Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny

2009 ◽  
Vol 16 (10) ◽  
pp. 1353-1367 ◽  
Author(s):  
David Sankoff ◽  
Chunfang Zheng ◽  
P. Kerr Wall ◽  
Claude dePamphilis ◽  
Jim Leebens-Mack ◽  
...  
Keyword(s):  
Gene Order ◽  
Ancestral Gene ◽  
Angiosperm Phylogeny

Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny

2008 ◽  
pp. 252-264 ◽  
Author(s):  
David Sankoff ◽  
Chunfang Zheng ◽  
P. Kerr Wall ◽  
Claude dePamphilis ◽  
Jim Leebens-Mack ◽  
...  
Keyword(s):  
Gene Order ◽  
Internal Validation ◽  
Ancestral Gene ◽  
Angiosperm Phylogeny ◽  
Order Reconstruction

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

Algorithms ◽  
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.

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

Zootaxa ◽  
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. 

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

1999 ◽  
Vol 73 (6) ◽  
pp. 4705-4712 ◽  
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.

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

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.

scholarly journals Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study

2007 ◽  
Vol 8 (11) ◽  
pp. R236 ◽  
Author(s):  
Arjun Bhutkar ◽  
William M Gelbart ◽  
Temple F Smith
Keyword(s):  
Gene Order ◽  
Ancestral Gene ◽  
Genome Scale

scholarly journals Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection

2021 ◽  
Vol 7 (10) ◽  
pp. 864
Author(s):  
Lajos Acs-Szabo ◽  
Laszlo Attila Papp ◽  
Matthias Sipiczki ◽  
Ida Miklos
Keyword(s):  
Natural Selection ◽  
Gene Order ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Cleavage Sites ◽  
Evolutionary Patterns ◽  
Ancestral Gene ◽  
Gene Structures ◽  
Stable Genome

Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.

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