RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Garcia Seco, Daniel ^a   Zhang, Yang ^b   Gutierrez Mañero, Francisco J ^a   Martin, Cathie ^b   Ramos Solano, Beatriz ^a  

^a UNIVERSIDAD SAN PABLO CEU   (Spain)

^b JOHN INNES CENTRE   (United Kingdom)

Author keywords

Alternative splicing; Blackberry; Chimera; De novo; RNA seq; SNP; Transcriptome

Indexed keywords

CHALCONE SYNTHASE; COMPLEMENTARY DNA; PRIMER DNA; RNA; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; BLACKBERRY; CHIMERA; CONSENSUS SEQUENCE; CONTIG MAPPING; CONTROLLED STUDY; DNA SEQUENCE; FRUIT; FRUIT DEVELOPMENT; GENE MAPPING; GENE SEQUENCE; GENETIC CODE; NONHUMAN; PLANT BREEDING; PLANT GENETICS; PROTEIN ANALYSIS; RNA ANALYSIS; RNA SEQUENCE; ROSACEAE; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; RUBUS; SEQUENCE ANALYSIS;

FRAGARIA; FRAGARIA VESCA; ROSACEAE; RUBUS;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; RUBUS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84924073103     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-014-1198-1     Document Type: Article

References (46)

1. Kalkman C. Rosaceae. In: Flowering plants · dicotyledons. Berlin Heidelberg: Springer; 2004. p. 343-86.
2. Martin C, Zhang Y, Tonelli C, Petroni K. Plants, diet, and health. Annu Rev Plant Biol. 2013;64:19-46.
3. Kaume L, Howard LR, Devareddy L. The blackberry fruit: a review on its composition and chemistry, metabolism and bioavailability, and health benefits. J Agric Food Chem. 2012;60(23):5716-27.
4. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, et al. The genome of the domesticated apple (Malus domestica Borkh.). Nat Genet. 2010;42(10):833-9.
5. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet. 2010;43(2):109-16.
6. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45(5):487-94.
7. Pindo M, Montanari S, Cestaro A, Velsaco R. A draft genome sequence of European pear (Pyrus communis L.'Bartlett'). In: 6th Rosaceous Genomics Conference (RGC6), Mezzocorona (TN), 30th September-4th October 2012: 2012. 2012.
8. Genome Database for Rosaceae (GDR). [http://www.rosaceaeorg ].
9. Focke WO. Species ruborum. Stuttgart: Schweizerbart; 1910.
10. Monasterio-Huelin E. Revisión taxonómica del género Rubus L (Rosaceae) en la Península Ibérica e Islas Baleares, Thesis. Madrid, Spain: Universidad Complutense de Madrid; 1992.
11. Alice LA, Campbell CS. Phylogeny of Rubus (rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Am J Bot. 1999;86(1):81-97.
12. Brooks RM. The brooks and olmo register of fruit & nut varieties. Alexandria, VA: Ashs Press; 1997.
13. Kassim A, Poette J, Paterson A, Zait D, McCallum S, Woodhead M, et al. Environmental and seasonal influences on red raspberry anthocyanin antioxidant contents and identification of quantitative traits loci (QTL). Mol Nutr Food Res. 2009;53(5):625-34.
14. Zheng D, Schröder G, Schröder J, Hrazdina G. Molecular and biochemical characterization of three aromatic polyketide synthase genes from Rubus idaeus. Plant Mol Biol. 2001;46(1):1-15.
15. Zheng D, Hrazdina G. Molecular and biochemical characterization of benzalacetone synthase and chalcone synthase genes and their proteins from raspberry (Rubus idaeus L.). Arch Biochem Biophys. 2008;470(2):139-45.
16. Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W. The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theor Appl Genet. 2004;109(4):740-9.
17. Zheng D, Hrazdina G. Cloning and characterization of an expansin gene, RiEXP1, and a 1-aminocyclopropane-1-carboxylic acid synthase gene, RiACS1 in ripening fruit of raspberry (Rubus idaeus L.). Plant Sci. 2010;179(1):133-9.
18. Kumar A, Ellis BE. A family of polyketide synthase genes expressed in ripening Rubus fruits. Phytochemistry. 2003;62(3):513-26.
19. Woodhead M, Weir A, Smith K, McCallum S, MacKenzie K, Graham J. Functional markers for red raspberry. J Am Soc Hortic Sci. 2010;135(5):418-27.
20. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005;23(1):48-55.
21. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, et al. Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol. 2009;60:305-33.
22. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991;252(5013):1651-6.
23. Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Op Plant Biol. 2009;12(2):107-18.
24. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57-63.
25. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 2010;28(5):511-5.
26. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol. 2011;29(7):644-52.
27. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24(5):713-4.
28. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, et al. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003;19(5):651-2.
29. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402.
30. Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. ISMB. 1999;1999:138-47.
31. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35 suppl 1:D61-5.
32. Bairoch A, Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991;19(Suppl):2247.
33. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
34. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4(1):41.
35. Consortium GO. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32 suppl 1:D258-61.
36. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674-6.
37. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34 suppl 2:W293-7.
38. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621-8.
39. Legendre M, Pochet N, Pak T, Verstrepen KJ. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. 2007;17(12):1787-96.
40. Castillo NR, Reed BM, Graham J, Fernández-Fernández F, Bassil NV. Microsatellite markers for raspberry and blackberry. J Am Soc Hortic Sci. 2010;135(3):271-8.
41. Nakasugi K, Crowhurst R, Bally J, Waterhouse P. Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant nicotiana benthamiana. PLoS One. 2014;9(3):e91776.
42. Ramos-Solano B, Garcia-Villaraco A, Gutierrez-Mañero F, Lucas J, Bonilla A, Garcia-Seco D. Annual changes in bioactive contents and production in field-grown blackberry after inoculation with Pseudomonas fluorescens. Plant Physiol Bioch. 2014;74:1-8.
43. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011;12(10):671-82.
44. de Bruijn NG, Erdos P. A combinatorial problem. K Ned Akad Van Wet-P. 1946;49(49):758-64.
45. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35 suppl 2:W71-4.
46. Sokal RR, Rohlf F. Biometry. 2nd ed. New York: WH Feeman and Company; 1981.