Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Clépet, Christian; Joobeur, Tarek; Zheng, Yi; Jublot, Delphine; Huang, Mingyun; Truniger, Verónica; Boualem, Adnane; Hernandez-Gonzalez, Maria Elena; Dolcet-Sanjuan, Ramón; Portnoy, Vitaly; Mascarell-Creus, Albert; Caño‐Delgado, Ana I.; Katzir, Nurit; Bendahmane, Abdelhafid; Giovannoni, James J.; Aranda, Miguel A.; García-Más, Jordi; Fei, Zhangjun

doi:10.1186/1471-2164-12-252

Cited by 52 publications

(42 citation statements)

References 70 publications

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“…Sixty-three genes putatively involved in sugar metabolism were annotated, belonging to 16 phylogenetic groups (Dataset S5). Twenty-one of these genes were not previously reported in melon (37,38), of which 8 had EST support. A gene putatively encoding a UDP-glc phyrophosphorylase (CmUGP-LIKE1), for which a single gene was described (CmUGP), was annotated (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

The genome of melon ( Cucumis melo L.)

García-Más

Benjak

Sanseverino

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucinerich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.de novo genome sequence | phylome M elon (Cucumis melo L.) is a eudicot diploid plant species (2n = 2x = 24) of interest for its specific biological properties and for its economic importance. It belongs to the Cucurbitaceae family, which also includes cucumber (Cucumis sativus L.), watermelon [Citrullus lanatus (Thunb.) Matsum.

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Section: Resultsmentioning

confidence: 99%

The genome of melon ( Cucumis melo L.)

García-Más

Benjak

Sanseverino

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

649

531

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“…Genes belonging to the organic acid metabolism pathway were selected based on the literature and the International Cucurbit Genomics Initiative database (Clepet et al 2011; http://www.ICUGI.org). In addition, an exhaustive search for additional paralogues, based on BLAST analysis of a melon fruit EST database derived from a 454 transcriptome analysis ) was also performed.…”

Section: Organic Acid Metabolism Genes: Identiwcation and Mappingmentioning

confidence: 99%

Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.)

et al. 2012

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Sweet melon cultivars contain a low level of organic acids and, therefore, the quality and flavor of sweet melon fruit is determined almost exclusively by fruit sugar content. However, genetic variability for fruit acid levels in the Cucumis melo species exists and sour fruit accessions are characterized by acidic fruit pH of <5, compared to the sweet cultivars that are generally characterized by mature fruit pH values of >6. In this paper, we report results from a mapping population based on recombinant inbred lines (RILs) derived from the cross between the non-sour 'Dulce' variety and the sour PI 414323 accession. Results show that a single major QTL for pH co-localizes with major QTLs for the two predominant organic acids in melon fruit, citric and malic, together with an additional metabolite which we identified as uridine. While the acidic recombinants were characterized by higher citric and malic acid levels, the non-acidic recombinants had a higher uridine content than did the acidic recombinants. Additional minor QTLs for pH, citric acid and malic acid were also identified and for these the increased acidity was unexpectedly contributed by the non-sour parent. To test for co-localization of these QTLs with genes encoding organic acid metabolism and transport, we mapped the genes encoding structural enzymes and proteins involved in organic acid metabolism, transport and vacuolar H+ pumps. None of these genes co-localized with the major pH QTL, indicating that the gene determining melon fruit pH is not one of the candidate genes encoding this primary metabolic pathway. Linked markers were tested in two additional inter-varietal populations and shown to be linked to the pH trait. The presence of the same QTL in such diverse segregating populations suggests that the trait is determined throughout the species by variability in the same gene and is indicative of a major role of the evolution of this gene in determining the important domestication trait of fruit acidity within the species.

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“…Como resultado de este proyecto, y de otros anteriores llevados a cabo por los distintos grupos participantes, se había desarrollado un mapa genético de densidad moderada, construido fundamentalmente con marcadores codominantes de tipo SSR (Fernández-Silva et al, 2008), un mapa físico (González et al, 2010), una colección de líneas de introgresión (Eduardo et al, 2005) y una colección de 30.000 ESTs (Expressed Sequence Tags), obtenidos mediante secuenciación por Sanger (González-Ibeas et al, 2007), entre otras herramientas genómicas. La colección de ESTs, que posteriormente se amplió con nuevas genotecas (Clepet et al, 2011), permitió la construcción del primer microarray en melón (Mascarell-Creus et al, 2009) y el avance de los estudios de expresión relacionados con resistencias y calidad del fruto en este cultivo (Dai et al, 2011;González-Ibeas et al, 2012). Muchas de estas herramientas se integraron y se encuentran accesibles en la base de datos de ICuGI (International Cucurbit Genomics Initiative, http://www.icugi.org/).…”

Section: Melón (C Melo)unclassified

“…melo var. cantalupensis Naudin), fueron ensambladas con las secuencias ESTs de Sanger ya disponibles (MELOGEN, ICuGI), (Clepet et al, 2011), para obtener una versión más completa del transcriptoma de melón. Este trabajo supuso la primera aplicación de técnicas de secuenciación masiva en melón.…”

Section: Melón (C Melo)unclassified

“…La primera colección masiva de SSRs y SNPs generada en 2007 requirió un importante esfuerzo y, a su vez, una cuantiosa inversión económica, de varios grupos de investigación para la generación de colecciones de secuencias (González-Ibeas et al, 2007 (Blanca et al, 2011c), lo que supone triplicar el número de SSRs identificados y multiplicar por 100 los SNPs respecto a la colección de 2007 (González-Ibeas et al, 2007). Por otra parte, y anterior a la publicación del transcriptoma de melón que se presenta en esta Tesis (Blanca et al, 2011c), el esfuerzo inicial en la generación de ESTs por Sanger continuó con una iniciativa internacional que permitió aumentar la colección existente con 93.756 ESTs adicionales que, ensamblados con los aproximadamente 35.000 previamente disponibles, dieron lugar a 24.444 unigenes, de los cuales 3.279 contenían motivos SSRs (4.068) y 1.331 contenían SNPs (3.073) (Clepet et al, 2011). Incluso con este avance en el descubrimiento de marcadores, el aumento en más de 12 veces del número de SNPs identificados gracias al nuevo transcriptoma obtenido por pirosecuenciación marca una nueva era en la generación de colecciones de secuencias e identificación masiva de marcadores para la especie.…”

Section: Melónunclassified

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Desarrollo y aplicación de herramientas genómicas para la mejora de especies cucurbitáceas por calidad y resistencia a enfermedades.

Gómez¹

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Melon (Cucumis melo) and summer squash (Cucurbita pepo) are economically important cucurbits cultivated worldwide. New, better-adapted, cultivars, resistant to pests and diseases, and varieties displaying better quality traits are required to optimize their production and to meet market demands. Crop breeding must be carried out efficiently and competitively, using the existing genetic knowledge and the molecular tools available for each species. The development of genomic tools to speed up Cucurbits breeding programs is the main objective of this Doctoral Thesis.Molecular markers are essential tools for the construction of genetic maps, for an efficient MAS selection, for QTL (Quantitative Trait Loci) analysis and mapping and for the development of new breeding populations. Molecular markers are also necessary tools for biodiversity analysis. High-quality markers, such as microsatellites (Simple Sequence Repeats, SSRs) and SNPs (Single Nucleotide Polymorphisms) have been developed and/or validated for both species in this Thesis. The generation of sequence information, required for the development of SSRs and SNPs has dramatically changed in the last 6 years due to the advent of new technological advances. In fact, a fairly complete melon transcriptome has been produced using high-throughput 454 sequencing (NGS, Next Generation Sequencing) and combining the newly produced ESTs with the previously existing Sanger sequences. The melon transcriptome characterization presented is the most complete to date (53.252 unigenes with over 63% of them annotated). The generation of large SSRs and SNPs collections for these species, by mapping the ESTs (Expressed Sequence Tags) against the new version of the transcriptome has been a great achievement starting a new era in melon breeding.The obtained collection of molecular markers (more than 3.000 SSRs and 38.000 SNPs) has allowed the construction of melon maps with increased marker density. 6Similar resources have been developed for the first time in C. pepo. SSRs identified in the C. pepo transcriptome sequencing project has been applied to localize landraces with favourable commercial traits and whose alleles might be exploited in breeding programs. Likewise, the usefulness of both EST-SSRs and genomic SSRs for depicting genetic relationships has been proved. On the other hand, the employment of the first SNP set identified for Cucurbita through a massive genotyping platform, GoldenGate, has been a success (90%). The genetic map obtained, with more than 300 SNPs, has allowed to map a large set of QTLs related to early flowering, femaleness tendency, shape, size and fruit color, and other traits of interest in breeding.Therefore, these works report the validation and application of previously developed markers and the generation of new genomic tools to speed up the breeding process of these crops. The paper-based format of this Thesis confirms the interest of the obtained results. 7 RESUMENEl melón (Cucumis melo) y el calabacín (Cucurbita pepo) son especies cucurbi...

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Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Cited by 52 publications

References 70 publications

The genome of melon ( Cucumis melo L.)

The genome of melon ( Cucumis melo L.)

Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.)

Desarrollo y aplicación de herramientas genómicas para la mejora de especies cucurbitáceas por calidad y resistencia a enfermedades.

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