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Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jsp Database URL https://www.echinobase.org/.
5P41HD095831-03 Eunice Kennedy Shriver National Institute of Child Health and Human Development, ACI-1445606 National Science Foundation, ACI-1548562 National Science Foundation, ACI-1928147 National Science Foundation, P41 HD095831 NICHD NIH HHS
Figure 1. Flowchart describing the Echinobase nomenclature pipeline. Following processing by NCBI and the Echinobase orthology pipeline, gene identifiers are assigned depending on orthology relationships to humans.
Adomako-Ankomah,
Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo.
2014, Pubmed,
Echinobase
Adomako-Ankomah,
Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo.
2014,
Pubmed
,
Echinobase
Alliance of Genome Resources Consortium,
Alliance of Genome Resources Portal: unified model organism research platform.
2020,
Pubmed
Altenhoff,
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
2018,
Pubmed
Angerer,
Patterning the sea urchin embryo: gene regulatory networks, signaling pathways, and cellular interactions.
2003,
Pubmed
,
Echinobase
Annunziata,
Development and evolution of gut structures: from molecules to function.
2019,
Pubmed
,
Echinobase
Barrière,
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes.
2009,
Pubmed
Britten,
The single-copy DNA sequence polymorphism of the sea urchin Strongylocentrotus purpuratus.
1978,
Pubmed
,
Echinobase
Bruford,
Guidelines for human gene nomenclature.
2020,
Pubmed
Buckley,
Techniques for analyzing gene expression using BAC-based reporter constructs.
2019,
Pubmed
,
Echinobase
Burt,
The Chicken Gene Nomenclature Committee report.
2009,
Pubmed
Carlisle,
Molecular mechanisms and evolution of fertilization proteins.
2021,
Pubmed
,
Echinobase
Cary,
EchinoBase: Tools for Echinoderm Genome Analyses.
2018,
Pubmed
,
Echinobase
Cary,
Echinoderm development and evolution in the post-genomic era.
2017,
Pubmed
,
Echinobase
Cary,
Genomic resources for the study of echinoderm development and evolution.
2019,
Pubmed
,
Echinobase
Davidson,
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.
2020,
Pubmed
,
Echinobase
Davidson,
Network design principles from the sea urchin embryo.
2009,
Pubmed
,
Echinobase
Dehal,
Two rounds of whole genome duplication in the ancestral vertebrate.
2005,
Pubmed
Emms,
OrthoFinder: phylogenetic orthology inference for comparative genomics.
2019,
Pubmed
Ernst,
Offerings from an urchin.
2011,
Pubmed
,
Echinobase
Ettensohn,
Encoding anatomy: developmental gene regulatory networks and morphogenesis.
2013,
Pubmed
,
Echinobase
Foley,
Integration of 1:1 orthology maps and updated datasets into Echinobase.
2021,
Pubmed
,
Echinobase
Hall,
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
2017,
Pubmed
,
Echinobase
Hu,
An integrative approach to ortholog prediction for disease-focused and other functional studies.
2011,
Pubmed
Hu,
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier.
2019,
Pubmed
James-Zorn,
Xenbase: Core features, data acquisition, and data processing.
2015,
Pubmed
,
Echinobase
Janies,
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.
2016,
Pubmed
,
Echinobase
Kelley,
Detection and correction of false segmental duplications caused by genome mis-assembly.
2010,
Pubmed
Koga,
The echinoderm larval skeleton as a possible model system for experimental evolutionary biology.
2014,
Pubmed
,
Echinobase
Kusumi,
Developing a community-based genetic nomenclature for anole lizards.
2011,
Pubmed
Lechner,
Proteinortho: detection of (co-)orthologs in large-scale analysis.
2011,
Pubmed
Lowe,
Omics approaches to study gene regulatory networks for development in echinoderms.
2017,
Pubmed
,
Echinobase
Martik,
Developmental gene regulatory networks in sea urchins and what we can learn from them.
2016,
Pubmed
,
Echinobase
McClay,
Sea Urchin Morphogenesis.
2016,
Pubmed
,
Echinobase
Ostlund,
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
2010,
Pubmed
Peter,
Methods for the experimental and computational analysis of gene regulatory networks in sea urchins.
2019,
Pubmed
,
Echinobase
Peter,
Regulatory states in the developmental control of gene expression.
2017,
Pubmed
,
Echinobase
Putnam,
The amphioxus genome and the evolution of the chordate karyotype.
2008,
Pubmed
Raff,
Chapter 7. Axis formation and the rapid evolutionary transformation of larval form.
2009,
Pubmed
,
Echinobase
Rafiq,
The genomic regulatory control of skeletal morphogenesis in the sea urchin.
2012,
Pubmed
,
Echinobase
Rast,
Genomic insights into the immune system of the sea urchin.
2006,
Pubmed
,
Echinobase
Remm,
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
2001,
Pubmed
Rhie,
Towards complete and error-free genome assemblies of all vertebrate species.
2021,
Pubmed
Ruzicka,
The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources.
2019,
Pubmed
Shashikant,
From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms.
2018,
Pubmed
,
Echinobase
Smith,
The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications.
2015,
Pubmed
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Tu,
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
2012,
Pubmed
,
Echinobase
Tweedie,
Genenames.org: the HGNC and VGNC resources in 2021.
2021,
Pubmed
Wattam,
PATRIC, the bacterial bioinformatics database and analysis resource.
2014,
Pubmed
Wessel,
Germ Line Mechanics--And Unfinished Business.
2016,
Pubmed
,
Echinobase
Wilt,
Developmental biology meets materials science: Morphogenesis of biomineralized structures.
2005,
Pubmed
,
Echinobase
Wright,
Human and orthologous gene nomenclature.
2006,
Pubmed
Wright,
HCOP: the HGNC comparison of orthology predictions search tool.
2005,
Pubmed
