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פותח על ידי קלירמאש פתרונות בע"מ -
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
Year:
2011
Source of publication :
BMC Genomics
Authors :
פורטנוי, ויטלי
;
.
קציר, נורית
;
.
Volume :
12
Co-Authors:
Clepet, C., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Joobeur, T., Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, United States, Seminis Vegetable Seeds, 37437 State Highway 16, Woodland, CA 95695, United States
Zheng, Y., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States
Jublot, D., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Huang, M., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States
Truniger, V., Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
Boualem, A., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Hernandez-Gonzalez, M.E., Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, United States
Dolcet-Sanjuan, R., IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Portnoy, V., Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
Mascarell-Creus, A., Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Caño-Delgado, A.I., Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Katzir, N., Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
Bendahmane, A., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France, Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
Giovannoni, J.J., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States, USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, United States
Aranda, M.A., Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
Garcia-Mas, J., IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Fei, Z., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States, USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, United States
Facilitators :
From page:
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(
Total pages:
1
)
Abstract:
Background: Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.Result: We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.Conclusion: The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns. © 2011 Clepet et al; licensee BioMed Central Ltd.
Note:
Related Files :
Cucumis melo
Cucurbitaceae
gene expression
genetic markers
Genetics
genomics
עוד תגיות
תוכן קשור
More details
DOI :
10.1186/1471-2164-12-252
Article number:
252
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
31995
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 01:06
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Scientific Publication
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
12
Clepet, C., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Joobeur, T., Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, United States, Seminis Vegetable Seeds, 37437 State Highway 16, Woodland, CA 95695, United States
Zheng, Y., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States
Jublot, D., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Huang, M., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States
Truniger, V., Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
Boualem, A., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France
Hernandez-Gonzalez, M.E., Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, United States
Dolcet-Sanjuan, R., IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Portnoy, V., Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
Mascarell-Creus, A., Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Caño-Delgado, A.I., Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Katzir, N., Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
Bendahmane, A., URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS., 2 Rue Gaston Crémieux, 91057 Evry, France, Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
Giovannoni, J.J., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States, USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, United States
Aranda, M.A., Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
Garcia-Mas, J., IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
Fei, Z., Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, United States, USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, United States
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
Background: Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.Result: We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.Conclusion: The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns. © 2011 Clepet et al; licensee BioMed Central Ltd.
Scientific Publication
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