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 |
S\311931 |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
Bernardello LM, Anderson GJ. Karyotypic studies in Solanum section Basarthrum (Solanaceae). Am J Bot. 1990;77:420–31. |
es_ES |
dc.description.references |
Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Report. 2004;9:208–18. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.references |
Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006;127:1309–21. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
Heiser CB. Origin and Variability of the Pepino (Solanum Muricatum). In: Preliminary Report. 1964. |
es_ES |
dc.description.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.description.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.description.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.description.references |
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
Consortium TG. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635–41. |
es_ES |
dc.description.references |
Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189–95. |
es_ES |
dc.description.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.description.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.description.references |
Swiss Prot [ http://web.expasy.org/docs/swiss-prot_guideline.html ]. Accessed 29 Apr 2016. |
es_ES |
dc.description.references |
SGN release versionITAG2.4 [ ftp://ftp.sgn.cornell.edu/tomato_genome/annotation/ ]. Accessed 29 Apr 2016. |
es_ES |
dc.description.references |
Uniref [ http://www.ebi.ac.uk/uniprot/database/download.html ]. Accessed 29 Apr 2016. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
Garrison E. FreeBayes. In: Marth Lab. 2010. |
es_ES |
dc.description.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.description.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.description.references |
Mooers AØ, Holmes EC. The evolution of base composition and phylogenetic inference. Trends Ecol Evol. 2000;15:365–9. |
es_ES |
dc.description.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.description.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.description.references |
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005;23:48–55. |
es_ES |
dc.description.references |
Anderson GJ. The variation and evolution of selected species of Solanum section Basarthrum. Brittonia. 1975;27:209–22. |
es_ES |
dc.description.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.description.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.description.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.description.references |
FASTAQC [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]. Accessed 29 Apr 2016. |
es_ES |
dc.description.references |
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. |
es_ES |
dc.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.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.description.references |
EMBOSS [ http://www.bioinformatics.nl/emboss-explorer/ ]. Accessed 29 Apr 2016. |
es_ES |
dc.description.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.description.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.description.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 |