The Plant Orthology Browser: An Orthology and Gene‐Order Visualizer for Plant Comparative Genomics

Innovative web‐based orthology and annotation visualization tool Intuitive, highly interactive pairwise comparison and visualization of genomic traits Interactive synteny plots for exploration and discovery of gene impact/localization Free‐text, Google‐like search with as‐you‐type suggestions and highlighting Easy retrieval of orthologs, comparative results, and publication‐quality figures

[1]  M. Clark,et al.  Comparative Genomics , 2020, Springer US.

[2]  Henning Redestig,et al.  Homoeologs: What Are They and How Do We Infer Them? , 2016, Trends in plant science.

[3]  Dave Kudrna,et al.  Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement , 2015, Scientific Reports.

[4]  Dan M. Bolser,et al.  Ensembl Genomes 2016: more genomes, more complexity , 2015, Nucleic Acids Res..

[5]  Mihaela M. Martis,et al.  Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes , 2015, The plant genome.

[6]  Congting Ye,et al.  PlantOrDB: a genome-wide ortholog database for land plants and green algae , 2015, BMC Plant Biology.

[7]  Yi Wang,et al.  OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species , 2015, Nucleic Acids Res..

[8]  Dan Tulpan,et al.  Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants , 2015, BMC Genomics.

[9]  Yves Van de Peer,et al.  PLAZA 3.0: an access point for plant comparative genomics , 2014, Nucleic Acids Res..

[10]  J. Batley,et al.  A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome , 2014, Science.

[11]  Shelby L. Bidwell,et al.  An improved genome release (version Mt4.0) for the model legume Medicago truncatula , 2014, BMC Genomics.

[12]  Thomas Rosleff Sörensen,et al.  The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) , 2013, Nature.

[13]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[14]  Damian Szklarczyk,et al.  eggNOG v4.0: nested orthology inference across 3686 organisms , 2013, Nucleic Acids Res..

[15]  Salvador Capella-Gutiérrez,et al.  PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome , 2013, Nucleic Acids Res..

[16]  Dan M. Bolser,et al.  Gramene 2013: comparative plant genomics resources , 2013, Nucleic Acids Res..

[17]  Aaron R. Phillips,et al.  SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes , 2013, Bioinform..

[18]  C. Dessimoz,et al.  Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals , 2013, Genome biology and evolution.

[19]  Wenlong Yang,et al.  Draft genome of the wheat A-genome progenitor Triticum urartu , 2013, Nature.

[20]  Huanming Yang,et al.  Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation , 2013, Nature.

[21]  Tae-Ho Lee,et al.  PGDD: a database of gene and genome duplication in plants , 2012, Nucleic Acids Res..

[22]  Evgeny M. Zdobnov,et al.  OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs , 2012, Nucleic Acids Res..

[23]  Eugene V. Koonin,et al.  A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes , 2012, Genome biology and evolution.

[24]  Saravanaraj N. Ayyampalayam,et al.  The banana (Musa acuminata) genome and the evolution of monocotyledonous plants , 2012, Nature.

[25]  Justin N. Vaughn,et al.  Reference genome sequence of the model plant Setaria , 2012, Nature Biotechnology.

[26]  Jian Wang,et al.  Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential , 2012, Nature Biotechnology.

[27]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[28]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[29]  Souhir Marsit,et al.  Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters , 2011, Bioinform..

[30]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[31]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..

[32]  Leszek P. Pryszcz,et al.  MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score , 2010, Nucleic acids research.

[33]  Gaston H. Gonnet,et al.  OMA 2011: orthology inference among 1000 complete genomes , 2010, Nucleic Acids Res..

[34]  Mark Gerstein,et al.  Getting Started in Gene Orthology and Functional Analysis , 2010, PLoS Comput. Biol..

[35]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[36]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[37]  Erik L. L. Sonnhammer,et al.  InParanoid 7: new algorithms and tools for eukaryotic orthology analysis , 2009, Nucleic Acids Res..

[38]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[39]  Christophe Dessimoz,et al.  Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..

[40]  Matthew R. Laird,et al.  InnateDB: facilitating systems-level analyses of the mammalian innate immune response , 2008, Molecular systems biology.

[41]  H. Budak,et al.  Brachypodium Genomics , 2008, International journal of plant genomics.

[42]  Tao Liu,et al.  TreeFam: 2008 Update , 2007, Nucleic Acids Res..

[43]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[44]  Nicholas H. Putnam,et al.  The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation , 2007, Proceedings of the National Academy of Sciences.

[45]  Leonid Peshkin,et al.  Roundup: a multi-genome repository of orthologs and evolutionary distances , 2006, Bioinform..

[46]  Feng Chen,et al.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..

[47]  Berend Snel,et al.  Keeping Afloat: A Strategy for Small Island Nations , 2005, BMC Bioinformatics.

[48]  Steven Salzberg,et al.  DAGchainer: a tool for mining segmental genome duplications and synteny , 2004, Bioinform..

[49]  Andreas Graner,et al.  A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. , 2004, The Plant journal : for cell and molecular biology.

[50]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[51]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[52]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[53]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[54]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[55]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[56]  Duncan J. Quincey,et al.  Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement , 2018 .

[57]  Matthew R. Laird,et al.  BMC Bioinformatics BioMed Central Methodology article Improving the specificity of high-throughput ortholog prediction , 2006 .

[58]  Z. Chen,et al.  Evolution of genome size in Brassicaceae. , 2005, Annals of botany.

[59]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.