Plant ortholog database. database construction.

Plant ortholog database 5. Adrian M. absence of a gold standard for plant ortholog y. It is no longer easy to JGI Plant Gene Atlas Gene expression across diverse plant species. , 2015), PO B uses . More info about data types here. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants. database construction. Nucleic Acids Research , 45(D1):D1040-D1045. 2008; Gupta et al. 1 gene annotation, with links to wheat expression browser and KnetMiner 17 wheat cultivars from the 10+ genome project and other sources including comparative analysis across the different lines Panel d : Pairwise Ortholog Gene Details from publication: PlantOrDB: A genome-wide ortholog database for land plants and green algae | Genes with different functions are originally generated from Mar 15, 2006 · The OrthologID Web application is developed, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-Based Orthology determination on a genomic scale possible. Data are mean ± s. The highly interactive web interfaces provided by PlantOrDB can display useful information on individual gene, and its homolog gene families and ortholog genes interactively and dynamically. Jun 1, 2015 · Foxtail millet (Setaria italica) is a member of the Poaceae grasses that was initially domesticated from the wild species of S. However, one cannot assume that it is an ortholog, because the “true” ortholog in species X may reside in the unsequenced portion of that genome. There are 798,547 plants, and 881,222 images in this world class database of plants, which is collaboratively developed by over 5,000 Garden. It is widely accepted that orthologs are homologous genes evolved from Background <p>Genes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. sativa), using the alga Chlamydomonas as outgroup. Built on 35 plant and 6 green algal genomes released from Phytozome v9, PlantOrDB is a genome-wide ortholog database for land plants and green algae. biomedcentral. 0: Accessibility: Eukaryotes 1,271: Prokaryotes 6,013: Genes 37M: Loading. 0 assembly from the IWGSC, including: The IWGSC RefSeq v1. d. Jul 31, 2008 · Lipocalins are a large and diverse family of small, mostly extracellular proteins implicated in many important functions. , species X) against Arabidopsis, it often is possible to identify a highly significant homolog(s) in the Arabidopsis genome. Jun 1, 2006 · A plant-specific ortholog database called OrthologID was recently built [22] from the three finished plant genomes (A. org members from around the globe. Nucleic Acids Res. See full list on bmcplantbiol. Select the matching entry from the suggestions menu or you can select the orthologs option (e. Jun 26, 2015 · PlantOrDB: a genome-wide ortholog database for land plants and green algae. The POB provides gene-order and synteny visualization capabilities of orthologous genes and their functional annotations. . descendants from a single gene of the last common ancestor, are termed orthologs and referred to below as ortholog groups or OGs (1, 2). thaliana protein(s) and sequences from other plant Plant GARDEN (Genome And Resource Database Entry) is a portal site that curates genome and marker information of various plant species. The PlanTAPDB developed by Rensing and his colleagues is a comprehensive phylogeny-based resource of plant transcription associated proteins ( 9). sativa / A. Result of our automatic clustering is manually annotated and analyzed by a phylogenetic-based approach to predict homologous relationships. Feb 1, 2008 · Using the plant comparative genomics database, the homologs of a functional gene in different species can be quickly explored (Conte et al. Mar 1, 2017 · Here, we present the POB (http://nrcmonsrv01. 2016;Irish and Benfey 2004). It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, crop information, automated tools, web links, and references. The JGI Plant Gene Atlas is an updateable transcriptome resource generated from a multi-laboratory collaboration following documented growth, sequencing and data analysis protocols for a number of evolutionarily distant JGI flagship plant species. GreenPhylDB: a database for plant comparative genomics GreenPhylDB: a database for plant comparative genomics. This family has been studied in bacteria, invertebrate and vertebrate animals but little is known about these proteins in plants. Altenhoff, Adrian Schneider, Gaston H. The Ortholuge method improves the specificity of high-throughput orthology prediction. I can go for such a search in Gramene database. miamioh. Amino acid sequences of 73 species (62 land plants and 11 green algae), containing 2,682,261 sequences, were obtained from the National Center for Biotechnology Information (NCBI) Reference Sequence database. MOTIVATION The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of Dec 8, 2022 · Sets of TF binding motifs for 156 species (157 organisms) Back to Top A set of manually curated, non-redundancy and high-quality TF binding Motifs derived from experiments (Motif information, All motifs in one file, and Individual motifs) are projected to 156 species using BLAST reciprocal best hits in the same family (see Methods for details). We provide browsable orthology predictions, APIs, flat file downloads and a standalone version of the inference algorithm. e. Zahn-Zabal et al. Ensembl Plants hosts the RefSeq v1. Canonical protein sequences of the gene in fasta format were downloaded from the UniProtKB (Swiss-Prot) database for each taxon ID. With the rapid increase of genomic data, identifying and The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the United States and its territories. Reconstructing ancestral genome content based on symmetrical best alignments Jan 1, 2006 · Affiliation 1 Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104-6018, USA. The PGDBj Ortholog Database, created under the auspices of the Plant Genome Database Japan (PGDBj), contains information about orthologous genes in plants based on their corresponding amino acid sequence similarity. Integrating new plant genomes is then not only needed to correct for the pseudo-ortholog bias described above, but it can also help functional transfer from and to model plant species. , 2014) using the non-redundant plant division of UniProtKB in order to remove spurious annotations. To find orthologs enter a gene symbol (e. Starting from genome sequence information for over 35 plant Dec 8, 2022 · Plant transcription factor database, a portal for the functional and evolutionary study of plant transcription factors PlantTFDB - Plant Transcription Factor Database @ CBI, PKU PlantRegMap /PlantTFDB v5. EZlab BUSCO LEMMI miRmap NewickUtils Jan 7, 2025 · Background Ortholog prediction, essential for various genomic research areas, faces growing inconsistencies amidst the expanding array of ortholog databases. thaliana protein(s) and sequences from other plant species. Jan 1, 2025 · The KO (KEGG Orthology) database is a database of molecular functions represented in terms of functional orthologs. sativa/A. Using 35 plant and 6 green algal genomes from Phytozome v9, we clustered 1,291,670 peptide sequences into 49,355 homologous gene families in terms of sequence similarity. , 2010). primate RAG1). Feb 19, 2015 · I would like to know any resources available for ortholog genes/proteins of a set of rice genes. (B) The flowering time of plants in (A) indicated by rosette leaf numbers at bolting. The following component databases can be accessed directly: the Ortholog DB (b), the DNA marker DB (c) and the See also. 0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. TreeFam is a database of phylogenetic trees of gene families found in animals. Dozens of ortholog resources have been available and broadly used over the past decades. com Plant Homolog Database is a database composed of plant homologous genes. , Nishide H. It is widely accepted that orthologs are homologous genes evolved from Apr 10, 2019 · Land plants originated from charophytes, came ashore as bryophytes, and then evolved as vascular plants including gymnosperms and angiosperms (Harrison, 2017). Plant comparative genomics database, focusing on dicots, monocots and green algae. Orthologs are the cornerstone of almost all comparative genomics studies. Keywords: Homolog, Ortholog, Paralog, Database, Land plants, Green algae, Gene family, PlantOrDB Background Genes with different functions are originally generated from some ancestral genes by gene duplication, muta-tion and functional recombination. thaliana and P. Search for Cluster of Orthologous Groups (COG), pairwise orthology predictions, functional annotation and phylogenetic data for more than 2000 species. How To ︎ About this site ︎ The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The common strategy of computing consensus orthologs introduces additional arbitrariness, emphasizing the need to examine the causes of such inconsistencies and identify proteins Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. Latest News. ( 8) has constructed a database of transcription factors for five plant species and made the first attempt for construction of a comprehensive plant transcription factor database. Similarity scores between all the pairs of amino acid sequences in the Sequence DB were calculated by the BLAST with default parameters. Initially, we planned to cluster and run phylogenomic analyses in four plant genomes, but we rapidly observed that annotation quality was a major limiting point. It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events. OrthoDB is the largest resource of evolutionary and functional annotations of orthologs, relating genes across animal, plant, fungal, protist, bacterial, and viral genomes. trichocarpa, O. Dec 19, 2013 · The PGDBj portal website ( The cross-search form on the front page is shown in (a). Dec 17, 2016 · PLAZA 3. With excellent Affiliations 1 Department of Genome Informatics, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. trichocarpa (Figure 1A), and protein pairs highlight in green confirmed the ortholog relationships between human and A. Eukaryotes 5,827: Prokaryotes 18,158: Viruses 7,962: Genes : Loading. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. The PO is under active development to expand to encompass terms and annotations from all plants. trichocarpa. The common strategy of computing consensus orthologs introduces additional arbitrariness, emphasizing the need to examine the causes of such inconsistencies and identify proteins susceptible to prediction errors. Nov 5, 2007 · GreenPhylDB also provides bootstrap support for ortholog predictions to quantify reliability of prediction and tree construction. , 2009). Citations (13) References . Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. To explore the evolutionary relationship between these genes, a collinear graph was constructed comparing human, A. thaliana putative orthologs, a feature missing in all other plant ortholog databases. Year founded: 2007: Last update: 2007-01-01: Version: v1. EZlab BUSCO LEMMI miRmap NewickUtils Nov 5, 2018 · Homologs with a reference to a specific phylogeny radiation, i. To adjust to the rather severe aspects of land environments relative to water environments, plant gene copy numbers have amplified over time, and genes have diversified after duplication (Zhang, 2003; Rensing et al. ca/pob/), an interactive web-based gene orthology and annotation visualization browser that uses 1,021,611 predicted orthologs from 20 plant species. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. Finally, users can insert their own sequences from another plant species and search for O. It combines phylogenetic and heuristic best-match approaches, yielding an accurate collection of more than 14,000 homologous groups covering multiple different species (including rice, Arabidopsis thaliana, tomato, maize, sorghum, etc). The calculation was divided into organism pairs and done for each of those pairs in two directions, i. (C) Flowering time comparison of EL8 with WT, 35S::AGL24 and Aug 11, 2015 · Therefore, gene descriptions (taken from the closest plant ortholog), GO terms, Enzyme Commission codes (ECs), and InterPro signatures were provided by Sma3s (Muñoz-Mérida et al. Using gene models for 20 fully sequenced plant genomes, … Jan 1, 2025 · The first of these is the Functional Annotation module, which (1) incorporates ortholog information by integrating OrthoLoger [7] to map orthologs to OrthoDB v12 [11]; (2) implements DIAMOND [17] to align sequences against the UniProtKB-Plants [18] (Viridiplantae) database, which now includes algae in recognition of the evolutionary importance Integrating new plant genomes is then not only needed to correct for the pseudo-ortholog bias described above, but it can also help functional transfer from and to model plant species. Please help EMBL-EBI keep the data flowing to the scientific community! Uchiyama I. For example, if I upload a list of genes and select the target plant organisms, it need to show the ortholog ids of the selected plants (any standard ids). 3 Similarity Database. In the following years, we built a database of plant TFs (PlantTFDB, http Mar 1, 2017 · The synteny view page consists of three parts: (i) a form where the user can select the two plant species, the type of orthology prediction, and the chromosomes in each plant; (ii) a plotting area, which includes an interactive dot plot representation of orthologs; and (iii) an interactive information area with three tabs (genes, blocks University/Institution: Peking University: Address: 1 State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People’s Republic of China. , the sequences of one organism and those of another were reciprocally used for the queries and the DB of the BLAST calculation. Machine learning-based integration of 17 ortholog prediction methods. Results We introduce the We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel bl … DATABASE Open Access PlantOrDB: a genome-wide ortholog database for land plants and green algae Lei Li1,2, Guoli Ji1,4*, Congting Ye1,2, Changlong Shu3, Jie Zhang3 and Chun Liang2,3* Abstract Oct 10, 2024 · The ortholog database gives a detailed account of the genetic information of the plant species which can be accessed through an amino acid or keyword information search. g. thaliana, P. , Mihara M. KEGG maps were retrieved directly from the KEGG site using the Ortholog-Finder is a tool developed to build ortholog data sets for phylogenetic analysis. nrc. DATABASE Open Access PlantOrDB: a genome-wide ortholog database for land plants and green algae Lei Li1,2, Guoli Ji1,4*, Congting Ye1,2, Changlong Shu3, Jie Zhang3 and Chun Liang2,3* Abstract Jan 7, 2025 · Background: Ortholog prediction, essential for various genomic research areas, faces growing inconsistencies amidst the expanding array of ortholog databases. For each gene family, we have generated a peptide sequence alignment and phylogenetic tree, and identified the speciation/duplication events for every node within the tree. A functional ortholog is manually defined in the context of KEGG molecular networks, namely, KEGG pathway maps, BRITE hierarchies and KEGG modules, and is given a KO identifier called K number. After revisions, this will be a very valuable resource for many biologists seeking to use this tool. But I would like to scan some more plant species. Jun 26, 2015 · Background: Genes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. The marker and QTL section includes an array of information related to the sequence-tagged DNA markers thereby enhancing a more accurate and precise genome comparisons between The OMA orthology database in 2015: function predictions, better plant support, synteny view, and other improvements Nucleic Acids Research, 2015, 43(D1): D240-D249 Full text. 2. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. 5) was used to search for ortholog genes to evaluate the overlap between human aging genes and genomes of other model species. OMA is a method and database for the inference of orthologs among complete genomes. Foxtail millet is distributed in natural and agricultural ecosystems worldwide, and it is grown as a cereal crop for both human food and fodder (Bettinger et al. Apr 10, 2019 · We designed the Gcorn plant database for the retrieval of information on homology and evolution of a plant gene of interest. ( View more stats ) » View our plant-specific databases. 0 Dec 8, 2022 · ©2010-2022, Center for Bioinformatics, Peking University Last Modified: 2022-12-08 Questions or Comments, please contact Aug 10, 2015 · POGs/PlantRBP is a relational database that integrates data from rice, Arabidopsis, and maize by placing the complete Arabidopsis and rice proteomes and available maize sequences into ‘putative orthologous groups’ (POGs). 6 days ago · The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. PGDBj Ortholog DB is a database that provides orthologous relationships of genes that are computationally determined according to similarities between amino acid sequences, and currently consists of 40 species of Viridiplantae (green plants) and 213 species of Cyanobacteria (blue-green algae). However, the inconsistency between these resources has drawn growing concerns, especially when more proteomes are available and ortholog databases expand. With the rapid increase of genomic data, identifying and distinguishing these Built on 35 plant and 6 green algal genomes released from Phytozome v9, PlantOrDB is a genome-wide ortholog database for land plants and green algae. Jun 26, 2015 · Keywords: Homolog, Ortholog, Paralog, Database, Land plants, Green algae, Gene family, PlantOrDB Background Genes with different functions are originally generated Jun 26, 2015 · Built on 35 plant and 6 green algal genomes released from Phytozome v9, PlantOrDB is a genome-wide ortholog database for land plants and green algae. Rag1 orthologs) to see all … Continue reading Searching for orthologous genes at NCBI → nomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. viridis in Northern China over 8700 years ago (Barton et al. , 2013) and Plaza (Proost et al. Year founded: 2006: Last update: Version: Accessibility: Keywords: Homolog, Ortholog, Paralog, Database, Land plants, Green algae, Gene family, PlantOrDB Background Genes with different functions are originally generated from some ancestral genes by gene duplication, muta-tion and functional recombination. The ever increasing body of information on genomics and functional genomics from model plants, and new tools of comparative genomics, provide an opportunity to accelerate the development of molecular markers for increasing the efficiency of breeding of lesser studied crops, so-called “orphan crops. The PlanTAPDB developed by Rensing and his colleagues is a comprehensive phylogeny-based resource of plant transcription associated proteins ( 9 ). from 20 plants of each line. 2015; 43:D270–D276. Expand This FAIRsharing record describes: The PGDBj Ortholog Database, created under the auspices of the Plant Genome Database Japan (PGDBj), contains information about orthologous genes in plants based on their corresponding amino acid sequence similarity. HMMER search. RAG1) or a gene symbol combined with a taxonomic group (e. Dec 17, 2016 · 3. ” Conserved ortholog set (COS) markers represent orthologous genes in widely divergent plant 3. Dec 25, 2024 · An OrthoFinder tool (v2. PlantOrDB offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research. [PMC free article] [Google Scholar] 11. Synteny Analysis and Gene Structure Visualization. With the rapid increase of genomic data, identifying and distinguishing these Feb 11, 2022 · Orthology prediction is challenging yet rewarding. edu/plantordb ) is a genome-wide ortholog database for land plants and green algae. ; 2 Department of It contains annotated plant abiotic stress ortholog sets which will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics. , 2008; Hori et al Apr 21, 2008 · Integrating new plant genomes is then not only needed to correct for the pseudo-ortholog bias described above, but it can also help functional transfer from and to model plant species. Here we present PlantExp (Figure 1 ), a web-based retrieval and analysis platform that builds upon 131 423 publicly available RNA-seq samples from 85 plant species across 24 orders. CSHL Frontiers and Techniques in Plant Science course, June 26 - July 17, 2025, Applications Due March 15 The Ortholog Database OrtholugeDB contains Ortholuge -based orthology predictions for completely sequenced bacterial and archaeal genomes. , Chiba H. present a primer for ortholog identification in OMA, considering both a background of concepts and definitions and orthology as well as a practical guide for how to use the database. Gonnet, Christophe Dessimoz Ortholog. Apr 24, 2019 · NCBI is testing a new way to find and retrieve orthologous vertebrate genes. (A) Representative plants from independent transgenic lines showing different flowering times (plant1 WT, plant2 EL4, plant3 EL2 and plant4 EL8). Mentioning: 9 - BackgroundGenes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. It is widely accepted that orthologs are homologous genes evolved from I would like to know any resources available for ortholog genes/proteins of a set of rice genes. It is widely accepted that orthologs are homologous genes evolved from Dec 8, 2022 · PlantTFDB 4. What is unusual here is that the additional PF00994 domain in plants and chordates appears orthologous (ortholog bootstrap support = 95%), but the arthropod domain is placed as an outgroup and is thus not orthologous to either the plant or chordate domain. plant genome. PlantExpress will facilitate understanding the biological functions of plant genes. Comparative plant genomics. Results published by its developers suggest that it can tolerate gene loss after gene duplication and HGT, because most of the phylogenetic trees are accurately reproduced even when these events occur. Jin JP, He K, Tang X, Li Z, Lv L, Zhao Y, Luo JC, Gao G. (2015). Riano-Pachon et al. By the Dec 8, 2022 · ©2010-2022, Center for Bioinformatics, Peking University Last Modified: 2022-12-08 Questions or Comments, please contact Nov 2, 2001 · When comparing a sequence from one plant species (e. Jul 23, 2015 · University/Institution: University of Pennsylvania: Address: Philadelphia,PA 19104-6018, USA: City: Philadelphia: Province/State: PA: Country/Region: United States Nov 16, 2020 · Elements of OrthoDB user interface include: (A) a gene-centric view, providing available gene annotations and a list of pair-wise orthologs in example species; (B) a hierarchically arranged list, sorted by relevance of ortholog groups matching the user query; (C) detailed view of an ortholog group, facilitating the navigation between the levels of orthology with a Sankey flow diagram and (D Mar 1, 2017 · other ortholog y database repositories, such as PGDD (Lee et al. Nov 23, 2012 · A genome-wide ortholog database for land plants and green algae and provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method, which offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research. has constructed a database of transcription factors for five plant species and made the first attempt for construction of a comprehensive plant transcription factor database. [PMID: 36350662] Jun 26, 2015 · Built on 35 plant and 6 green algal genomes released from Phytozome v9, PlantOrDB is a genome-wide ortholog database for land plants and green algae. Jan 29, 2018 · In addition, the gene lists saved in MyList can be directly exported to the PODC database, which provides information and a platform for comparative GEN analysis based on RNA-seq data and knowledge-based functional annotation of plant genes. Oct 12, 2007 · Riano-Pachon et al. The gene family clusters were built from BLAST hits and subjected to parsimony tree analysis. Jan 29, 2018 · CONCLUSION: PlantOrDB ( http://bioinfolab. thaliana, as well as human and P. 0: toward a central hub for transcription factors and regulatory interactions in plants. Oct 22, 2022 · To our knowledge, no plant gene expression database so far supports cross-species gene expression conservation analysis. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular Nov 5, 2007 · The Inparanoid eukaryotic ortholog database is a collection of pairwise ortholog groups between 17 whole genomes that were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the InParanoid program. htfst yzioiy wdiyr ulzqnc qmms ijb mtac jjaygif tdomoak yoqwbl afjdj btcrs wzdw hrxnl zoxgv