Revised eutherian gene collections.

Objectives: The most recent research projects in scientific field of eutherian comparative genomics included intentions to sequence every extant eutherian species genome in foreseeable future, so that future revisions and updates of eutherian gene data sets were expected.

Data Description: Using 35 public eutherian reference genomic sequence assemblies and free available software, the eutherian comparative genomic analysis protocol RRID:SCR_014401 was published as guidance against potential genomic sequence errors. The protocol curated 14 eutherian third-party data gene data sets, including, in aggregate, 2615 complete coding sequences that were deposited in European Nucleotide Archive.

Comparative genomic analysis of eutherian interferon genes.

The eutherian interferons were implicated as paradigmatic effector proteins in innate and acquired immunity. Yet, familiar interferon classification and nomenclature disagreed with functional genomics, phylogenetic and evolutionary analyses. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets, the present analysis attempted to resolve major disagreements in descriptions of eutherian interferons.

Comparative genomic analysis of eutherian fibroblast growth factor genes.

Background: The eutherian fibroblast growth factors were implicated as key regulators in developmental processes. However, there were major disagreements in descriptions of comprehensive eutherian fibroblast growth factors gene data sets including either 18 or 22 homologues. The present analysis attempted to revise and update comprehensive eutherian fibroblast growth factor gene data sets, and address and resolve major discrepancies in their descriptions using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets.

Author Correction: Comparative genomic analysis of eutherian connexin genes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Comparative genomic analysis of eutherian connexin genes.

The eutherian connexins were characterized as protein constituents of gap junctions implicated in cell-cell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses. However, conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive eutherian connexin gene data sets, due to ambiguities and inconsistencies in connexin gene and protein nomenclatures. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets, the present analysis attempted to update and revise comprehensive eutherian connexin gene data sets, and address and resolve major discrepancies in their descriptions.

Comparative genomic analysis of eutherian adiponectin genes.

The present study proposed updated and standardized classification and nomenclature of eutherian adiponectin genes implicated in regulation of systemic metabolism and inflammation and activation of classical complement pathway. The revisions of comprehensive adiponectin gene data sets used eutherian comparative genomic analysis protocol and public reference genomic sequence assemblies. Among 438 potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated most comprehensive curated third-party data gene data set of eutherian adiponectin genes that included 211 complete coding sequences.

Comparative genomic analysis of eutherian kallikrein genes.

The present study made attempts to update and revise eutherian kallikrein genes implicated in major physiological and pathological processes and in medical molecular diagnostics. Using eutherian comparative genomic analysis protocol and free available genomic sequence assemblies, the tests of reliability of eutherian public genomic sequences annotated most comprehensive curated third party data gene data set of eutherian kallikrein genes including 121 complete coding sequences among 335 potential coding sequences. The present analysis first described 13 major gene clusters of eutherian kallikrein genes, and explained their differential gene expansion patterns.

Curated eutherian third party data gene data sets.

The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences.

Third party data gene data set of eutherian growth hormone genes.

Among 146 potential coding sequences, the most comprehensive eutherian growth hormone gene data set annotated 100 complete coding sequences. The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes. The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments.

Comparative genomic analysis of eutherian tumor necrosis factor ligand genes.

The present analysis made attempts to resolve discrepancies in descriptions of eutherian tumor necrosis factor ligand genes implicated in cell signalling pathways, as well as in major physiological and pathological processes. Among 455 potential coding sequences, the eutherian comparative genomic analysis protocol annotated 211 complete coding sequences using public genomic sequence assemblies. The most comprehensive third party data gene data set first described 8 superclusters of eutherian tumor necrosis factor ligand genes, including 18 major gene clusters.

Third party annotation gene data set of eutherian lysozyme genes.

The eutherian comparative genomic analysis protocol annotated most comprehensive eutherian lysozyme gene data set. Among 209 potential coding sequences, the third party annotation gene data set of eutherian lysozyme genes included 116 complete coding sequences that first described seven major gene clusters. As one new framework of future experiments, the present integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new classification and nomenclature of eutherian lysozyme genes.

Initial description of primate-specific cystine-knot Prometheus genes and differential gene expansions of D-dopachrome tautomerase genes.

Using eutherian comparative genomic analysis protocol and public genomic sequence data sets, the present work attempted to update and revise two gene data sets. The most comprehensive third party annotation gene data sets of eutherian adenohypophysis cystine-knot genes (128 complete coding sequences), and d-dopachrome tautomerases and macrophage migration inhibitory factor genes (30 complete coding sequences) were annotated. For example, the present study first described primate-specific cystine-knot Prometheus genes, as well as differential gene expansions of D-dopachrome tautomerase genes.

Comparative genomic analysis of eutherian Mas-related G protein-coupled receptor genes.

The present study made attempts to update comprehensive eutherian Mas-related G protein-coupled receptor gene data sets, using public eutherian genomic sequence data sets and new genomics and molecular evolution tests. Among 254 potential coding sequences, the most comprehensive gene data set of eutherian Mas-related G protein-coupled receptor genes included 119 complete coding sequences that described eight major gene clusters. The present analysis integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis and first explained differential gene expansion patterns of eutherian Mas-related G protein-coupled receptor genes.

Comparative genomic analysis of eutherian ribonuclease A genes.

The present study attempted to update comprehensive eutherian ribonuclease A gene data sets, using public eutherian genomic sequence data sets and new genomics and molecular evolution tests. Among 448 ribonuclease A potential coding sequences, the present analysis annotated 255 complete coding sequences. The most comprehensive data set of eutherian ribonuclease A genes first characterized 13 major gene clusters, 9 of which showed evidence of differential gene expansions.

Comparative genomic analysis of eutherian interferon-γ-inducible GTPases.

The interferon-γ-inducible GTPases, IFGGs, are intracellular proteins involved in immune response against pathogens. A comprehensive comparative genomic review and analysis of eutherian IFGGs was carried out using public genomic sequences. The 64 eutherian IFGG genes were examined in detail and annotated.

Positive selection in prion protein.

The prion diseases, such as Creutzfeldt-Jakob disease of humans and bovine spongiform encephalopathy, involve the aberrant metabolism and accumulation of prion protein PrP. There are three contradictory hypotheses about evolution of prion protein gene PRNP. Population genetic studies have proposed that PRNP could be under balancing selection, strong purifying selection, or mainly positive selection.

Comparative genomic analysis of prion genes.

Background: The homologues of human disease genes are expected to contribute to better understanding of physiological and pathogenic processes. We made use of the present availability of vertebrate genomic sequences, and we have conducted the most comprehensive comparative genomic analysis of the prion protein gene PRNP and its homologues, shadow of prion protein gene SPRN and doppel gene PRND, and prion testis-specific gene PRNT so far.

Results: While the SPRN and PRNP homologues are present in all vertebrates, PRND is known in tetrapods, and PRNT is present in primates.

The complete set of ribosomal proteins from the marine sponge Suberites domuncula.

The siliceous marine sponge Suberites domuncula is a member of the most ancient and simplest extant phylum of multicellular animals-Porifera, which have branched off first from the common ancestor of all Metazoa. We have determined primary structures of 79 ribosomal proteins (r-proteins) from S. domuncula: 32 proteins from the small ribosomal subunit and 47 proteins from the large ribosomal subunit.

The prion protein gene: identifying regulatory signals using marsupial sequence.

The function of the prion protein gene (PRNP) and its normal product PrP(C) is elusive. We used comparative genomics as a strategy to understand the normal function of PRNP. As the reliability of comparisons increases with the number of species and increased evolutionary distance, we isolated and sequenced a 66.

Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis.

Recent findings of new genes in fish related to the prion protein (PrP) gene PRNP, including our recent report of SPRN coding for Shadoo (Sho) protein found also in mammals, raise issues of their function and evolution. Here we report additional novel fish genes found in public databases, including a duplicated SPRN gene, SPRNB, in Fugu, Tetraodon, carp, and zebrafish encoding the Sho2 protein, and we use comparative genomic analysis to analyze the evolutionary relationships and to infer evolutionary trajectories of the complete data set. Phylogenetic footprinting performed on aligned human, mouse, and Fugu SPRN genes to define candidate regulatory promoter regions, detected 16 conserved motifs, three of which are known transcription factor-binding sites for a receptor and transcription factors specific to or associated with expression in brain.

Shadoo, a new protein highly conserved from fish to mammals and with similarity to prion protein.

We report evidence from cDNA isolation and expression analysis as well as analyses of genome, expressed sequence tag (EST), cDNA and expression databases for a new gene named SPRN (shadow of prion protein). SPRN comprises two exons, with the open reading frame (ORF) contained within exon 2, and codes for a protein of 130-150 amino acids named Shadoo (Japanese shadow), predicted to be extracellular and GPI-anchored. The SPRN gene was found in fish (zebrafish, Fugu) and mammals (mouse, rat, human).