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Boris Sagredo

Bio: Boris Sagredo is an academic researcher from University of La Frontera. The author has contributed to research in topics: Ripening & Prunus. The author has an hindex of 10, co-authored 24 publications receiving 2125 citations.

Papers
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Journal ArticleDOI
Xun Xu1, Shengkai Pan1, Shifeng Cheng1, Bo Zhang1, Mu D1, Peixiang Ni1, Gengyun Zhang1, Shuang Yang1, Ruiqiang Li1, Jun Wang1, Gisella Orjeda2, Frank Guzman2, Torres M2, Roberto Lozano2, Olga Ponce2, Diana Martinez2, De la Cruz G3, Chakrabarti Sk3, Patil Vu3, Konstantin G. Skryabin4, Boris B. Kuznetsov4, Nikolai V. Ravin4, Tatjana V. Kolganova4, Alexey V. Beletsky4, Andrey V. Mardanov4, Di Genova A5, Dan Bolser5, David M. A. Martin5, Li G, Yang Y, Hanhui Kuang6, Hu Q6, Xiong X7, Gerard J. Bishop8, Boris Sagredo, Nilo Mejía, Zagorski W9, Robert Gromadka9, Jan Gawor9, Pawel Szczesny9, Sanwen Huang, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Youjun Zhang, Xie B, Du Y, Qu D, Merideth Bonierbale10, Marc Ghislain10, Herrera Mdel R, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, O'Brien K11, Sergio Enrique Feingold, Barreiro Le, Massa Ga, Luis Aníbal Diambra12, Brett R Whitty13, Brieanne Vaillancourt13, Lin H13, Alicia N. Massa13, Geoffroy M13, Lundback S13, Dean DellaPenna13, Buell Cr14, Sanjeev Kumar Sharma14, David Marshall14, Robbie Waugh14, Glenn J. Bryan14, Destefanis M15, Istvan Nagy15, Dan Milbourne15, Susan Thomson16, Mark Fiers16, Jeanne M. E. Jacobs16, Kåre Lehmann Nielsen17, Mads Sønderkær17, Marina Iovene18, Giovana Augusta Torres18, Jiming Jiang18, Richard E. Veilleux19, Christian W. B. Bachem20, de Boer J20, Theo Borm20, Bjorn Kloosterman20, van Eck H20, Erwin Datema20, Hekkert Bt20, Aska Goverse20, van Ham Rc20, Richard G. F. Visser20 
10 Jul 2011-Nature
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

1,813 citations

Journal ArticleDOI
TL;DR: The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.
Abstract: The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.

236 citations

Journal ArticleDOI
TL;DR: The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.
Abstract: Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.

110 citations

Journal ArticleDOI
26 May 2015-PLOS ONE
TL;DR: These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.
Abstract: Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a ‘Rainier’ x ‘Rivedel’ (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in ‘Rainier’, ‘Rivedel’ and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for ‘Rainier’, ‘Rivedel’ and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both ‘Rainier’ and ‘Rivedel’ maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

74 citations

Journal ArticleDOI
TL;DR: A comparative study of the most contrasting genotypes revealed that these morpho-anatomical changes would be playing a key role in survival of the tolerant Prunus genotype during O2 deprivation caused by waterlogging.

46 citations


Cited by
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Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations

Journal ArticleDOI
Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu  +320 moreInstitutions (51)
31 May 2012-Nature
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

2,687 citations

Journal ArticleDOI
Xun Xu1, Shengkai Pan1, Shifeng Cheng1, Bo Zhang1, Mu D1, Peixiang Ni1, Gengyun Zhang1, Shuang Yang1, Ruiqiang Li1, Jun Wang1, Gisella Orjeda2, Frank Guzman2, Torres M2, Roberto Lozano2, Olga Ponce2, Diana Martinez2, De la Cruz G3, Chakrabarti Sk3, Patil Vu3, Konstantin G. Skryabin4, Boris B. Kuznetsov4, Nikolai V. Ravin4, Tatjana V. Kolganova4, Alexey V. Beletsky4, Andrey V. Mardanov4, Di Genova A5, Dan Bolser5, David M. A. Martin5, Li G, Yang Y, Hanhui Kuang6, Hu Q6, Xiong X7, Gerard J. Bishop8, Boris Sagredo, Nilo Mejía, Zagorski W9, Robert Gromadka9, Jan Gawor9, Pawel Szczesny9, Sanwen Huang, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Youjun Zhang, Xie B, Du Y, Qu D, Merideth Bonierbale10, Marc Ghislain10, Herrera Mdel R, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, O'Brien K11, Sergio Enrique Feingold, Barreiro Le, Massa Ga, Luis Aníbal Diambra12, Brett R Whitty13, Brieanne Vaillancourt13, Lin H13, Alicia N. Massa13, Geoffroy M13, Lundback S13, Dean DellaPenna13, Buell Cr14, Sanjeev Kumar Sharma14, David Marshall14, Robbie Waugh14, Glenn J. Bryan14, Destefanis M15, Istvan Nagy15, Dan Milbourne15, Susan Thomson16, Mark Fiers16, Jeanne M. E. Jacobs16, Kåre Lehmann Nielsen17, Mads Sønderkær17, Marina Iovene18, Giovana Augusta Torres18, Jiming Jiang18, Richard E. Veilleux19, Christian W. B. Bachem20, de Boer J20, Theo Borm20, Bjorn Kloosterman20, van Eck H20, Erwin Datema20, Hekkert Bt20, Aska Goverse20, van Ham Rc20, Richard G. F. Visser20 
10 Jul 2011-Nature
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

1,813 citations

Journal ArticleDOI
04 Oct 2012-Nature
TL;DR: The sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy and transcriptomes of development and stress response and the proteome of the shell are reported, showing that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes.
Abstract: The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

1,806 citations

Journal ArticleDOI
TL;DR: The computational problems surrounding repeats are discussed and strategies used by current bioinformatics systems to solve them are described.
Abstract: Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.

1,451 citations