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1. The Impact of MOSE (Experimental Electromechanical Module) Flood Barriers on Microphytobenthic Community of the Venice Lagoon

Author

Laura Baldassarre, Vanessa Natali, Fabio De Pascale, Alessandro Vezzi, Elisa Banchi, Matteo Bazzaro, Federica Relitti, Davide Tagliapietra, and Tamara Cibic

Subjects
microphytobenthos, benthic diatoms, Venice Lagoon, next generation sequencing, classic taxonomy, Biology (General), QH301-705.5
Abstract

MOSE is a system of mobile gates engineered to temporarily isolate the Venice Lagoon from the Adriatic Sea and to protect the city from flooding during extreme high tides. Within the framework of the Venezia2021 program, we conducted two enclosure experiments in July 2019 (over 48 h) and October 2020 (over 28 h) by means of 18 mesocosms, in order to simulate the structural alterations that microphytobenthos (MPB) assemblages might encounter when the MOSE system is operational. The reduced hydrodynamics inside the mesocosms favored the deposition of organic matter and the sinking of cells from the water column towards the sediment. Consequently, MPB abundances increased over the course of both experiments and significant changes in the taxonomic composition of the community were recorded. Species richness increased in summer while it slightly decreased in autumn, this latter due to the increase in relative abundances of taxa favored by high organic loads and fine grain size. By coupling classical taxonomy with 18S rRNA gene metabarcoding we were able to obtain a comprehensive view of the whole community potential, highlighting the complementarity of these two approaches in ecological studies. Changes in the structure of MPB could affect sediment biostabilization, water turbidity and lagoon primary production.

Published
2023
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2. Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters

Author

Vincenzo Manna, Francesca Malfatti, Elisa Banchi, Federica Cerino, Fabio De Pascale, Annalisa Franzo, Riccardo Schiavon, Alessandro Vezzi, Paola Del Negro, and Mauro Celussi

Subjects
particulate organic matter, particle-attached, free-living, 16S rRNA, microbial community, extracellular enzymes, Microbiology, QR1-502
Abstract

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L–1) and intense (10 μg of Chlorophyll a L–1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes’ abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.

Published
2020
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3. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Author

Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D’Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi, and Giorgio Valle

Subjects
Variant prioritization, Exome sequencing, Variant annotation, Data integration, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/ .

Published
2017
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4. Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential

Author

Alessandra Fontana, Irene Falasconi, Paola Molinari, Laura Treu, Arianna Basile, Alessandro Vezzi, Stefano Campanaro, and Lorenzo Morelli

Subjects
lactic acid bacteria, Lactobacillus helveticus, bile salts tolerance, exopolysaccharides, antibiotic resistance, comparative genomics, Microbiology, QR1-502
Abstract

Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.

Published
2019
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5. Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Author

Abdul-Salam Juhmani, Alessandro Vezzi, Mohammad Wahsha, Alessandro Buosi, Fabio De Pascale, Riccardo Schiavon, and Adriano Sfriso

Subjects
bacterial community, seaweeds, Illumina, lagoon of Venice, anthropogenic stressors, Biology (General), QH301-705.5
Abstract

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Published
2020
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6. A Snapshot of the Emerging Tomato Genome Sequence

Author

Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song-Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung-Hwan Jo, Cheol-Goo Hur, Doil Choi, Chang-Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, Jinfeng Shi, Shouhong Sun, Jianjun Chen, Xiaohua Yang, Chen Lu, Mingsheng Chen, Zhukuan Cheng, Chuanyou Li, Hongqing Ling, Yongbiao Xue, Ying Wang, Graham B. Seymour, Gerard J. Bishop, Glenn Bryan, Jane Rogers, Sarah Sims, Sarah Butcher, Daniel Buchan, James Abbott, Helen Beasley, Christine Nicholson, Clare Riddle, Sean Humphray, Karen McLaren, Saloni Mathur, Shailendra Vyas, Amolkumar U. Solanke, Rahul Kumar, Vikrant Gupta, Arun K. Sharma, Paramjit Khurana, Jitendra P. Khurana, Akhilesh Tyagi, Sarita, Parul Chowdhury, Smriti Shridhar, Debasis Chattopadhyay, Awadhesh Pandit, Pradeep Singh, Ajay Kumar, Rekha Dixit, Archana Singh, Sumera Praveen, Vivek Dalal, Mahavir Yadav, Irfan Ahmad Ghazi, Kishor Gaikwad, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh, Dóra Szinay, Hans de Jong, Sander Peters, Marjo van Staveren, Erwin Datema, Mark W.E.J. Fiers, Roeland C.H.J. van Ham, P. Lindhout, Murielle Philippot, Pierre Frasse, Farid Regad, Mohamed Zouine, Mondher Bouzayen, Erika Asamizu, Shusei Sato, Hiroyuki Fukuoka, Satoshi Tabata, Daisuke Shibata, Miguel A. Botella, M. Perez-Alonso, V. Fernandez-Pedrosa, Sonia Osorio, Amparo Mico, Antonio Granell, Zhonghua Zhang, Jun He, Sanwen Huang, Yongchen Du, Dongyu Qu, Longfei Liu, Dongyuan Liu, Jun Wang, Zhibiao Ye, Wencai Yang, Guoping Wang, Alessandro Vezzi, Sara Todesco, Giorgio Valle, Giulia Falcone, Marco Pietrella, Giovanni Giuliano, Silvana Grandillo, Alessandra Traini, Nunzio D'Agostino, Maria Luisa Chiusano, Mara Ercolano, Amalia Barone, Luigi Frusciante, Heiko Schoof, Anika Jöcker, Rémy Bruggmann, Manuel Spannagl, Klaus X.F. Mayer, Roderic Guigó, Francisco Camara, Stephane Rombauts, Jeffrey A. Fawcett, Yves Van de Peer, Sandra Knapp, Dani Zamir, and Willem Stiekema

Subjects
Plant culture, SB1-1110, Genetics, QH426-470
Abstract

The genome of tomato ( L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Published
2009
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7. PABS: An online platform to assist BAC-by-BAC sequencing projects

Author

Sara Todesco, Davide Campagna, Fabrizio Levorin, Michela D'Angelo, Riccardo Schiavon, Giorgio Valle, and Alessandro Vezzi

Subjects
Biology (General), QH301-705.5
Abstract

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC.

Published
2008
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8. Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes

Author

Nicola Vitulo, Alessandro Vezzi, Giulio Galla, Sandra Citterio, Giada Marino, Benedetto Ruperti, Monica Zermiani, Emidio Albertini, Giorgio Valle, and Gianni Barcaccia

Subjects
Mob genes, protein structure, phylogenesis, cytokinesis, apoptosis, morphogenesis, Evolution, QH359-425
Abstract

The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the 43 eukaryotic genomes so far sequenced. We show that genes for Mob-like proteins are present in at least 41 of these genomes, confi rming the universal distribution of this protein family and suggesting its prominent biological function. The phylogenetic analysis reveals fi ve distinct MOB domain classes, showing a progressive expansion of this family from unicellular to multicellular organisms, reaching the highest number in mammals. Plant Mob genes appear to have evolved from a single ancestor, most likely after the loss of one or more genes during the early stage of Viridiplantae evolutionary history. Three of the Mob classes are widespread among most of the analyzed organisms. The possible biological and molecular function of Mob proteins and their role in conserved signaling pathways related to cell proliferation, cell death and cell polarity are also presented and critically discussed.

Published
2007

9. Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Author

Riccardo Schiavon, Mohammad Wahsha, Alessandro Vezzi, Alessandro Buosi, Adriano Sfriso, Abdul-Salam Juhmani, and Fabio De Pascale

Subjects
Settore BIO/07 - Ecologia, Microbiology (medical), Host response, anthropogenic stressors, Microbiology, bacterial community, lagoon of Venice, Article, 03 medical and health sciences, Nutrient, Algae, Illumina, Anthropogenic stressors, Bacterial community, Lagoon of Venice, Seaweeds, Virology, lcsh:QH301-705.5, Illumina dye sequencing, 030304 developmental biology, metagenomics, 0303 health sciences, biology, 030306 microbiology, Ecology, Seaweed associated microbial communities, metagenomics, Lagoon of Venice, biology.organism_classification, Affected site, seaweeds, Seaweed associated microbial communities, Taxon, lcsh:Biology (General), Metabolic activity, Bacteria
Abstract

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds&rsquo, performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities&rsquo, composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Published
2020

10. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Author

Claudio Forcato, Susanna Negrisolo, Giovanni Birolo, Erika Feltrin, Alessandra Zanetti, Riccardo Schiavon, Alessandro Vezzi, Franca Anglani, Francesca D’Avanzo, Giorgio Valle, Nicola Vitulo, Georgine Faulkner, Rosella Tomanin, Fabio De Pascale, and Loris Bertoldi

Subjects
0301 basic medicine, Exome sequencing, Variant prioritization, Exome sequencing, Variant annotation, Data integration, Process (engineering), Interface (Java), Data integration, Variant annotation, Variant prioritization, Disease, Exome, Genome, Human, Humans, Internet, Databases, Genetic, Genetic Variation, Software, Computational biology, Biology, computer.software_genre, lcsh:Computer applications to medicine. Medical informatics, Biochemistry, Field (computer science), 03 medical and health sciences, Inheritance (object-oriented programming), Databases, 0302 clinical medicine, Genetic, Structural Biology, Molecular Biology, lcsh:QH301-705.5, Flexibility (engineering), Information retrieval, Genome, Applied Mathematics, Computer Science Applications, 030104 developmental biology, XML Schema (W3C), lcsh:Biology (General), lcsh:R858-859.7, computer, 030217 neurology & neurosurgery, Human
Abstract

Background Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1654-4) contains supplementary material, which is available to authorized users.

Published
2017

11. Genomic Comparison of

Author

Alessandra, Fontana, Irene, Falasconi, Paola, Molinari, Laura, Treu, Arianna, Basile, Alessandro, Vezzi, Stefano, Campanaro, and Lorenzo, Morelli

Subjects
lactic acid bacteria, antibiotic resistance, probiotics, exopolysaccharides, food and beverages, bile salts tolerance, comparative genomics, Microbiology, Lactobacillus helveticus, Original Research
Abstract

Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.

Published
2019

12. Chromosome Scale Genome Assembly and Transcriptome Profiling of Nannochloropsis gaditana in Nitrogen Depletion

Author

Tomas Morosinotto, Claudio Forcato, Giorgio Valle, Giorgio M. Giacometti, Riccardo Schiavon, Michela D'Angelo, Elisa Corteggiani Carpinelli, Andrea Telatin, Nicola Vitulo, and Alessandro Vezzi

Subjects
0106 biological sciences, chromosomes, Nitrogen, nitrogen deprivation, Sequence assembly, Plant Science, de novo assembly, 01 natural sciences, 7. Clean energy, Genome, Transcriptome, lipids, 03 medical and health sciences, Nannochloropsis, Gene, Molecular Biology, 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, Genetics, 0303 health sciences, biology, Gene Expression Profiling, SOLiD, Molecular Sequence Annotation, Gene Annotation, biology.organism_classification, biofuel, genome, telomeres, transcriptome, Chromosomes, Gene Expression Regulation, Stramenopiles, Gene expression profiling, 010606 plant biology & botany
Abstract

Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae. Here, we report a high-quality genomic assembly of Nannochloropsis gaditana , consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of the chromosomes. We identified 10646 complete genes and characterized possible alternative transcripts. The annotation of the predicted genes and the analysis of cellular processes revealed traits relevant for the genetic improvement of this organism such as genes involved in DNA recombination, RNA silencing, and cell wall synthesis. We also analyzed the modification of the transcriptional profile in nitrogen deficiency—a condition known to stimulate lipid accumulation. While the content of lipids increased, we did not detect major changes in expression of the genes involved in their biosynthesis. At the same time, we observed a very significant down-regulation of mitochondrial gene expression, suggesting that part of the Acetyl-CoA and NAD(P)H, normally oxidized through the mitochondrial respiration, would be made available for fatty acids synthesis, increasing the flux through the lipid biosynthetic pathway. Finally, we released an information resource of the genomic data of N. gaditana , available online at www.nannochloropsis.org. SUMMARY The paper describes the genome sequence, gene annotation, and transcriptional profiling of the microalga Nannochloropsis gaditana B-31. The study identifies possible targets of genetic modification that could improve the yield of the strain for biodiesel production. The genome resource is available online at www.nannochloropsis.org with multiple tools for information retrieval.

Published
2014
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13. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island

Author

Sariel Hübner, Alessandro Vezzi, Eduard Fadeev, Dikla Aharonovich, Fabio De Pascale, and Daniel Sher

Subjects
0301 basic medicine, Microbiology (medical), lcsh:QR1-502, Sequence assembly, Bacterial genome size, Genome sequencing, Genome, Microbiology, DNA sequencing, lcsh:Microbiology, 03 medical and health sciences, Plasmid, genomic island, Genomic island, plasmid, Alteromonas, Genome assembly, Metal resistance, Original Research, Genetics, biology, biology.organism_classification, 030104 developmental biology, genome assembly, Alteromonas macleodii, metal resistance
Abstract

Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de-novo methods. In general, the de-novo assemblies clearly outperformed the reference-based or hybrid ones, covering>99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (~4.5Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to Alteromonas macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island, containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire flexible genomic island suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon.

Published
2016
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14. The Ocean Sampling Day Consortium

Author

Oleksandra Bobrova, Petra ten Hoopen, Rodrigo Costa, Rania Siam, Rehab Z. Abdallah, Jorge A. Herrera Silveira, Catarina Magalhães, Nedime Serakinci, Marie E. DeLorenzo, Riccardo Rosselli, Paul Malthouse, Lise Øvreås, Eyjólfur Reynisson, Susan Gebbels, Francesca Malfatti, Frank Oliver Glöckner, Federico M. Lauro, Hans Erik Karlsen, David Wallom, Christian Jeanthon, Mark J. Costello, Fergal O'Gara, Nadezhda Todorova, Ana C. Costa, Monia El Bour, Paul D. van Ruth, Ivaylo Kostadinov, Martin Ostrowski, Jed A. Fuhrman, Viggo Marteinsson, Thierry Cariou, Hiroyuki Ogata, Maria Luiza Pedrotti, Emilie Villar, Federico Baltar, Sandi Orlić, Valentina Turk, Katja Lehmann, Dawn Field, Renzo Kottmann, Florence Jude-Lemeilleur, Daniel Vaulot, Alessandro Vezzi, Neil M Davies, Mahrous M. Kandil, Véronique Berteaux-Lecellier, Christopher D. Sinigalliano, Timothy W. Davis, Peter N. Golyshin, Stéphane L'Haridon, Jonathan A. Martinez, Sandra Ramos, Pascal Conan, Ma. Leopoldina Aguirre-Macedo, Antonio Fernandez-Guerra, Soumya Essayeh, Clara Loureiro, Edvardsen Bente, Noureddine Boukhatem, Rachelle M. Jensen, Sophie Pitois, Bouchra Chaouni, Kate Munnik, Anke Kremp, Stephane Pesant, Roberto Danovaro, Cecilia Alonso, Said Barrijal, Jodie van de Kamp, Michail M. Yakimov, Nicole J. Poulton, Zackary I. Johnson, Adriana Zingone, Bernardo Duarte, Ilkay Salihoglu, Paraskevi N. Polymenakou, Jack A. Gilbert, Melody S. Clark, Ian Salter, Hassan Ghazal, Julie LaRoche, J. Mortelmans, Ranjith Edirisinghe, Grazia Marina Quero, Dion Matthew Frederick Frampton, Isabel Caçador, Georgios Tsiamis, Declan C. Schroeder, Jamie Hinks, Ana Martins, Noga Stambler, Rachel Collin, João Canning-Clode, Tinkara Tinta, Mesude Bicak, Scott Jones, Valentina Amaral, Matthias S. Ullrich, Gunnar Gerdts, Klaas Deneudt, Michael Steinke, Mohamed Bennani, Rafael Santana, Fabio De Pascale, Jennifer Tolman, Juan Iriberri, Levente Bodrossy, Abderrahim Bouali, Antonella Penna, Bruno Cataletto, Josep M. Gasol, Florencia Biancalana, Maribeth L. Gidley, Stephen A. Jackson, Mahmut Cerkez Ergoren, Carolin R. Löscher, Antje Wichels, Ventzislav Karamfilov, R. Eric Collins, Sara Ettamimi, Riccardo Schiavon, Mohammed Timinouni, Christina Bienhold, Julia Schnetzer, Marc E. Frischer, Wayne J. Fuller, Simon Claus, Ibon Cancio, Guy Cochrane, Patrick Martin, Gian Marco Luna, Snejana Moncheva, Linda A. Amaral-Zettler, Eva C. Sonnenschein, Paul Anders Fronth Nyhus, Shiao Y. Wang, Antonina Dos Santos, Eyal Rahav, Eileen Bresnan, Anna Kopf, Barker Katherine, Michèle Barbier, Naiara Rodríguez-Ezpeleta, Kemal Can Bizsel, Tim Ingleton, Patricia Wecker, Julia A. Busch, Kelly D. Goodwin, El Houcine Zaid, Rajaa Chahboune, Takashi Yoshida, Fatima El Otmani, Marianna Mea, Nina Dzhembekova, Anne-Lise Ducluzeau, Christopher P. Meyer, Georgios Kotoulas, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Jacobs University [Bremen], University of Oxford, Centre for Ecology & Hydrology, Oxfordshire UK, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Israel Oceanographic and Limnological Research (IOLR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Hellenic Centre for Marine Research (HCMR), American University in Cairo, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Institut Ruder Boskovic, Institut Ruđer Bošković (IRB), University of Essex, Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Universidade de Lisboa = University of Lisbon (ULISBOA), Smithonian Environmental Research Center, Research Center, Odessa National I.I.Mechnikov University, Matis Ltd, Universidade dos Açores, Istituto di Science Marine (ISMAR ), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Finnish Environment Institute (SYKE), National Oceanic and Atmospheric Administration (NOAA), University of Bergen (UiB), Dalhousie University [Halifax], Università di Urbino, Skidaway Institute of Oceanography, Smithsonian Institution, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mississippi State University [Mississippi], Bigelow Laboratory for Ocean Sciences, Smithsonian Marine Station, Smithsonian Tropical Research Institute, University of Southern California (USC), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Universidad de la República [Montevideo] (UDELAR), Bar-Ilan University [Israël], The Interuniversity Institute for marine Science in Eilat, IAMC-CNR, Istituto per l'Ambiente Marino Costiero &ndash, University of Otago [Dunedin, Nouvelle-Zélande], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Macquarie University, South Australian Research and Development Institute (SARDI), South Australian Research and Development Institute, Flanders Marine Institute, VLIZ, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), University of Algarve [Portugal], Marine Biological Association of the UK, Department of Chemistry, Alexandria University [Alexandrie], Argentine Institute of Oceanography, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of Tasmania [Hobart, Australia] (UTAS), Waters, wetlands & coasts Sydney, Lwande technologies Cape Town, AZTI (AZTI), AZTI, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Université Mohammed Premier [Oujda], Université Mohammed V de Rabat [Agdal] (UM5), Université Sidi Mohamed Ben Abdellah (USMBA), Université Abdelmalek Essaâdi (UAE), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), Faculty of Sciences, Rabat, Morocco., Bulgarian Academy of Sciences (BAS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Université de Brest (UBO), Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Università degli Studi di Padova = University of Padua (Unipd), Singapore centre for environmental life sciences engineering, Nanyang Technological University [Singapour], Indigo V Expeditions, Newcastle University [Newcastle], Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universität Bremen, Istituto Nazionale di Geofisica e di Oceanografia Sperimentale (OGS), Rajarata University of Sri-Lanka (RUSL), University of Southern Mississippi (USM), Mediterranean Science Commission, National institute of biology Fornace, Near East University, Marine Scotland Marine Laboratory, Kind of Blue Project ABS, University of Oslo (UiO), Marine biology research station, Bangor University, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Fridtjof Nansen Institute of oceanology, Duke University [Durham], Miami University, Miami University [Ohio] (MU), Stazione Zoologica Anton Dohrn (SZN), Polytechnic University of Marche, University of Patras, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), INSTIM, University of Alaska [Fairbanks] (UAF), University of Hawaii, University of Auckland [Auckland], Marine Biological Laboratory (MBL), University of Chicago, Brown University, Zhejiang University, Argonne National Laboratory [Lemont] (ANL), Department of Mathematics [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Repositório da Universidade de Lisboa, Kopf, A, Bicak, M, Kottmann, R, Schnetzer, J, Kostadinov, I, Lehmann, K, Fernandez-Guerra, A, Jeanthon, C, Rahav, E, Ullrich, M, Wichels, A, Gerdts, G, Polymenakou, P, Kotoulas, G, Siam, R, Abdallah, Rz, Sonnenschein, Ec, Cariou, T, O'Gara, F, Jackson, S, Orlic, S, Steinke, M, Busch, J, Duarte, B, Cacador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, Cm, Luna, Gm, Quero, Gm, Loscher, Cr, Kremp, A, Delorenzo, Me, Ovreas, L, Tolman, J, Laroche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, Cp, Ramos, S, Magalhaes, C, Jude-Lemeilleur, F, Aguirre-Macedo, Ml, Wang, S, Poulton, N, Jones, S, Collin, R, Fuhrman, Ja, Conan, P, Alonso, C, Stambler, N, Goodwin, K, Yakimov, Mm, Baltar, F, Bodrossy, L, Van De Kamp, J, Frampton, Dmf, Ostrowski, M, Van Ruth, P, Malthouse, P, Claus, S, Deneudt, K, Mortelmans, J, Pitois, S, Wallom, D, Salter, I, Costa, R, Schroeder, Dc, Kandil, Mm, Amaral, V, Biancalana, F, Santana, R, Pedrotti, Ml, Yoshida, T, Ogata, H, Ingleton, T, Munnik, K, Rodriguez-Ezpeleta, N, Berteaux-Lecellier, V, Wecker, P, Cancio, I, Vaulot, D, Bienhold, C, Ghazal, H, Chaouni, B, Essayeh, S, Ettamimi, S, Zaid, E, Boukhatem, N, Bouali, A, Chahboune, R, Barrijal, S, Timinouni, M, El Otmani, F, Bennani, M, Mea, M, Todorova, N, Karamfilov, V, ten Hoopen, P, Cochrane, G, L'Haridon, S, Bizsel, Kc, Vezzi, A, Lauro, Fm, Martin, P, Jensen, Rm, Hinks, J, Gebbels, S, Rosselli, R, De Pascale, F, Schiavon, R, dos Santos, A, Villar, E, Pesant, S, Cataletto, B, Malfatti, F, Edirisinghe, R, Silveira, Jah, Barbier, M, Turk, V, Tinta, T, Fuller, Wj, Salihoglu, I, Serakinci, N, Ergoren, Mc, Bresnan, E, Iriberri, J, Nyhus, Paf, Bente, E, Karlsen, He, Golyshin, Pn, Gasol, Jm, Moncheva, S, Dzhembekova, N, Johnson, Z, Sinigalliano, Cd, Gidley, Ml, Zingone, A, Danovaro, R, Tsiamis, G, Clark, M, Costa, Ac, El Bour, M, Martins, Am, Collins, Re, Ducluzeau, Al, Martinez, J, Costello, Mj, Amaral-Zettler, La, Gilbert, Ja, Davies, N, Field, D, Glockner, Fo, European Commission, University of Oxford [Oxford], Israel Oceanographic and Limnological Research - IOLR (ISRAEL), Danmarks Tekniske Universitet (DTU), Carl Von Ossietzky Universität Oldenburg, Universidade de Lisboa (ULISBOA), Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Universidad de la República [Montevideo] (UCUR), Kyoto University [Kyoto], Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), University of Mohammed V, Sidi Mohammed Ben Abdellah University, Universita degli Studi di Padova, Rajarata University of Sri-Lanka, University of Patras [Patras], University of California [Berkeley], and University of California-University of California

Subjects
0106 biological sciences, Biodiversity, Marine life, 01 natural sciences, Bacteria, Genomics, Health Index, Marine, Metagenomics, Micro B3, Microorganism, OSD, Ocean sampling day, Standards, 11. Sustainability, Data and Information, Ocean Sampling Day, biodiversity, genomics, health index, bacteria, microorganism, metagenomics, marine, standards, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, Environmental resource management, Geology, Computer Science Applications, Interdisciplinary Natural Sciences, Microbial biodiversity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ocean sampling day, OSD, Biodiversity, Genomics, Health Index, Bacteria, Microorganism, Metagenomics,Marine, Micro B3, Standards, Oceans and Seas, Microorganisms, Marine Biology, Health Informatics, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Ecology and Environment, Metagenomic, 03 medical and health sciences, Health index, Medisinske Fag: 700 [VDP], SDG 14 - Life Below Water, 14. Life underwater, 030304 developmental biology, business.industry, 010604 marine biology & hydrobiology, Ocean sampling, 13. Climate action, Commentary, Genomic, Database Management Systems, Global Ocean, business
Abstract

Kopf, Anna ... et. al.-- 5 pages, 1 figure.-- This manuscript is NOAA-GLERL contribution number 1763, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits, This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589

Published
2015

15. Gene disruption and basic phenotypic analysis of nine novel yeast genes from chromosome XIV

Author

Stefano Campanaro, Giorgio Valle, Francesca Sartorello, Michela D'Angelo, Alessandro Vezzi, Chiara Capozzo, and Francesca Dal Pero

Subjects
Genetics, Saccharomyces cerevisiae, Bioengineering, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Biochemistry, Molecular biology, Phenotype, Homology (biology), Green fluorescent protein, Essential gene, ORFS, Ploidy, Gene, Biotechnology
Abstract

In this work, we describe the disruption of nine ORFs of S. cerevisiae (YNL123w, YNL119w, YNL115c, YNL108c, YNL110c, YNL124w, YNL233w, YNL232w and YNL231c) in two genetic backgrounds: FY1679 and CEN.PK2. For the construction of the deletant strains, we used the strategy of short flanking homology (SFH) PCR. The SFH-deletion cassette was made by PCR amplification of the KanMX4 module with primers containing a 5′ region of 40 bases homologous to the target yeast gene and with a 3′ region of 20 bases homologous to pFA6a–KanMX4 MCS. Sporulation and tetrad analysis of heterozygous deletants revealed that YNL110c, YNL124w and YNL232w are essential genes. The subcellular localization of the protein encoded by the essential gene YNL110c was investigated using the green fluorescent protein (GFP) approach, revealing a nuclear pattern. Basic phenotypic analysis of the non-essential genes revealed that the growth of ynl119wΔ haploid cells was severely affected at 37°C in N3 medium, indicating that this gene is required at high temperatures with glycerol as a non-fermentable substrate. The ynl233wΔ haploid cells also showed a particular phenotype under light microscopy and were studied in detail in a separate work. Copyright © 2000 John Wiley & Sons, Ltd.

Published
2000

16. Life at Depth: Photobacterium profundum Genome Sequence and Expression Analysis

Author

Alessandro Cestaro, Dh Bartlett, Stefano Campanaro, Francesca Simonato, Nicola Cannata, Barbara Simionati, Alessandro Vezzi, Chiara Romualdi, G Malacrida, Giorgio Valle, Michela D'Angelo, Fm Lauro, and Nicola Vitulo

Subjects
Geologic Sediments, Transcription, Genetic, Amino Acid Transport Systems, Physiological, Hydrostatic pressure, Genome, Chromosomes, Open Reading Frames, Genetic, Polysaccharides, Piezophile, Hydrostatic Pressure, Extreme environment, Seawater, Adaptation, rRNA Operon, Oligonucleotide Array Sequence Analysis, Whole genome sequencing, Multidisciplinary, biology, Photobacterium, Gene Expression Profiling, Bacterial, Photobacterium profundum, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, DNA, Chromosomes, Bacterial, biology.organism_classification, Adaptation, Physiological, Atmospheric Pressure, Genes, Gene Expression Regulation, Genes, Bacterial, Evolutionary biology, Carbohydrate Metabolism, Genome, Bacterial, RRNA Operon, Transcription, Sequence Analysis
Abstract

Deep-sea life requires adaptation to high pressure, an extreme yet common condition given that oceans cover 70% of Earth's surface and have an average depth of 3800 meters. Survival at such depths requires specific adaptation but, compared with other extreme conditions, high pressure has received little attention. Recently, Photobacterium profundum strain SS9 has been adopted as a model for piezophily. Here we report its genome sequence (6.4 megabase pairs) and transcriptome analysis. The results provide a first glimpse into the molecular basis for life in the largest portion of the biosphere, revealing high metabolic versatility.

Published
2005

17. A snapshot of the emerging tomato genome sequence

Author

Sandra Knapp, Ying Wang, Antonio Granell, Dongyu Qu, Erika Asamizu, Pierre Frasse, Hongling Jiang, Mohamed Zouine, Pradeep Kumar Singh, Vivek Dalal, Luigi Frusciante, Robert M. Buels, Hans de Jong, Dongyuan Liu, James J. Giovannoni, Sander Peters, Sarita, Satoshi Tabata, Isaak Y. Tecle, Mara Ercolano, Jun Wang, Longfei Liu, Rekha Dixit, Heiko Schoof, Yongbiao Xue, Kishor Gaikwad, Julia Vrebalov, Alessandra Traini, Nunzio D’Agostino, Ruth White, Zhibiao Ye, Amparo Mico, Cheol-Goo Hur, Jitendra P. Khurana, Roderic Guigó, Arun Sharma, Paramjit Khurana, Jiuhai Zhao, Hiroyuki Fukuoka, Byung-Dong Kim, Smriti Shridhar, René Klein Lankhorst, Yuanyuan Dai, Dani Zamir, Sumera Praveen, Helen Beasley, Manuel Spannagl, Erwin Datema, Klaus X.F. Mayer, Yves Van de Peer, Akhilesh K. Tyagi, Aureliano Bombarely, P. Lindhout, Mark Fiers, Silvana Grandillo, Jane Rogers, Zhangjun Fei, Changbao Li, Giorgio Valle, Karen McLaren, Alok Singh, Sung-Hwan Jo, Sarah Butcher, Willem J. Stiekema, Murielle Philippot, Huajie Fan, Glenn J. Bryan, Fei Lu, Doil Choi, Jun He, Daniel W. A. Buchan, Stephane Rombauts, Jinfeng Chen, Yongchen Du, Xiao-Hua Yang, Shailendra Vyas, Daisuke Shibata, Maria Luisa Chiusano, Rajesh Kumar, Song Bin Chang, Marjo J. van Staveren, Gerard J. Bishop, Victoria Fernandez-Pedrosa, Hong-Qing Ling, Graham B. Seymour, Lukas A. Mueller, Mondher Bouzayen, Stephen M. Stack, Rémy Bruggmann, Ajay Kumar, Zhonghua Zhang, Christine Nicholson, Guoping Wang, Saloni Mathur, Sean Humphray, Vikrant Gupta, Jinfeng Shi, Roeland C. H. J. van Ham, Debasis Chattopadhyay, Amolkumar U. Solanke, Mingsheng Chen, Shusei Sato, Sanwen Huang, Sonia Osorio, Chen Lu, Zhukuan Cheng, Tilak Raj Sharma, Dóra Szinay, James Abbott, Awadhesh Pandit, Yu Geng, Mahavir Yadav, Sara Todesco, Manuel Pérez-Alonso, Giovanni Giuliano, Amalia Barone, Trilochan Mohapatra, Irfan Ahmad Ghazi, Wencai Yang, Francisco Camara, Giulia Falcone, Anika Jöcker, Clare Riddle, Alessandro Vezzi, Jianjun Chen, Shouhong Sun, Marco Pietrella, Joyce Van Eck, Lindsay A. Shearer, Adri A. Mills, Steven D. Tanksley, Miguel A. Botella, Chuanyou Li, Sarah Sims, Farid Regad, Jeffrey A. Fawcett, Parul Chowdhury, Naama Menda, Suzanne M. Royer, Nagendra K. Singh, Mueller, L. A., Lankhorst, R. K., Tanksley, S. D., Giovannoni, J. J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A. A., Menda, N., Tecle, I. Y., Bombarely, A., Stack, S., Royer, S. M., Chang, S. B., Shearer, L. A., Kim, B. D., Jo, S. H., Hur, C. G., Choi, D., Li, C. B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G. B., Bishop, G. J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., Mclaren, K., Mathur, S., Vyas, S., Solanke, A. U., Kumar, R., Gupta, V., Sharma, A. K., Khurana, P., Khurana, J. P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I. A., Gaikwad, K., Sharma, T. R., Mohapatra, T., Singh, N. K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M. W. E. J., van Ham, R. C. H. J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M. A., Perez Alonso, M., Fernandez Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, Nunzio, Chiusano, MARIA LUISA, Ercolano, MARIA RAFFAELLA, Barone, Amalia, Frusciante, Luigi, Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K. X. F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J. A., Van de Peer, Y., Knapp, S., Zamir, D., and Stiekema, W.

Subjects
0106 biological sciences, lcsh:QH426-470, Bioinformatics, Genomics, Plant Science, Computational biology, lcsh:Plant culture, Biology, Laboratorium voor Erfelijkheidsleer, ENCODE, 01 natural sciences, Genome, 03 medical and health sciences, Laboratorium voor Plantenveredeling, Bioinformatica, Genetics, Life Science, lcsh:SB1-1110, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Bacterial artificial chromosome, EPS-4, fungi, food and beverages, Biology and Life Sciences, Genome project, PRI Bioscience, lcsh:Genetics, Plant Breeding, GenBank, Laboratory of Genetics, Agronomy and Crop Science, 010606 plant biology & botany, Reference genome
Abstract

The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Published
2009

18. PABS: an online platform to assist BAC-by-BAC sequencing projects

Author

Michela D'Angelo, Fabrizio Levorin, Sara Todesco, Giorgio Valle, Alessandro Vezzi, Davide Campagna, and Riccardo Schiavon

Subjects
Genetics, Chromosomes, Artificial, Bacterial, Internet, Contig, Base Sequence, Shotgun sequencing, Molecular Sequence Data, food and beverages, Computational Biology, Hybrid genome assembly, Computational biology, Sequence Analysis, DNA, Biology, Pipeline (software), Genome, General Biochemistry, Genetics and Molecular Biology, Deep sequencing, DNA sequencing, genome sequencing, Solanum lycopersicum, Primer walking, Genome, Plant, Biotechnology
Abstract

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC.

Published
2008

19. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile

Author

Alessandro Vezzi, Nicola Vitulo, Stefano Campanaro, Chiara Romualdi, and Giorgio Valle

Subjects
Chromosome Mapping, DNA Mutational Analysis, Genetic Variation, Genome, Bacterial, Phylogeny, Species Specificity, Vibrionaceae, Biological Evolution, Evolution, Molecular, Evolution, lcsh:Computer applications to medicine. Medical informatics, Genome, Biochemistry, Structural Biology, Phylogenetics, ORFS, Gene, Molecular Biology, lcsh:QH301-705.5, Genetics, biology, Phylogenetic tree, Applied Mathematics, Research, Bacterial, Photobacterium profundum, Molecular, Phylogenetic network, biology.organism_classification, Computer Science Applications, lcsh:Biology (General), Evolutionary biology, Horizontal gene transfer, lcsh:R858-859.7
Abstract

Background Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In this work we propose an improved phylogenetic profile analysis on 14 Vibrionaceae genomes, to study the evolution of this family on the basis of gene content. The phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently present or absent within different genomes. This allows the prediction of hypothetical functions on the basis of a shared phylogenetic profiles. Moreover this approach is useful to identify putative laterally transferred elements on the basis of their presence on distantly phylogenetically related bacteria. Results Vibrionaceae ORFs were aligned against all the available bacterial proteomes. Phylogenetic profile is defined as an array of distances, based on aminoacid substitution matrixes, from single genes to all their orthologues. Final phylogenetic profiles, derived from non-redundant list of all ORFs, was defined as the median of all the profiles belonging to the cluster. The resulting phylogenetic profiles matrix contains gene clusters on the rows and organisms on the columns. Cluster analysis identified groups of "core genes" with a widespread high similarity across all the organisms and several clusters that contain genes homologous only to a limited set of organisms. On each of these clusters, COG class enrichment has been calculated. The analysis reveals that clusters of core genes have the highest number of enriched classes, while the others are enriched just for few of them like DNA replication, recombination and repair. Conclusion We found that mobile elements have heterogeneous profiles not only across the entire set of organisms, but also within Vibrionaceae; this confirms their great influence on bacteria evolution even inside the same family. Furthermore, several hypothetical proteins highly correlate with mobile elements profiles suggesting a possible horizontal transfer mechanism for the evolution of these genes. Finally, we suggested the putative role of some ORFs having an unknown function on the basis of their phylogenetic profile similarity to well characterized genes.

Published
2007

20. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Author

Graziano Pesole, Benjamin Noel, François Artiguenave, Alberto Policriti, Federica Cattonaro, Alessandro Vezzi, Delphine Jublot, Valérie Laucou, Michel Gouyvenoux, Eléonore Durand, Didier Merdinoglu, Cristian Del Fabbro, Giorgio Valle, Isabelle Le Clainche, Michael Alaux, Irena Juman, Erica Mica, Béatrice Segurens, Alberto Casagrande, Claude Scarpelli, Massimo Delledonne, Gabriele Di Gaspero, Jean-Marc Aury, David S. Horner, Marco Moroldo, M. Enrico Pè, Philippe Hugueney, Mario Pezzotti, Michel Caboche, Anne-Françoise Adam-Blondon, Véronique Anthouard, Nicola Vitulo, Alain Lecharny, Alain Billault, Virginie Vico, Olivier Jaillon, Christian Clepet, Sébastien Aubourg, Michele Morgante, Jean Weissenbach, Patrick Wincker, Nathalie Choisne, Aurélie Canaguier, Corinne Dasilva, Edgardo Ugarte, Philippe Chatelet, Clémence Bruyère, Vincent Dumas, Sophie Paillard, Fabrice Legeai, Nicoletta Felice, Simone Scalabrin, G Malacrida, Julie Poulain, Francis Quetier, Claire Jubin, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Università degli Studi di Udine - University of Udine [Italie], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), CRIBI (CRIBI), Università degli Studi di Padova = University of Padua (Unipd), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano = University of Milan (UNIMI), Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Istituto Tecnologie Biomediche, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Dipartimento Scientifico e Tecnologico (DST), Università degli studi di Verona = University of Verona (UNIVR), Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, VIGNA-CRA Initiative (VIGNA-CRA INITIATIVE), Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Universita degli Studi di Padova, Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Verona (UNIVR), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Milano [Milano], Università degli studi di Bari, Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Università degli Studi di Verona, O., Jaillon, J., Aury, B., Noel, A., Policriti, C., Clepet, Casagrande, Alberto, N., Choisne, S., Aubourg, N., Vitulo, C., Jubin, A., Vezzi, F., Legeai, P., Hugueney, C., Dasilva, D., Horner, E., Mica, D., Jublot, J., Poulain, C., Bruyère, A., Billault, B., Seguren, M., Gouyvenoux, E., Ugarte, F., Cattonaro, V., Anthouard, V., Vico, C., DEL FABBRO, M., Alaux, G., DI GASPERO, V., Duma, N., Felice, S., Paillard, I., Juman, M., Moroldo, S., Scalabrin, A., Canaguier, I., LE CLAINCHE, G., Malacrida, E., Durand, G., Pesole, V., Laucou, P., Chatelet, D., Merdinoglu, M., Delledonne, M., Pezzotti, A., Lecharny, C., Scarpelli, F., Artiguenave, M. E., Pè, G., Valle, M., Morgante, M., Caboche, A., ADAM BLONDON, J., Weissenbach, F., Quétier, and P., Wincker

Subjects
0106 biological sciences, genotype, Arabidopsis, POLYPLOIDY, adaptation, 01 natural sciences, Genome, RNA, Transfer, Gene duplication, plant genomics, plant genome evolution, Sequencing, Vitis, vitis vinifera, genome sequencing, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, Multidisciplinary, food and beverages, Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Paleopolyploidy, Populus, RNA, Plant, ARABIDOPSIS-THALIANA, DNA-SEQUENCE, GENE, DUPLICATION, MAP, IDENTIFICATION, EVOLUTION, DNA, Intergenic, vine, Genome, Plant, assembly, Bioinformatics, Molecular Sequence Data, Genomics, Biology, Genes, Plant, Monocotyledon, DNA sequencing, Evolution, Molecular, Polyploidy, 03 medical and health sciences, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, angiosperm, genome, 030304 developmental biology, Whole genome sequencing, fungi, Oryza, Sequence Analysis, DNA, 15. Life on land, chronology, Introns, grapevine, MicroRNAs, polyploidy, Karyotyping, vitis classification, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract

International audience; The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

Published
2007

21. Piezophilic adaptation: a genomic point of view

Author

Douglas H. Bartlett, Nicola Vitulo, Federico M. Lauro, Stefano Campanaro, Alessandro Vezzi, Giorgio Valle, Francesca Simonato, and Michela D'Angelo

Subjects
Acclimatization, Ecology (disciplines), barophile, Hydrostatic pressure, Bioengineering, Genomics, Biology, Bacterial Physiological Phenomena, Applied Microbiology and Biotechnology, piezophile, Photobacterium profundum, Hydrostatic Pressure, Seawater, Ecosystem, high pressure, deep-sea, Biotechnology, DNA Damage, Genome, Bacterial, Photobacterium, Water Microbiology, Ecological niche, Genome, Ecology, Bacterial, General Medicine, High pressure, Food preparation, Adaptation
Abstract

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.

Published
2006

22. Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

Author

Alessandro Vezzi, Nicola Vitulo, Douglas H. Bartlett, Giulio Bertoloni, Federico M. Lauro, Stefano Campanaro, G Malacrida, Michela D'Angelo, Alessandro Cestaro, Giorgio Valle, and Francesca Simonato

Subjects
Transcription, Genetic, lcsh:QH426-470, Oceans and Seas, lcsh:Biotechnology, Models, Biological, Genome, Photobacterium profundum, Open Reading Frames, lcsh:TP248.13-248.65, Piezophile, Image Processing, Computer-Assisted, Pressure, Genetics, Seawater, RNA, Messenger, Codon, gene transfer, Phylogeny, DNA Primers, Oligonucleotide Array Sequence Analysis, biology, Strain (chemistry), Photobacterium, Temperature, Genomic signature, Gene Expression Regulation, Bacterial, biology.organism_classification, high pressure, lcsh:Genetics, Atmospheric Pressure, Gene Expression Regulation, Genes, Bacterial, RNA, Ribosomal, gene transfer, high pressure , Photobacterium profundum, Gene pool, Genome, Bacterial, GC-content, Research Article, Biotechnology
Abstract

Background Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. Results These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. Conclusion These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Published
2005

23. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Author

Jean Weissenbach, William C. Nierman, Christopher D. Town, A Perez-Perez, R. Cooke, Brian J. Haas, Samir Kaul, T Kato, Claire Fujii, J Militscher, Mitsuyo Kohara, Steven L. Salzberg, A Conrad, Hans-Werner Mewes, D. Haase, M. Scharfe, S Bangert, Hean L. Koo, W. Ansorge, Laurence Cattolico, Patrick Wincker, Rama Maiti, Marcel Salanoubat, Erika Asamizu, Bénédicte Purnelle, Luke J. Tallon, M flores, Grace Pai, P Brottier, Kumi Idesawa, Richard Holland, P Sellers, J C Venter, S Nakayama, Michela D'Angelo, Holger Erfle, Berthold Fartmann, Ai Matsuno, Elena Casacuberta, Barbara Simionati, T Wada, R Wiedelmann, Amparo Monfort, Chiaki Kiyokawa, M. Rizzo, Jeremy Peterson, D. Vitale, Joan Climent, M. Schäfer, C Takeuchi, Gertrud Mannhaupt, Terrance Shea, P Navarro, Gerald Nyakatura, Pere Puigdomènech, R Mache, Leslie A. Grivell, S. van Aken, Paolo Zaccaria, Stephen Rudd, H. Voss, B Ottenwälder, Todd Creasy, J Reichelt, C Berger-Llauro, M Laudie, K Hornischer, H Drzonek, J P Alcaraz, Kai Lemcke, M Unseld, N Jordan, C Robert, Shusei Sato, T Kimura, S Müller-Auer, Naomi Nakazaki, W Saurin, Daphne Preuss, M. de Haan, J Jenkins, Francis Quetier, D Duchemin, Xiaoying Lin, Alberto Pallavicini, A Watanabe, Petra Brandt, Klaus F. X. Mayer, Heiko Schoof, M Yamada, Javier Terol, Satoshi Tabata, Benes, John Gill, François Artiguenave, Yoshie Kishida, Nathalie Choisne, O Schön, C. Gabel, E Wurmbach, Michael A. Rieger, Alessandro Vezzi, T Kaneko, T. H. Löhnert, Owen White, G Kauer, M Matsumoto, M. Fuchs, A Walts, G Nordsiek, Michel Delseny, Shigemi Sasamoto, H Kranz, Rosario Liguori, Yasukazu Nakamura, David Masuy, H. Blöcker, De Simone, Miho Yasuda, Tamara Feldblyum, B. Obermaier, Giorgio Valle, Manuel Pérez-Alonso, Sayaka Shinpo, Kumiko Kawashima, A Cottet, Anagnostis Argiriou, T Rooney, A.C. Maarse, Dongying Wu, C Collado, T. Utterback, Claire M. Fraser, M. D. Bargues, Stefano Toppo, Marc Boutry, Akiko Muraki, Salanoubat, M., Lemcke, K., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Blocker, H., Perezalonso, M., Obermaier, B., Delseny, M., Boutry, M., Grivell, L. A., Mache, R., Puigdomenech, P., DE SIMONE, V., Choisne, N., Artiguenave, F., Robert, C., Brottier, P., Wincker, P., Cattolico, L., Weissenbach, J., Saurin, W., Quetier, F., Schafer, M., Mullerauer, S., Gabel, C., Fuchs, M., Benes, V., Wurmbach, E., Drzonek, H., Erfle, H., Jordan, N., Bangert, S., Wiedelmann, R., Kranz, H., Voss, H., Holland, R., Brandt, P., Nyakatura, G., Vezzi, A., D'Angelo, M., Pallavicini, Alberto, Toppo, S., Simionati, B., Conrad, A., Hornischer, K., Kauer, G., Lohnert, T. H., Nordsiek, G., Reichelt, J., Scharfe, M., Schon, O., Bargues, M., Terol, J., Climent, J., Navarro, P., Collado, C., Perezperez, A., Ottenwalder, B., Duchemin, D., Cooke, R., Laudie, M., Bergerllauro, C., Purnelle, B., Masuy, D., DE HAAN, M., Maarse, A. C., Alcaraz, J. P., Cottet, A., Casacuberta, E., Monfort, A., Argiriou, A., Flores, M., Liguori, R., Vitale, D., Mannhaupt, G., Haase, D., and Schoof, H.

Subjects
DNA, Plant, Sequence analysis, Arabidopsis, plant, Genome, Complete sequence, Gene Duplication, Centromere, Plant genomics, model organism, Humans, genomic structure, Gene, Plant Proteins, Genetics, Multidisciplinary, biology, Chromosome, Chromosome Mapping, Sequence Analysis, DNA, biology.organism_classification, genome sequencing, Chromosome 3, Genome, Plant
Abstract

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.

Published
2000

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