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1.
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20 p, 3.6 MB |
Improved high-quality genome assembly and annotation of pineapple (Ananas comosus) cultivar md2 revealed extensive haplotype diversity and diversified frs/frf gene family
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Yow, Ashley (North Carolina State University. Department of Horticultural Science) ;
Bostan, Hamed (North Carolina State University. Plants for Human Health Institute) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Biomeets Consulting (Barcelona)) ;
Mengist, Mengist F. (North Carolina State University. Plants for Human Health Institute) ;
Curaba, Julien (North Carolina State University. Plants for Human Health Institute) ;
Young, Roberto (Standard Fruit de Honduras. Research Department of Dole) ;
Gillitt, Nicholas (David H. Murdock Research Institute) ;
Iorizzo, Massimo (North Carolina State University. Plants for Human Health Institute)
Pineapple (Ananas comosus (L. ) Merr. ) is the second most important tropical fruit crop globally, and 'MD2' is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. [...]
2022 -  10.3390/genes13010052
Genes, Vol. 13, Issue 1 (January 2022) , art. 52
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2.
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18 p, 7.7 MB |
Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior
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Pereira, Lara (Centre de Recerca en Agrigenòmica) ;
Santo Domingo, Miguel (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Phillips, Michael A. (University of Toronto. Department of Biology) ;
Zhao, Guangwei (Zhengzhou Fruit Research Institute) ;
Lian, Qun (Agricultural Genomics Institute at Shenzhen) ;
Xu, Yongyang (Zhengzhou Fruit Research Institute) ;
He, Yuhua (Zhengzhou Fruit Research Institute) ;
Huang, Sanwen (Agricultural Genomics Institute at Shenzhen) ;
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. [...]
2020 - 10.1038/s41438-020-00411-z
Horticulture research, Vol. 7 (November 2020) , art. 187
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3.
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65 p, 1.6 MB |
Status and Prospects of systems biology in grapevine research
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Matus, José Tomás (Universitat de València. Institut de Biologia Integrativa de Sistemes) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Romero, Francisco José (Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial) ;
Moretto, Marco (Fondazione Edmund Mach. Centro Ricerca e Innovazione) ;
Wong, Darren Chern Jan (Australian National University. Research School of Biology)
The cultivated grapevine, Vitis vinifera L. , has gathered a vast amount of omics data throughout the last two decades, driving the imperative use of computational resources for its analysis and integration. [...]
[s. l.] : Springer, 2019 (Compendium of Plant Genomes) - 10.1007/978-3-030-18601-2_8
The Grape Genome, 2019, p. 137-166
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4.
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10 p, 1.1 MB |
An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes
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Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
The published melon (Cucumis melo L. ) reference genome assembly (v3. 6. 1) has still 41. 6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. [...]
2020 - 10.3389/fpls.2019.01815
Frontiers in plant science, Vol. 10 (January 2020) , art. 1815
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5.
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35 p, 12.9 MB |
A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits
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Zhao, Guangwei (Zhengzhou Fruit Research Institute) ;
Lian, Qun (Agricultural Genomics Institute at Shenzhen) ;
Zhang, Zhonghua (Chinese Academy of Agricultural Sciences. Institute of Vegetables and Flowers) ;
Fu, Qiushi (Chinese Academy of Agricultural Sciences. Institute of Vegetables and Flowers) ;
He, Yuhua (Zhengzhou Fruit Research Institute) ;
Ma, Shuangwu (Zhengzhou Fruit Research Institute) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Monforte, Antonio J. (Instituto de Biologia Molecular y Celular de Plantas (València, Espanya)) ;
Wang, Pingyong (Zhengzhou Fruit Research Institute) ;
Julca, Irene (Centre de Recerca en Agrigenòmica) ;
Wang, Huaisong (Chinese Academy of Agricultural Sciences. Institute of Vegetables and Flowers) ;
Liu, Junpu (Zhengzhou Fruit Research Institute) ;
Xu, Yong (Beijing Key Laboratory of Vegetable Germplasm Improvement) ;
Wang, Runze (Nanjing Agricultural University) ;
Ji, Jiabing (Agricultural Genomics Institute at Shenzhen) ;
Xu, Zhihong (Zhengzhou Fruit Research Institute) ;
Kong, Weihu (Zhengzhou Fruit Research Institute) ;
Zhong, Yang (Agricultural Genomics Institute at Shenzhen) ;
Shang, Jianli (Zhengzhou Fruit Research Institute) ;
Pereira, Lara (Centre de Recerca en Agrigenòmica) ;
Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Zhang, Jian (Zhengzhou Fruit Research Institute) ;
Mayobre, Carlos (Centre de Recerca en Agrigenòmica) ;
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica) ;
Oren, Elad (NeweYa'ar Research Center) ;
Ou, Diandian (Zhengzhou Fruit Research Institute) ;
Wang, Jiming (Zhengzhou Fruit Research Institute) ;
Sun, Dexi (Zhengzhou Fruit Research Institute) ;
Zhao, Shengjie (Zhengzhou Fruit Research Institute) ;
Zhu, Yingchun (Zhengzhou Fruit Research Institute) ;
Li, Na (Zhengzhou Fruit Research Institute) ;
Katzir, Nurit (NeweYa'ar Research Center) ;
Gur, Amit (NeweYa'ar Research Center) ;
Dogimont, Catherine (Institut National de la Recherche Agronomique (França)) ;
Schaefer, Hanno (Technical University of Munich. Department of Ecology and Ecosystem Management) ;
Fan, Wei (Agricultural Genomics Institute at Shenzhen) ;
Bendahmane, Abdelhafid (Institut National de la Recherche Agronomique (França)) ;
Fei, Zhangjun (Cornell University. Boyce Thompson Institute for Plant Research) ;
Pitrat, Michel (Institut National de la Recherche Agronomique (França)) ;
Gabaldón, Toni (Centre de Regulació Genòmica) ;
Lin, Tao (Agricultural Genomics Institute at Shenzhen) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Xu, Yongyang (Zhengzhou Fruit Research Institute) ;
Huang, Sanwen (Agricultural Genomics Institute at Shenzhen)
Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. [...]
2019 - 10.1038/s41588-019-0522-8
Nature genetics, Vol. 51, issue 11 (Nov. 2019) , p. 1607-1615
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6.
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13 p, 2.7 MB |
Exploiting genetic and genomic resources to enhance heat-tolerance in tomatoes
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Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Calafiore, Roberta (University of Naples Federico II. Department of Agricultural Sciences) ;
Schettini, Carlo (ALMA SEGES Soc. Coop.) ;
Rigano, Maria Manuela (University of Naples Federico II. Department of Agricultural Sciences) ;
Olivieri, Fabrizio (University of Naples Federico II. Department of Agricultural Sciences) ;
Frusciante, Luigi (University of Naples Federico II. Department of Agricultural Sciences) ;
Barone, Amalia (University of Naples Federico II. Department of Agricultural Sciences)
High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. [...]
2019 - 10.3390/agronomy9010022
Agronomy, Vol. 9, Issue 1 (January 2019) , art. 22
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7.
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17 p, 3.0 MB |
QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map
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Pereira, Lara (Centre de Recerca en Agrigenòmica) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Pérez, S. (Centre de Recerca en Agrigenòmica) ;
Alexiou, Konstantinos G. (Centre de Recerca en Agrigenòmica) ;
Fernández, Marta (Semillas Fitó, S.L) ;
Jahrmann, Torben (Semillas Fitó, S.L.) ;
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Background: Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. [...]
2018 - 10.1186/s12870-018-1537-5
BMC plant biology, Vol. 18 (2018) , art. 324
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8.
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9 p, 1.8 MB |
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
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Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Pujol Abajo, Marta (Institut de Recerca i Tecnologia Agroalimentàries) ;
Yano, Ryoichi (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Nonaka, Satoko (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Ezura, Hiroshi (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Latrasse, David (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Boualem, Adnane (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Benhamed, Moussa (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Bendahmane, Abdelhafid (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Aiese Cigliano, Riccardo (Sequentia Biotech SL) ;
Sanseverino, Walter (Sequentia Biotech SL) ;
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
We report an improved assembly (v3. 6. 1) of the melon (Cucumis melo L. ) genome and a new genome annotation (v4. 0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. [...]
2018 - 10.1038/s41598-018-26416-2
Scientific reports, Vol. 8 (May 2018) , art. 8088
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9.
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20 p, 2.1 MB |
QTL analyses in multiple populations employed for the fine mapping and identification of candidate genes at a locus affecting sugar accumulation in melon (Cucumis melo L.)
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Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Díaz, Aurora (Instituto de Biología Molecular y Celular de Plantas) ;
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Fernández, Marta (Semillas Fitó, S.L.) ;
Jahrmann, Torben (Semillas Fitó, S.L.) ;
Gibon, Yves (Institut National de la Recherche Agronomique (França)) ;
Picó, Belén (Universitat Politècnica de València. Instituto de Conservación y Mejora de la Agrodiversidad Valenciana) ;
Martín-Hernández, Ana Montserrat (Centre de Recerca en Agrigenòmica) ;
Monforte, Antonio J. (Instituto de Biología Molecular y Celular de Plantas) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Sugar content is the major determinant of both fruit quality and consumer acceptance in melon (Cucumis melo L), and is a primary target for crop improvement. Near-isogenic lines (NILs) derived from the intraspecific cross between a "Piel de Sapo" (PS) type and the exotic cultivar "Songwhan Charmi" (SC), and several populations generated from the cross of PS × Ames 24294 ("Trigonus"), a wild melon, were used to identify QTL related to sugar and organic acid composition. [...]
2017 - 10.3389/fpls.2017.01679
Frontiers in plant science, Vol. 8 (Sep. 2017) art. 1679
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