates the vegetative to reproductive transition. Plant Physiol Biochem 58: 98-105. doi:10.1016/j.plaphy.2012.06.011. PubMed: 22796899.
56. Chen MK, Hsu WH, Lee PF, Thiruvengadam M, Chen HI et al. (2011) The MADS box gene, FOREVER YOUNG FLOWER, acts as a repressor controlling floral organ senescence and abscission in Arabidopsis. Plant J 68: 168-185. doi:10.1111/j.1365-313X.2011.04677.x. PubMed: 21689171.
57. Simon R, Igeño MI, Coupland G (1996) Activation of floral meristem identity genes in Arabidopsis. Nature 384: 59-62. doi:10.1038/384059a0. PubMed: 8900276. (Pubitemid 26374585)
58. Wu M, Fan S, Song M, Pang C, Shu X (2010) Cloning and Expression Analysis of GhCO Gene in Gossypium hirsutum L. Journal of Cotton Sci 22: 387-392.
59. Mouradov A, Cremer F, Coupland G (2002) Control of flowering time: Interacting pathways as a basis for diversity. Plant Cell 14: S111-S130. PubMed: 12045273. (Pubitemid 34609234)
60. Metzger JDeDThe Netherlands: Kluwer Academic Publishers), pp. 617-648 (1995) Hormones and reproductive development. In: PJ Davies. In Plant Hormones. Dordrecht, The Netherlands: Kluwer Academic Publishers. pp. Dordrecht, The Netherlands: Kluwer Academic Publishers.
61. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111: 206-217 (Pubitemid 41033753)
62. Itoh H, Ueguchi-Tanaka M, Kawaide H, Chen X, Kamiya Y et al. (1999) The gene encoding tobacco gibberellin 3β-hydroxylase is expressed at the site of GA action during stem elongation and flower organ development. Plant J 20: 15-24. doi:10.1046/j.1365-313X. 1999.00568.x. PubMed: 10571861.
63. Itoh H, Ueguchi-Tanaka M, Sentoku N, Kitano H, Matsuoka M et al. (2001) Cloning and functional analysis of two gibberellin 3 beta - hydroxylase genes that are differently expressed during the growth of rice. Proc Natl Acad Sci U S A 98: 8909-8914. doi:10.1073/pnas.141239398. PubMed: 11438692. (Pubitemid 32678126)
64. Martin C, Bhatt K, Baumann K, Jin H, Zachgo S et al. (2002) The mechanics of cell fate determination in petals. Philos Trans R Soc Lond B Biol Sci 357: 809-813. doi:10.1098/rstb.2002.1089. PubMed: 12079676. (Pubitemid 34735688)
65. Peng J (2009) Gibberellin and jasmonate crosstalk during stamen development. J Integr Plant Biol 51: 1064-1070. doi:10.1111/j.1744-7909.2009. 00881.x. PubMed: 20021553.
66. Gocal GF, Sheldon CC, Gubler F, Moritz T, Bagnall DJ et al. (2001) GAMYB-like genes, flowering, and gibberellin signaling in Arabidopsis. Plant Physiol 127: 1682-1693. doi:10.1104/pp.010442. PubMed: 11743113. (Pubitemid 34050036)
67. Cheng H, Song S, Xiao L, Soo HM, Cheng Z et al. (2009) Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis. PLoS Genet 5: e1000440. PubMed: 19325888.
68. Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V et al. (2011) Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 18: 305-320. doi:10.1093/dnares/dsr017. PubMed: 21768136.
69. Bao S, Corke H, Sun M (2002) Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theor Appl Genet 105: 898-905 (Pubitemid 36080319)
70. Dresselhaus T, Cordts S, Heuer S, Sauter M, Lörz H et al. (1999) Novel ribosomal genes from maize are differentially expressed in the zygotic and somatic cell cycles. Mol Gen Genet 261: 416-427. doi:10.1007/s004380050983. PubMed: 10102378. (Pubitemid 29140057)
71. Gao LF, Jing RL, Huo NX, Li Y, Li XP et al. (2004) One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108: 1392-1400. doi:10.1007/s00122-003-1554-z. PubMed: 14968301. (Pubitemid 38630183)
72. Li S, Jia J, Wei X, Zhang X, Li L et al. (2007) A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breeding 20: 167-178. doi:10.1007/s11032-007-9080-3. (Pubitemid 47099815)
73. Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura N et al. (2012) A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics 13: 136. doi:10.1186/1471-2164-13-136. PubMed: 22507374.
74. Zhang H, Wei L, Miao H, Zhang T, Wang C (2012) Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics 13: 316. doi:10.1186/1471-2164-13-316. PubMed: 22800194.
75. 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. doi:10.1186/1471-2164-12-451. PubMed: 21929789.
76. 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
77. Zeng S, Xiao G, Guo J, Fei Z, Xu Y et al. (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11: 94. doi:10.1186/1471-2164-11-94. PubMed: 20141623.
78. Luro FL, Costantino G, Terol J, Argout X, Allario T et al. (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9: 287. doi: 10.1186/1471-2164-9-287. PubMed: 18558001.
79. Chen C, Zhou P, Choi YA, Huang S, Gmitter JFG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112: 1248- 1257. doi:10.1007/s00122-006-0226-1. PubMed: 16474971.
80. Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K et al. (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108: 414-422. doi:10.1007/s00122-003-1450-6. PubMed: 13679975. (Pubitemid 38300119)
81. 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. doi:10.1186/1471-2164-6-23. PubMed: 15720707.
82. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55. doi:10.1016/j.tibtech.2004.11.005. PubMed: 15629858. (Pubitemid 40075526)
83. 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 Res 18: 471-482. doi:10.1093/dnares/dsr034. PubMed: 22086998.
84. Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breeding 23: 85-97. doi:10.1007/s11032- 008-9216-0.
85. An ZW, Zhao YH, Cheng H, Li WG, Huang HS (2009) Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg Hereditas 31: 311-319.
86. Gur-Arie R, Cohen CJ, Eitan Y, Shelef L, Hallerman EM et al. (2000) Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res 10: 62-71. PubMed: 10645951. (Pubitemid 30095256)
87. Li X, Cui H, Zhang M (2006) Molecular markers derived from EST: Their development and applications in comparative genomics. Biodiversity Sci 14: 541-547. doi:10.1360/biodiv.060148.
88. Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F et al. (2001) Structural and functional features of eukaryotic mRNA untranslated regions. Gene 276: 73-81. doi:10.1016/S0378-1119(01)00674-6. PubMed: 11591473. (Pubitemid 32925261)
89. Fan S, Guo A, Shan L, Hu X (2003) Analysis of genetic code preference in Arabidopsis thaliana. Prog Biochem Biophys 30: 221-225. (Pubitemid 36793608)
90. Sook J, Abbott A, Jesudurai C (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae EST. Funct Integr Genomics 5: 136-143. doi:10.1007/s10142-005-0139-0. (Pubitemid 40823255)
91. Cloutier S, Niu Z, Datla R, Duguid S (2009) Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119: 53-63
92. Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC et al. (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92: 353-358. doi:10.1016/j.ygeno.2008.07.008. PubMed: 18721872.
93. Bus VGM, Rikkerink EHA, van de Weg WE, Rusholme RL, Gardiner SE et al. (2005) The Vh2 and Vh4 scab resistance genes in two differential hosts derived from Russian apple R12740-7A map to the same linkage group of apple. Mol Breeding 15: 103-116. doi:10.1007/ s11032-004-3609-5.
94. Costa F, Stella S, Van de Weg WE, Guerra W, Cecchinel M et al. (2005) Role of the genes Md-ACO1 and Md-ACS1 in ethylene production and shelf life of apple (Malus domestica Borkh). Euphytica 141: 181-190. doi:10.1007/s10681-005- 6805-4. (Pubitemid 40564419)
95. Gao ZS, van de Weg WE, Schaart JG, Schouten HJ, Tran DH et al. (2005) Genomic cloning and linkage mapping of the Mal d 1 (PR-10) gene family in apple (Malus domestica). Theor Appl Genet 111: 171-183. doi:10.1007/s00122-005-2018-4. PubMed: 15883791. (Pubitemid 40912340)
96. Li F, Kitashiba H, Inaba K, Nishio T (2009) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 16: 311-323. doi:10.1093/dnares/dsp020. PubMed: 19884167.
97. Blanca J, Esteras C, Ziarsolo P, Perez D, Ndez-Pedrosa Ferna V, et Blanca J, Esteras C, Ziarsolo P, Pérez D, Ndez-Pedrosa Fernã V, Collado C, Rodrã Guez de Pablos R, Ballester A, Roig C, Cañizares J, Picó Bal (2012) Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics 13: 280 doi:10.1186/1471-2164-13-280. PubMed: 22726804. doi:10.1186/1471-2164-13-280. PubMed: 22726804.