Reconstruction of ancestral gene order after segmental duplication and gene loss

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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Horizontal transfer and gene loss shaped the evolution of alpha-amylases in bilaterians

10.1101/670273 ◽

2019 ◽

Author(s):

Andrea Desiderato ◽

Marcos Barbeitos ◽

Clément Gilbert ◽

Jean-Luc Da Lage

Keyword(s):

Horizontal Transfer ◽

Gene Loss ◽

Unexpected Finding ◽

Ancestral Gene ◽

Unicellular Eukaryotes ◽

Horizontal Transfers ◽

Alpha Amylases

AbstractThe subfamily GH13_1 of alpha-amylases is typical of Fungi, but it is also found in some unicellular eukaryotes (e.g. Amoebozoa, choanoflagellates) and non-bilaterian Metazoa. Since a previous study in 2007, GH13_1 amylases were considered ancestral to the Unikonts, including animals, except Bilateria, such that it was thought to have been lost in the ancestor of this clade. The only alpha-amylases known to be present in Bilateria so far belong to the GH13_15 and 24 subfamilies (commonly called bilaterian alpha-amylases) and were likely acquired by horizontal transfer from a proteobacterium. The taxonomic scope of Eukaryota genomes in databases has been greatly increased ever since 2007. We have surveyed GH13_1 sequences in recent data from ca. 1600 bilaterian species, 60 non-bilaterian animals and also in unicellular eukaryotes. As expected, we found a number of those sequences in non-bilaterians: Anthozoa (Cnidaria) and in sponges, confirming the previous observations, but none in jellyfishes and in Ctenophora. Our main and unexpected finding is that such fungal (also called Dictyo-type) amylases were also consistently retrieved in several bilaterian phyla: hemichordates (deuterostomes), brachiopods and related phyla, some molluscs and some annelids (protostomes). We discuss evolutionary hypotheses possibly explaining the scattered distribution of GH13_1 across bilaterians, namely, the retention of the ancestral gene in those phyla only and/or horizontal transfers from non-bilaterian donors.

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

Nucleic Acids Research ◽

10.1093/nar/gkaa1007 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D373-D379

Author(s):

Adrian M Altenhoff ◽

Clément-Marie Train ◽

Kimberly J Gilbert ◽

Ishita Mediratta ◽

Tarcisio Mendes de Farias ◽

...

Keyword(s):

Gene Order ◽

Genome Mapping ◽

Local Order ◽

Ancestral Gene ◽

Gene Group ◽

Semantic Data ◽

Gene Order Conservation ◽

Domains Of Life ◽

Alternatively Spliced ◽

Phylogenetic Profiling

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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Fast ancestral gene order reconstruction of genomes with unequal gene content

BMC Bioinformatics ◽

10.1186/s12859-016-1261-9 ◽

2016 ◽

Vol 17 (S14) ◽

Cited By ~ 6

Author(s):

Pedro Feijão ◽

Eloi Araujo

Keyword(s):

Gene Order ◽

Gene Content ◽

Ancestral Gene ◽

Order Reconstruction

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Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400826 ◽

2019 ◽

Vol 10 (2) ◽

pp. 709-719 ◽

Cited By ~ 2

Author(s):

Andrea Desiderato ◽

Marcos Barbeitos ◽

Clément Gilbert ◽

Jean-Luc Da Lage

Keyword(s):

Horizontal Transfer ◽

Gene Loss ◽

Unexpected Finding ◽

Ancestral Gene ◽

Unicellular Eukaryotes ◽

Horizontal Transfers ◽

Alpha Amylases

The subfamily GH13_1 of alpha-amylases is typical of Fungi, but it is also found in some unicellular eukaryotes (e.g., Amoebozoa, choanoflagellates) and non-bilaterian Metazoa. Since a previous study in 2007, GH13_1 amylases were considered ancestral to the Unikonts, including animals, except Bilateria, such that it was thought to have been lost in the ancestor of this clade. The only alpha-amylases known to be present in Bilateria so far belong to the GH13_15 and 24 subfamilies (commonly called bilaterian alpha-amylases) and were likely acquired by horizontal transfer from a proteobacterium. The taxonomic scope of Eukaryota genomes in databases has been greatly increased ever since 2007. We have surveyed GH13_1 sequences in recent data from ca. 1600 bilaterian species, 60 non-bilaterian animals and also in unicellular eukaryotes. As expected, we found a number of those sequences in non-bilaterians: Anthozoa (Cnidaria) and in sponges, confirming the previous observations, but none in jellyfishes and in Ctenophora. Our main and unexpected finding is that such fungal (also called Dictyo-type) amylases were also consistently retrieved in several bilaterian phyla: hemichordates (deuterostomes), brachiopods and related phyla, some molluscs and some annelids (protostomes). We discuss evolutionary hypotheses possibly explaining the scattered distribution of GH13_1 across bilaterians, namely, the retention of the ancestral gene in those phyla only and/or horizontal transfers from non-bilaterian donors.

Download Full-text