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The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

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The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

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dc.contributor.author Herraiz García, Francisco Javier es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Ziarsolo Areitioaurtena, Pello es_ES
dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Plazas Ávila, María de la O es_ES
dc.contributor.author Anderson, Gregory Joseph es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.date.accessioned 2018-01-02T09:36:51Z
dc.date.available 2018-01-02T09:36:51Z
dc.date.issued 2016 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/93706
dc.description.abstract [EN] Background Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. Results Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. Conclusions This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny. es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Solanum muricatum es_ES
dc.subject Transcriptome es_ES
dc.subject S. caripense es_ES
dc.subject Pepino es_ES
dc.subject Potato es_ES
dc.subject Tomato es_ES
dc.subject Solanaceae es_ES
dc.subject Functional annotation es_ES
dc.subject Phylogeny es_ES
dc.subject Candidate genes es_ES
dc.subject Molecular markers es_ES
dc.subject.classification GENETICA es_ES
dc.title The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-016-2656-8 es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana es_ES
dc.description.bibliographicCitation Herraiz García, FJ.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Gramazio, P.; Plazas Ávila, MDLO.; Anderson, GJ.; Prohens Tomás, J.... (2016). The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. BMC Genomics. 17(321). doi:10.1186/s12864-016-2656-8 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12864-016-2656-8 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 17 es_ES
dc.description.issue 321 es_ES
dc.identifier.pmid 27142449 en_EN
dc.identifier.pmcid PMC4855764 en_EN
dc.relation.pasarela 311931 es_ES
dc.relation.references Anderson GJ, Jansen RK, Kim Y. The origin and relationships of the pepino, Solanum muricatum (Solanaceae): DNA restriction fragment evidence. Econ Bot. 1996;50:369–80. es_ES
dc.relation.references Anderson GJ, Martine CT, Prohens J, Nuez F. Solanum perlongistylum and S. catilliflorum, new endemic Peruvian species of Solanum, Section Basarthrum, are close relatives of the domesticated pepino, S. muricatum. Novon. 2006;16:161–7. es_ES
dc.relation.references Rodríguez-Burruezo A, Prohens J, Fita AM. Breeding strategies for improving the performance and fruit quality of the pepino (Solanum muricatum): A model for the enhancement of underutilized exotic fruits. Food Res Int. 2011;44:1927–35. es_ES
dc.relation.references Yalçin H. Effect of ripening period on composition of pepino (Solanum muricatum) fruit grown in Turkey. Afr J Biotechnol. 2010;9:3901–3. es_ES
dc.relation.references Abouelnasr H, Li Y-Y, Zhang Z-Y, Liu J-Y, Li S-F, Li D-W, Yu J-L, McBeath JH, Han C-G. First Report of Potato Virus H on Solanum muricatum in China. Plant Dis. 2014;98:1016. es_ES
dc.relation.references Spooner DM, Anderson GJ, Jansen RK. Chloroplast DNA evidence for the interrelationships of tomatoes, potatoes, and pepinos (Solanaceae). Am J Bot. 1993;80:676–88. es_ES
dc.relation.references Sarkinen T, Bohs L, Olmstead RG, Knapp S. A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evol Biol. 2013;13:214. es_ES
dc.relation.references Nakitandwe J, Trognitz FCH, Trognitz BR. Genetic mapping of Solanum caripense, a wild relative of pepino dulce, tomato and potato, and a genetic resource for resistance to potato late blight. In: VI International Solanaceae Conference: Genomics Meets Biodiversity 745. 2006. p. 333–42. es_ES
dc.relation.references Sakomoto K, Taguchi T. Regeneration of intergeneric somatic hybrid plants between Lycopersicon esculentum and Solanum muricatum. Theor Appl Genet. 1991;81:509–13. es_ES
dc.relation.references Bernardello LM, Anderson GJ. Karyotypic studies in Solanum section Basarthrum (Solanaceae). Am J Bot. 1990;77:420–31. es_ES
dc.relation.references Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Report. 2004;9:208–18. es_ES
dc.relation.references Spooner DM, Rodríguez F, Polgár Z, Ballard HE, Jansky SH. Genomic origins of potato polyploids: GBSSI gene sequencing data. Crop Sci. 2008;48(Supplement to crop science):27–36. es_ES
dc.relation.references Herraiz FJ, Vilanova S, Andújar I, Torrent D, Plazas M, Gramazio P, Prohens J. Morphological and molecular characterization of local varieties, modern cultivars and wild relatives of an emerging vegetable crop, the pepino (Solanum muricatum), provides insight into its diversity, relationships and breeding history. Euphytica. 2015;206:301–18. es_ES
dc.relation.references Trognitz FC, Trognitz BR. Survey of resistance gene analogs in Solanum caripense, a relative of potato and tomato, and update on R gene genealogy. Mol Genet Genomics. 2005;274:595–605. es_ES
dc.relation.references Hajjar R, Hodgkin T. The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica. 2007;156:1–13. es_ES
dc.relation.references Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006;127:1309–21. es_ES
dc.relation.references Blanca JM, Prohens J, Anderson GJ, Zuriaga E, Canizares J, Nuez F. AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication. Am J Bot. 2007;94:1219–29. es_ES
dc.relation.references Rodríguez-Burruezo A, Prohens J, Nuez F. Wild relatives can contribute to the improvement of fruit quality in pepino (Solanum muricatum). Euphytica. 2003;129:311–8. es_ES
dc.relation.references Herraiz FJ, Villaño D, Plazas M, Vilanova S, Ferreres F, Prohens J, Moreno DA. Phenolic profile and biological activities of the pepino (Solanum muricatum) fruit and its wild relative S. caripense. Int J Mol Sci. 2016;17:394. es_ES
dc.relation.references Leiva-Brondo M, Prohens J, Nuez F. Characterization of pepino accessions and hybrids resistant to Tomato mosaic virus (ToMV). J Food Agric Env. 2006;4:138. es_ES
dc.relation.references Nakitandwe J, Trognitz F, Trognitz B. Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping. Plant Methods. 2007;3:2. es_ES
dc.relation.references Andrivon D. The origin of Phytophthora infestans populations present in Europe in the 1840s: a critical review of historical and scientific evidence. Plant Pathol. 1996;45:1027–35. es_ES
dc.relation.references Prohens J, Ruiz JJ, Nuez F. The pepino (Solanum muricatum, Solanaceae): A “new” crop with a history. Econ Bot. 1996;50:355–68. es_ES
dc.relation.references Heiser CB. Origin and Variability of the Pepino (Solanum Muricatum). In: Preliminary Report. 1964. es_ES
dc.relation.references Ahmad H, Khan A, Muhammad K, Nadeem MS, Ahmad W, Iqbal S, Nosheen A, Akbar N, Ahmad I, Que Y. Morphogenetic study of pepino and other members of solanaceae family. Am J Plant Sci. 2014;5:3761. es_ES
dc.relation.references Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512. es_ES
dc.relation.references Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52. es_ES
dc.relation.references Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63. es_ES
dc.relation.references McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, de Pamphilis CW, Leebens-Mack J. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). Am J Bot. 2012;99:397–406. es_ES
dc.relation.references Barker MS, Vogel H, Schranz ME. Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biol Evol. 2009;1:391–9. es_ES
dc.relation.references Rensink W, Lee Y, Liu J, Iobst S, Ouyang S, Buell CR. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics. 2005;6:124. es_ES
dc.relation.references Koenig D, Jimenez-Gomez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat A V, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A. 2013;110:E2655–62. es_ES
dc.relation.references Blanca JM, Cañizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, Garcia-Mas J, Picó MB. Melon transcriptome characterization: Simple sequence repeats and single nucleotide polymorphisms discovery for high throughput genotyping across the species. Plant Genome. 2011;4:118–31. es_ES
dc.relation.references Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, Pico B. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 2011;12:104. es_ES
dc.relation.references Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JF. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics. 2013;14:137. es_ES
dc.relation.references Consortium TG. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635–41. es_ES
dc.relation.references Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189–95. es_ES
dc.relation.references Anderson GJ, Jansen RK. Biosystematic and molecular systematic studies of Solanum section Basarthrum and the origin and relationships of the pepino (S. muricatum). In: Proceedings of the VI Congreso Latinoamericano de botanica: Mar del Plata, Argentina. 1994. p. 2–8. es_ES
dc.relation.references Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402. es_ES
dc.relation.references Swiss Prot [ http://web.expasy.org/docs/swiss-prot_guideline.html ]. Accessed 29 Apr 2016. es_ES
dc.relation.references SGN release versionITAG2.4 [ ftp://ftp.sgn.cornell.edu/tomato_genome/annotation/ ]. Accessed 29 Apr 2016. es_ES
dc.relation.references Uniref [ http://www.ebi.ac.uk/uniprot/database/download.html ]. Accessed 29 Apr 2016. es_ES
dc.relation.references Wei D-D, Chen E-H, Ding T-B, Chen S-C, Dou W, Wang J-J. De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences. PLoS One. 2013;8:e80046. es_ES
dc.relation.references Li D, Deng Z, Qin B, Liu X, Men Z. 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. 2012;13:192. es_ES
dc.relation.references Lulin H, Xiao Y, Pei S, Wen T, Shangqin H. The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One. 2012;7:e38653. es_ES
dc.relation.references Mitraki A, Barge A, Chroboczek J, Andrieu JP, Gagnon J, Ruigrok RWH. Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB). Eur J Biochem. 1999;264:610–50. es_ES
dc.relation.references Sierro N, Battey JN, Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch MC, Ivanov N V. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol. 2013;14:R60. es_ES
dc.relation.references Garzon-Martinez GA, Zhu ZI, Landsman D, Barrero LS, Marino-Ramirez L. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. BMC Genomics. 2012;13:151. es_ES
dc.relation.references Wang L, Li J, Zhao J, He C. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae. Front Plant Sci. 2015;6:248. es_ES
dc.relation.references Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999;99:138–48. es_ES
dc.relation.references Peralta IE, Spooner DM. Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon). Am J Bot. 2001;88:1888–902. es_ES
dc.relation.references Martins TR, Barkman TJ, Smith JF. Reconstruction of Solanaceae phylogeny using the nuclear gene SAMT. Syst Bot. 2005;30:435–47. es_ES
dc.relation.references Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30:2725–9. es_ES
dc.relation.references Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics. 2008;180:391–408. es_ES
dc.relation.references Garrison E. FreeBayes. In: Marth Lab. 2010. es_ES
dc.relation.references Collins DW, Jukes TH. Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics. 1994;20:386–96. es_ES
dc.relation.references 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 (Ipomoea batatas L.) transcriptome. Planta. 2012;236:101–13. es_ES
dc.relation.references Mooers AØ, Holmes EC. The evolution of base composition and phylogenetic inference. Trends Ecol Evol. 2000;15:365–9. es_ES
dc.relation.references Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, et al. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics. 2010;11:210. es_ES
dc.relation.references Crookshanks M, Emmersen J, Welinder KG, Nielsen KL. The potato tuber transcriptome: analysis of 6077 expressed sequence tags. FEBS Lett. 2001;506:123–6. es_ES
dc.relation.references Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30. es_ES
dc.relation.references Lester RN. Evolutionary relationships of tomato, potato, pepino, and wild species of Lycopersicon and Solanum. In: Hawkes JG, Lester RN, Nee M, Estrad N, editors. Solanaceae III Taxonomy, Chem Evol Kew Linn Soc London. 1991. p. 283–301. es_ES
dc.relation.references Butelli E, Titta L, Giorgio M, Mock H-P, Matros A, Peterek S, Schijlen EGWM, Hall RD, Bovy AG, Luo J, Martin C. Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nat Biotech. 2008;26:1301–8. es_ES
dc.relation.references Clé C, Hill LM, Niggeweg R, Martin CR, Guisez Y, Prinsen E, Jansen MAK. Modulation of chlorogenic acid biosynthesis in Solanum lycopersicum; consequences for phenolic accumulation and UV-tolerance. Phytochemistry. 2008;69:2149–56. es_ES
dc.relation.references Niggeweg R, Michael AJ, Martin C. Engineering plants with increased levels of the antioxidant chlorogenic acid. Nat Biotechnol. 2004;22:746–54. es_ES
dc.relation.references Prohens J, Sánchez MC, Rodríguez-Burruezo A, Cámara M, Torija E, Nuez F. Morphological and physico-chemical characteristics of fruits of pepino (Solanum muricatum), wild relatives (S. caripense and S. tabanoense) and interspecific hybrids. Implications in pepino breeding. Eur J Hortic Sci. 2005;70:224. es_ES
dc.relation.references Blanca J, Montero-Pau J, Sauvage C, Bauchet G, Illa E, D’iez MJ, Francis D, Causse M, van der Knaap E, Cañizares J. Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics. 2015;16:1–19. es_ES
dc.relation.references Rong J, Lammers Y, Strasburg JL, Schidlo NS, Ariyurek Y, de Jong TJ, Klinkhamer PGL, Smulders MJM, Vrieling K. New insights into domestication of carrot from root transcriptome analyses. BMC Genomics. 2014;15:895. es_ES
dc.relation.references Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci. 2012;109(29):11878–83. es_ES
dc.relation.references Feng Z, Zhang B, Ding W, Liu X, Yang D-L, Wei P, Cao F, Zhu S, Zhang F, Mao Y. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 2013;23:1229–32. es_ES
dc.relation.references Park T, Vleeshouwers V, Jacobsen E, Van Der Vossen E, Visser RGF. Molecular breeding for resistance to Phytophthora infestans (Mont.) de Bary in potato (Solanum tuberosum L.): a perspective of cisgenesis. Plant Breed. 2009;128:109–17. es_ES
dc.relation.references Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006;22:2971–2. es_ES
dc.relation.references Zhai L, Xu L, Wang Y, Cheng H, Chen Y, Gong Y, Liu L. Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Mol Breed. 2014;33:611–24. es_ES
dc.relation.references Ahn Y-K, Tripathi S, Kim J-H, Cho Y-I, Lee H-E, Kim D-S, Woo J-G, Yoon M-K. Microsatellite marker information from high-throughput next-generation sequence data of Capsicum annuum varieties Mandarin and Blackcluster. Sci Hortic. 2014;170:123–30. es_ES
dc.relation.references Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 2000;10:72–80. es_ES
dc.relation.references Li Y, Korol AB, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol. 2002;11:2453–65. es_ES
dc.relation.references Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005;23:48–55. es_ES
dc.relation.references Anderson GJ. The variation and evolution of selected species of Solanum section Basarthrum. Brittonia. 1975;27:209–22. es_ES
dc.relation.references Murray BG, Hammett KRW, Grigg FDW. Seed set and breeding system in the pepino Solanum muricatum Ait., Solanaceae. Sci Hortic (Amsterdam). 1992;49:83–92. es_ES
dc.relation.references Perez-de-Castro AM, Vilanova S, Canizares J, Pascual L, Blanca JM, Diez MJ, Prohens J, Pico B. Application of genomic tools in plant breeding. Curr Genomics. 2012;13:179–95. es_ES
dc.relation.references Ruiz JJ, Prohens J, Nuez F. “Sweet Round” and “Sweet Long”: Two pepino cultivars for Mediterranean, climates. HortSci. 1997;32:751–2. es_ES
dc.relation.references FASTAQC [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]. Accessed 29 Apr 2016. es_ES
dc.relation.references Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. es_ES
dc.relation.references Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323. es_ES
dc.relation.references Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 2011;12:1–8. es_ES
dc.relation.references Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832. es_ES
dc.relation.references Lippman ZB, Cohen O, Alvarez JP, Abu-Abied M, Pekker I, Paran I, Eshed Y, Zamir D. The making of a compound inflorescence in tomato and related nightshades. PLoS Biol. 2008;6:e288. es_ES
dc.relation.references Zhang Y, Hu Z, Chu G, Huang C, Tian S, Zhao Z, Chen G. Anthocyanin accumulation and molecular analysis of anthocyanin biosynthesis-associated genes in eggplant (Solanum melongena L.). J Agric Food Chem. 2014;62:2906–12. es_ES
dc.relation.references Kohara A, Nakajima C, Hashimoto K, Ikenaga T, Tanaka H, Shoyama Y, Yoshida S, Muranaka T. A novel glucosyltransferase involved in steroid saponin biosynthesis in Solanum aculeatissimum. Plant Mol Biol. 2005;57:225–39. es_ES
dc.relation.references Gramazio P, Prohens J, Plazas M, Andujar I, Herraiz FJ, Castillo E, Knapp S, Meyer RS, Vilanova S. Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biol. 2014;14:350–014–0350–z. es_ES
dc.relation.references Klann E, Yelle S, Bennett AB. Tomato fruit Acid invertase complementary DNA: nucleotide and deduced amino Acid sequences. Plant Physiol. 1992;99:351–3. es_ES
dc.relation.references Lam Cheng KL. Golden2--like (GLK2) Transcription Factor: Developmental Control of Tomato Fruit Photosynthesis and Its Contribution to Ripe Fruit Characteristics. Davis: University of California; 2013. es_ES
dc.relation.references Mott R. EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci. 1997;13:477–8. es_ES
dc.relation.references EMBOSS [ http://www.bioinformatics.nl/emboss-explorer/ ]. Accessed 29 Apr 2016. es_ES
dc.relation.references Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45. es_ES
dc.relation.references Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–8. es_ES
dc.relation.references Abajian C. Sputnik. University of Washington Department of Molecular Biotechnology. 1994.[ http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota ]. Accessed 29 Apr 2016. es_ES


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