- -

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

Mostrar el registro completo del ítem

Gramazio, P.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Herraiz García, FJ.; Plazas Ávila, MDLO.; Prohens Tomás, J.; Vilanova Navarro, S. (2016). Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics. 17(300). https://doi.org/10.1186/s12864-016-2631-4

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/93708

Ficheros en el ítem

Metadatos del ítem

Título: Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding
Autor: Gramazio, Pietro Blanca Postigo, José Miguel Ziarsolo Areitioaurtena, Pello Herraiz García, Francisco Javier Plazas Ávila, María de la O Prohens Tomás, Jaime Vilanova Navarro, Santiago
Entidad UPV: Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana
Fecha difusión:
Resumen:
[EN] Background: Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. ...[+]
Palabras clave: Solanum incanum , S. aethiopicum , Eggplant genepool , De novo transcriptome , Gene annotation , Molecular marker discovery
Derechos de uso: Reconocimiento (by)
Fuente:
BMC Genomics. (issn: 1471-2164 )
DOI: 10.1186/s12864-016-2631-4
Editorial:
Springer (Biomed Central Ltd.)
Versión del editor: https://doi.org/10.1186/s12864-016-2631-4
Código del Proyecto:
info:eu-repo/grantAgreement/MINECO//AGL2015-64755-R/ES/MEJORA GENETICA DE LA CALIDAD FUNCIONAL Y APARENTE DE LA BERENJENA/
Agradecimientos:
This work has been partially funded by Spanish Ministerio de Economia y Competitividad and FEDER (grant AGL2015-64755-450 R).
Tipo: Artículo

References

The FAOSTAT Database. [ http://faostat.fao.org/ ]. Accessed 20 September 2015.

Collonnier C, Fock I, Kashyap V, Rotino G, Daunay M, Lian Y, et al. Applications of biotechnology in eggplant. Plant Cell Tiss Org. 2001;65(2):91–107.

Plazas M, Andújar I, Vilanova S, Gramazio P, Herraiz FJ, Prohens J. Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes. Front Plant Sci. 2014. doi: 10.3389/fpls.2014.00318 . [+]
The FAOSTAT Database. [ http://faostat.fao.org/ ]. Accessed 20 September 2015.

Collonnier C, Fock I, Kashyap V, Rotino G, Daunay M, Lian Y, et al. Applications of biotechnology in eggplant. Plant Cell Tiss Org. 2001;65(2):91–107.

Plazas M, Andújar I, Vilanova S, Gramazio P, Herraiz FJ, Prohens J. Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes. Front Plant Sci. 2014. doi: 10.3389/fpls.2014.00318 .

Rotino GL, Sala T, Toppino L. Eggplant. In: Pratap A, Kumar J, editors. Alien Gene Transfer in Crop Plants, vol. 2. New York: Springer; 2014. p. 381–409.

Meyer RS, Karol KG, Little DP, Nee MH, Litt A. Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Mol Phylogenet Evol. 2012;63(3):685–701.

Schippers RR. African indigenous vegetables: an overview of the cultivated species. Wallingford: UK: CAB International; 2000.

Maundu P, Achigan-Dako E, Morimoto Y. Biodiversity of African vegetables. In: Shackleton CM, Pasquini MW, Drescher AW, editors. African indigenous vegetables in urban agriculture. UK: MapSet Ltd; 2009. p. 65–104.

Vorontsova M, Stern S, Bohs L, Knapp S. African spiny Solanum (subgenus Leptostemonum, Solanaceae): a thorny phylogenetic tangle. Bot J Linn Soc. 2013;173(2):176–93.

Rizza F, Mennella G, Collonnier C, Sihachakr D, Kashyap V, Rajam M, et al. Androgenic dihaploids from somatic hybrids between Solanum melongena and S. aethiopicum group gilo as a source of resistance to Fusarium oxysporum f. sp. melongenae. Plant Cell Rep. 2002;20(11):1022–32.

Mennella G, Rotino GL, Fibiani M, D’Alessandro A, Francese G, Toppino L, et al. Characterization of health-related compounds in eggplant (Solanum melongena L.) lines derived from introgression of allied species. J Agric Food Chem. 2010;58(13):7597–603.

Prohens J, Plazas M, Raigón MD, Seguí-Simarro JM, Stommel JR, Vilanova S. Characterization of interspecific hybrids and first backcross generations from crosses between two cultivated eggplants (Solanum melongena and S. aethiopicum Kumba group) and implications for eggplant breeding. Euphytica. 2012;186(2):517–38.

Prohens J, Whitaker BD, Plazas M, Vilanova S, Hurtado M, Blasco M, et al. Genetic diversity in morphological characters and phenolic acids content resulting from an interspecific cross between eggplant, Solanum melongena, and its wild ancestor (S. incanum). Ann Appl Biol. 2013;162(2):242–57.

Plazas M, Prohens J, Cuñat AN, Vilanova S, Gramazio P, Herraiz FJ, Andújar I. Reducing Capacity, Chlorogenic Acid Content and Biological Activity in a Collection of Scarlet (Solanum aethiopicum) and Gboma (S. macrocarpon) Eggplants. Int J Mol Sci. 2014;15(10):17221–41.

Lester RN, Hasan SMZ. Origin and domestication of the brinjal eggplant, Solanum melongena, from S. incanum, in Africa and Asia. In: Hawkes JG, Lester RN, Nee MH, Estrada N, editors. Solanaceae III: taxonomy, chemistry, evolution. London, U.K: Royal Botanic Gardens, Kew; 1991. p. 369–88.

Knapp S, Vorontsova MS, Prohens J. Wild relatives of the eggplant (Solanum melongena L.: Solanaceae): new understanding of species names in a complex group. PLoS One. 2013;8(2):e57039.

Stommel JR, Whitaker BD. Phenolic acid content and composition of eggplant fruit in a germplasm core subset. J Am Soc Hort Sci. 2003;128(5):704–10.

Yamakawa K, Mochizuki H. Nature and inheritance of Fusarium-wilt resistance in eggplant cultivars and related wild Solanum species. Bulletin of the Vegetable and Ornamental Crops Research Station. 1979;6:19–27.

Anis M, Baksh S, Iqbal M. Cytogenetic Studies on the F1 Hybrid Solanum incanum * S. melongena var. American Wonder. Cytologia. 1994;59(4):433–6.

Behera T, Singh N. Inter-specific crosses between eggplant (Solanum melongena L.) with related Solanum species. Sci. Hortic. 2002;95(1):165–72.

Gramazio P, Prohens J, Plazas M, Andujar I, Herraiz FJ, Castillo E, et al. 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.

Schippers RR. African indigenous vegetables: an overview of the cultivated species. 2000.

Sunseri F, Polignano GB, Alba V, Lotti C, Bisignano V, Mennella G, et al. Genetic diversity and characterization of African eggplant germplasm collection. Afr J Plant Sci. 2010;4(7):231–41.

Lester R, Niakan L. Origin and domestication of the scarlet eggplant, Solanum aethiopicum, from S. anguivi in Africa. In: D’Arcy WG, editor. Solanaceae: Biology and systematics. Columbia: Columbia University Press; 1986. p. 433–56.

Cappelli C, Stravato VM, Rotino GL, Buonaurio R. Sources of resistance among Solanum spp. to an Italian isolate of Fusarium oxysporum f sp. Melongenae. Proceeding of the 9th EUCARPIA meeting on genetics and breeding of capsicum and eggplant. 1995. p. 221–4.

Collonnier C, Mulya K, Fock I, Mariska I, Servaes A, Vedel F, et al. Source of resistance against Ralstonia solanacearum in fertile somatic hybrids of eggplant (Solanum melongena L.) with Solanum aethiopicum L. Plant Sci. 2001;160(2):301–13.

Gisbert C, Prohens J, Raigón MD, Stommel JR, Nuez F. Eggplant relatives as sources of variation for developing new rootstocks: Effects of grafting on eggplant yield and fruit apparent quality and composition. Sci Hortic. 2011;128(1):14–22.

Nunome T, Ishiguro K, Yoshida T, Hirai M. Mapping of Fruit Shape and Color Development Traits in Eggplant (Solanum melongena L.) Based on RAPD and AFLP Markers. Breed Sci. 2001;51(1):19–26.

Doganlar S, Frary A, Daunay MC, Lester RN, Tanksley SD. A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae. Genetics. 2002;161(4):1697–711.

Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L, et al. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics. 2011;12:304.

Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, et al. Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet. 2012;125(1):47–56.

Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, et al. Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet. 2009;119(6):1143–53.

Vilanova S, Manzur JP, Prohens J. Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Mol Breed. 2012;30(2):647–60.

Yang X, Cheng YF, Deng C, Ma Y, Wang ZW, Chen XH, et al. Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis. BMC Genomics. 2014;15(1):412.

Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, et al. Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res. 2014;21(6):649–60.

The NCBI (National Center for Biotechnology Information) database. [ http://www.ncbi.nlm.nih.gov/ ]. Accessed 20 September 2015.

Jaiswal B. Solanum torvum: a review of its traditional uses, phytochemistry and pharmacology. Int J Pharm Biol Sci. 2012;3:4.

Mohan M, Kamble S, Gadhi P, Kasture S. Protective effect of Solanum torvum on doxorubicin-induced nephrotoxicity in rats. Food Chem Toxicol. 2010;48(1):436–40.

Gandhi GR, Ignacimuthu S, Paulraj MG, Sasikumar P. Antihyperglycemic activity and antidiabetic effect of methyl caffeate isolated from Solanum torvum Swartz. fruit in streptozotocin induced diabetic rats. Eur J Pharmacol. 2011;670(2):623–31.

Gousset C, Collonnier C, Mulya K, Mariska I, Rotino GL, Besse P, et al. Solanum torvum, as a useful source of resistance against bacterial and fungal diseases for improvement of eggplant (S. melongena L.). Plant Sci. 2005;168(2):319–27.

Bagnaresi P, Sala T, Irdani T, Scotto C, Lamontanara A, Beretta M, et al. Solanum torvum responses to the root-knot nematode Meloidogyne incognita. BMC Genomics. 2013;14:540.

Guri A, Sink K. Interspecific somatic hybrid plants between eggplant (Solanum melongena) and Solanum torvum. Theor Appl Genet. 1988;76(4):490–6.

Sihachakr D, Haicour R, Chaput M, Barrientos E, Ducreux G, Rossignol L. Somatic hybrid plants produced by electrofusion between Solanum melongena L. and Solanum torvum Sw. Theor Appl Genet. 1989;77(1):1–6.

Collonnier C, Fock I, Mariska I, Servaes A, Vedel F, Siljak-Yakovlev S, et al. GISH confirmation of somatic hybrids between Solanum melongena and S. torvum: assessment of resistance to both fungal and bacterial wilts. Plant Physiol Biochem. 2003;41(5):459–70.

Kumchai J, Wei Y, Lee C, Chen F, Chin S. Production of interspecific hybrids between commercial cultivars of the eggplant (Solanum melongena L.) and its wild relative S. torvum. Gen Mol Res. 2013;12(1):755–64.

YiKui W, YanYan F, Hong W, WenJia L, Yan L. Pollen development and anther callus induction in hybrid F1 by Solanum torvum SW. (♂) × Solanum melongena L. (♀). Journal of Southern Agriculture. 2014;45(12):1967–71.

Takeda H, Sato A, Nishihara E, Arao T. Reduction of cadmium concentration in eggplant (Solanum melongena) fruits by grafting with Solanum torvum rootstock. Japanese Journal of Soil Science and Plant Nutrition. 2007.

Sabatino L, Palazzolo E, D’Anna F. Grafting suitability of Sicilian eggplant ecotypes onto Solanum torvum: Fruit composition, production and phenology. Int j food, agric and environ. 2013;11(3):1195–200.

Miceli A, Sabatino L, Moncada A, Vetrano F, D’Anna F. Nursery and field evaluation of eggplant grafted onto unrooted cuttings of Solanum torvum Sw. Sci Hort. 2014;178:203–10.

Davey JW, Blaxter ML. RADSeq: next-generation population genetics. Brief Funct Genomics. 2010;9(5-6):416–23.

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. Nat Biotechnol. 2011;29(7):644–52.

Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint. arXiv. 2013;1303:3997.

Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014;30(9):418–26.

Lee S, Abecasis GR, Boehnke M, Lin X. Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet. 2014;95(1):5–23.

Faure D, Joly D. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences. Genetica. 2015;143(2):129–32.

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12(1):323.

Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45.

Erayman M, Sandhu D, Sidhu D, Dilbirligi M, Baenziger PS, Gill KS. Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res. 2004;32(12):3546–65.

Mizuno H, Kawahara Y, Wu J, Katayose Y, Kanamori H, Ikawa H, et al. Asymmetric distribution of gene expression in the centromeric region of rice chromosome 5. Front Plant Sci. 2011;2:16.

Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A. Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato. Gene. 2010;450(1):76–84.

Groves RA, Hagel JM, Zhang Y, Kilpatrick K, Levy A, Marsolais F, et al. Transcriptome profiling of khat (Catha edulis) and Ephedra sinica reveals gene candidates potentially involved in amphetamine-type alkaloid biosynthesis. PLoS One. 2015;10(3):e0119701.

Zhang J, Liu W, Han H, Song L, Bai L, Gao Z, et al. De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat. Genomics. 2015;106(2):129–36.

Zhang S, Shi Y, Cheng N, Du H, Fan W, Wang C. De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy. PLoS One. 2015;10(3):e0122170.

Mutz K, Heilkenbrinker A, Lönne M, Walter J, Stahl F. Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol. 2013;24(1):22–30.

The Swiss-Prot database. [ http://web.expasy.org/docs/swiss-prot_guideline.html ]. Accessed 20 September 2015.

The ITAG2.4 database. [ ftp://ftp.sgn.cornell.edu/tomato_genome/annotation/ ]. Accessed 20 September 2015.

The TAIR database: The Arabidopsis Information Resource. [ http://www.arabidopsis.org/ ]. Accessed 20 September 2015.

The UniRef90 database. [ http://www.ebi.ac.uk/uniprot/database/download.html ]. Accessed 20 September 2015.

Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832.

Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485(7400):635–41.

Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, et al. De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics. 2012;13:571.

Bao Y, Xu S, Jing X, Meng L, Qin Z. De Novo Assembly and Characterization of Oryza officinalis Leaf Transcriptome by Using RNA-Seq. Biomed Res Int. 2015;2015:982065.

Lu X, Kim H, Zhong S, Chen H, Hu Z, Zhou B. De novo transcriptome assembly for rudimentary leaves in Litchi chinesis Sonn. and identification of differentially expressed genes in response to reactive oxygen species. BMC Genomics. 2014;15(1):805.

Ranjan A, Ichihashi Y, Farhi M, Zumstein K, Townsley B, David-Schwartz R, et al. De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism. Plant Physiol. 2014;166(3):1186–99.

Laurent GS, Wahlestedt C, Kapranov P. The Landscape of long noncoding RNA classification. Trends Genet. 2015;31(5):239–51.

The lncRNA (Long Noncoding RNA) database. [ http://www.lncrnadb.org/ ]. Accessed 20 September 2015.

Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell. 2012;24(11):4333–45.

Liu J, Wang H, Chua N. Long noncoding RNA transcriptome of plants. Plant Biotech J. 2015;13(3):319–28.

Webb EC. Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. Academic Press. 1992.

Niederhuth CE, Patharkar OR, Walker JC. Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq. BMC Genomics. 2013;14:37.

Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.

Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Int Conf Intell Syst Mol Bio. 1999;7:138–48.

Mott R. EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci. 1997;13:477–8.

Kumar S, Banks TW, Cloutier S. SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics. 2012. doi: 10.1155/2012/831460 .

Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, et al. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2012;99(2):193–208.

Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, et al. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One. 2009;4(8):e6524.

Robbins MD, Sim SC, Yang W, Van Deynze A, van der Knaap E, Joobeur T, et al. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J Exp Bot. 2011;62(6):1831–45.

Sim S, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, et al. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One. 2012;7:e40563.

Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint. arXiv. 2012;1207:3907.

Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003;49(6):853–60.

Daunay M. Eggplant. In: Prohens J, Nuez F, editors. Vegetables II: Handbook of plant Breeding. New York: Springer; 2008. p. 163–220.

Amar MH, Biswas MK, Zhang Z, Guo W. Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Sci Hortic. 2011;128(3):220–7.

Pariasca-Tanaka J, Lorieux M, He C, McCouch S, Thomson MJ, Wissuwa M. Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. Euphytica. 2015;201(1):67–78.

Fan J, Chee MS, Gunderson KL. Highly parallel genomic assays. Nat Rev Genet. 2006;7(8):632–44.

Gupta P, Rustgi S, Mir R. Array-based high-throughput DNA markers for crop improvement. Heredity. 2008;101(1):5–18.

Abajian C. Sputnik. University of Washington Department of Molecular Biotechnology. 1994.

Ding Q, Li J, Wang F, Zhang Y, Li H, Zhang J, Gao J. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). Int J Genomics. 2015;2015:473028.

Chen H, Wang L, Wang S, Liu C, Blair MW, Cheng X. Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers. PLoS One. 2015;10(4):e0120273.

Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, et al. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics. 2010;11(1):94.

Pinosio S, González‐Martínez S, Bagnoli F, Cattonaro F, Grivet D, Marroni F, et al. First insights into the transcriptome and development of new genomic tools of a widespread circum‐Mediterranean tree species, Pinus halepensis Mill. Mol Ecol Resour. 2014;14(4):846–56.

Gao C, Xin P, Cheng C, Tang Q, Chen P, Wang C, et al. Diversity Analysis in Cannabis sativa Based on Large-Scale Development of Expressed Sequence Tag-Derived Simple Sequence Repeat Markers. PLoS One. 2014;9(10):e110638.

Stàgel A, Portis E, Toppino L, Rotino GL, Lanteri S. Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics. 2008;9(1):357.

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.

Schlautman B, Fajardo D, Bougie T, Wiesman E, Polashock J, Vorsa N, et al. Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.). Molecules. 2015;20(2):2001–13.

Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 2000;10(1):72–80.

Li YC, Korol AB, Fahima T, Nevo E. Microsatellites within genes: structure, function, and evolution. Mol Biol Evol. 2004;21(6):991–1007.

Gonzalez-Ibeas D, Blanca J, Roig C, Gonzalez-To M, Pico B, Truniger V, et al. MELOGEN: an EST database for melon functional genomics. BMC Genomics. 2007;8:306.

Durand J, Bodenes C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, et al. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics. 2010;11:570.

Zhou C, He X, Li F, Weng Q, Yu X, Wang Y, et al. Development of 240 novel EST-SSRs in Eucalyptus L’Hérit. Mol Breed. 2014;33(1):221–5.

Kumar B, Kumar U, Yadav HK. Identification of EST–SSRs and molecular diversity analysis in Mentha piperita. The Crop Journal. 2015;3(4):335–42.

Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005;23(1):48–55.

Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen JP, et al. Advances in plant gene-targeted and functional markers: a review. Plant Methods. 2013;9(1):6.

The FastQC software. [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]. Accessed 20 September 2015.

The NGS_CRUMBS software. [ https://bioinf.comav.upv.es/ngs_crumbs/ ]. Accessed 20 September 2015.

Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999;9(9):868–77.

Morgulis A, Gertz EM, Schäffer AA, Agarwala R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biology. 2006;13(5):1028–40.

The GOterm database. [ http://geneontology.org/ ]. Accessed 20 September 2015.

Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.

The eggplant genome database. [ http://eggplant.kazusa.or.jp/ ]. Accessed 20 September 2015.

The IGV software. [ http://www.broadinstitute.org/igv/ ]. Accessed 20 September 2015.

The Primer3 software. [ http://bioinfo.ut.ee/primer3-0.4.0/ ]. Accessed 20 September 2015.

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem