OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

Abstract OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise orthologs, functional annotations, local and global gene order conservation (synteny) information, among many other functions. This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. Other new and improved features are detailed, such as reporting of the evolutionarily best conserved isoforms of alternatively spliced genes, the inferred local order of ancestral genes, phylogenetic profiling, better cross-references, fast genome mapping, semantic data sharing via RDF, as well as a special coronavirus OMA with 119 viruses from the Nidovirales order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude with improvements to the documentation of the resource through primers, tutorials and short videos. OMA is accessible at https://omabrowser.org.

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Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers

Eukaryotic Cell ◽

10.1128/ec.1.2.304-310.2002 ◽

2002 ◽

Vol 1 (2) ◽

pp. 304-310 ◽

Cited By ~ 33

Author(s):

Jan O. Andersson ◽

Andrew J. Roger

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Gene Order ◽

Phylogenetic Analyses ◽

Single Gene ◽

Large Subunit ◽

Glutamate Synthase ◽

Small Subunit ◽

Gene Order Conservation ◽

Domains Of Life

ABSTRACT Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes—the diplomonads—while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.

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Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽

10.3390/a14060160 ◽

2021 ◽

Vol 14 (6) ◽

pp. 160

Author(s):

Qiaoji Xu ◽

Lingling Jin ◽

James H. Leebens-Mack ◽

David Sankoff

Keyword(s):

Phylogenetic Tree ◽

Gene Order ◽

Evolutionary Process ◽

Gene Content ◽

Ancestral Genome ◽

Maximum Weight ◽

Ancestral Gene ◽

Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

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First partial mitogenome of a new Seira Lubbock species (Collembola,Entomobryidae, Seirinae) from Cambodia reveals a possible separate lineage from the Neotropical Seirinae

Zootaxa ◽

10.11646/zootaxa.4890.4.1 ◽

2020 ◽

Vol 4890 (4) ◽

pp. 451-472

Author(s):

NERIVANIA NUNES GODEIRO ◽

FENG ZHANG ◽

NIKOLAS GIOIA CIPOLA

Keyword(s):

New Species ◽

Gene Order ◽

Colour Pattern ◽

Protein Coding ◽

Ancestral Gene ◽

Protein Coding Genes ◽

The Third ◽

Maximum Likelihood Phylogenetic Tree ◽

Genome Information ◽

A New Species

A new species of Seira from Koh Rong Sanloem Island, Cambodia, as well as its mitochondrial genome information, are herein described. Seira sanloemensis sp. nov. has a similar colour pattern compared to nine other species of Seira worldwide distributed, but the dorsal chaetotaxy is more similar to S. arunachala Mitra from India, S. camgiangensis Nguyễn from Vietnam, and S. gobalezai Christiansen & Bellinger from Hawaii. However, the new species differs from these species by dorsal chaetotaxy of head, Th II–III and Abd II, collophore chaetotaxy, and morphology of the empodial complex. This is the third Collembola species described for Cambodia. Its assembled incomplete mitogenome from MGI reads, has a length of 13,953 bp, and contains all protein-coding genes except for tree tRNAs missing; the gene order is the same of the Pancrustacean ancestral gene order. Based on the alignment of the 13 coding genes, a maximum likelihood phylogenetic tree of medium bootstrap values suggested that the Asian Seira species can represent a different lineage from the Neotropical Seirinae, but further biogeographic and divergence estimation analyses plus the inclusion of more Asian taxa are necessary to test such hypothesis.

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GC-rich intra-operonic spacers in prokaryotes: Possible relation to gene order conservation

FEBS Letters ◽

10.1016/j.febslet.2010.10.037 ◽

2010 ◽

Vol 584 (22) ◽

pp. 4633-4638

Author(s):

Anirban Dutta ◽

Sandip Paul ◽

Chitra Dutta

Keyword(s):

Gene Order ◽

Gene Order Conservation

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Phenotypic Consequences of Rearranging the P, M, and G Genes of Vesicular Stomatitis Virus

Journal of Virology ◽

10.1128/jvi.73.6.4705-4712.1999 ◽

1999 ◽

Vol 73 (6) ◽

pp. 4705-4712 ◽

Cited By ~ 86

Author(s):

L. Andrew Ball ◽

Craig R. Pringle ◽

Brian Flanagan ◽

Victoria P. Perepelitsa ◽

Gail W. Wertz

Keyword(s):

Gene Expression ◽

Vesicular Stomatitis Virus ◽

Gene Order ◽

Gene Rearrangement ◽

Matrix Protein ◽

Cultured Cells ◽

Growth Potential ◽

Wild Type Virus ◽

Ancestral Gene ◽

Vesicular Stomatitis

ABSTRACT The nonsegmented negative-strand RNA viruses (orderMononegavirales) include many important human pathogens. The order of their genes, which is highly conserved, is the major determinant of the relative levels of gene expression, since genes that are close to the single promoter site at the 3′ end of the viral genome are transcribed at higher levels than those that occupy more distal positions. We manipulated an infectious cDNA clone of the prototypic vesicular stomatitis virus (VSV) to rearrange three of the five viral genes, using an approach which left the viral nucleotide sequence otherwise unaltered. The central three genes in the gene order, which encode the phosphoprotein P, the matrix protein M, and the glycoprotein G, were rearranged into all six possible orders. Viable viruses were recovered from each of the rearranged cDNAs. The recovered viruses were examined for their levels of gene expression, growth potential in cell culture, and virulence in mice. Gene rearrangement changed the expression levels of the encoded proteins in concordance with their distance from the 3′ promoter. Some of the viruses with rearranged genomes replicated as well or slightly better than wild-type virus in cultured cells, while others showed decreased replication. All of the viruses were lethal for mice, although the time to symptoms and death following inoculation varied. These data show that despite the highly conserved gene order of the Mononegavirales, gene rearrangement is not lethal or necessarily even detrimental to the virus. These findings suggest that the conservation of the gene order observed among the Mononegavirales may result from immobilization of the ancestral gene order due to the lack of a mechanism for homologous recombination in this group of viruses. As a consequence, gene rearrangement should be irreversible and provide an approach for constructing viruses with novel phenotypes.

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Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

10.1101/2021.07.16.452543 ◽

2021 ◽

Author(s):

Abdoallah Sharaf ◽

Mallika Vijayanathan ◽

Miroslav Obornik ◽

iva Mozgova

Keyword(s):

Developmental Regulation ◽

Structural Diversity ◽

Polycomb Group ◽

Catalytic Subunit ◽

Set Domain ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2 ◽

Domains Of Life ◽

Domain Protein ◽

Phylogenetic Profiling

Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

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Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes

10.1101/852491 ◽

2019 ◽

Cited By ~ 2

Author(s):

David Moi ◽

Laurent Kilchoer ◽

Pablo S. Aguilar ◽

Christophe Dessimoz

Keyword(s):

Sexual Reproduction ◽

Large Scale ◽

Biological Process ◽

Locality Sensitive Hashing ◽

Computational Method ◽

Eukaryotic Species ◽

Efficient Retrieval ◽

Domains Of Life ◽

Phylogenetic Profiling ◽

Eukaryotic Genomes

AbstractPhylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require quadratic time or worse in the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profiles. We show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct networks and query for interactors of the kinetochore complex as well as conserved proteins involved in sexual reproduction: Hap2, Spo11 and Gex1. HogProf enables large-scale phylogenetic profiling across the three domains of life, and will be useful to predict biological pathways among the hundreds of thousands of eukaryotic species that will become available in the coming few years. HogProf is available at https://github.com/DessimozLab/HogProf.

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