scholarly journals Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony

2008 ◽  
Vol 24 (5) ◽  
pp. 606-612 ◽  
Author(s):  
Onur Sakarya ◽  
Kenneth S. Kosik ◽  
Todd H. Oakley
Keyword(s):  
Ancestral Genome ◽  
Dollo Parsimony ◽  
Genome Content

scholarly journals The evolutionary origin of host association in an ancient bacterial clade

2021 ◽  
Author(s):  
Max E. Schön ◽  
Joran Martijn ◽  
Julian Vosseberg ◽  
Stephan Köstlbacher ◽  
Thijs J. G. Ettema
Keyword(s):  
Secretion System ◽  
Type Iv Secretion ◽  
Type Iv Secretion System ◽  
Ancestral Genome ◽  
Bacterial Symbionts ◽  
Host Association ◽  
Free Living ◽  
Type Iv ◽  
Genome Content ◽  
Bacterial Clade

AbstractThe evolution of obligate host-association of bacterial symbionts and pathogens remains poorly understood. The Rickettsiales represent an order of obligate alphaproteobacterial endosymbionts and parasites that infect a wide variety of eukaryotic hosts, including humans, livestock, insects and protists. Induced by their host-associated lifestyle, Rickettsiales genomes have undergone reductive evolution, leading to small, AT-rich genomes with limited metabolic capacities. We describe several genomes of deep-branching, environmental alphaproteobacteria that branch basal to previously sampled Rickettsiales, and whose genome content are reminiscent of free-living and biofilm-associated lifestyles. Ancestral genome content reconstruction across the Rickettsiales tree revealed that the free-living to host-association transition of this group occurred more recently than previously anticipated, and likely involved the repurposing of a type IV secretion system.One-Sentence SummaryDeep-branching Rickettsiales provide insights into the evolution of obligate host-associated lifestyle

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.

Genetic Evidence for Allopolyploidy in the Neotropical Fern Hemionitis pinnatifida (Adiantaceae) and the Reconstruction of an Ancestral Genome

1989 ◽  
Vol 14 (4) ◽  
pp. 439 ◽  
Author(s):  
Thomas A. Ranker ◽  
Christopher H. Haufler ◽  
Pamela S. Soltis ◽  
Douglas E. Soltis
Keyword(s):  
Genetic Evidence ◽  
Ancestral Genome

scholarly journals Genome Sequence of Lentisphaera araneosa HTCC2155T, the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae

2010 ◽  
Vol 192 (11) ◽  
pp. 2938-2939 ◽  
Author(s):  
J. Cameron Thrash ◽  
Jang-Cheon Cho ◽  
Kevin L. Vergin ◽  
Robert M. Morris ◽  
Stephen J. Giovannoni
Keyword(s):  
Genome Sequence ◽  
Type Species ◽  
Microbial Evolution ◽  
Unusual Property ◽  
Oregon Coast ◽  
The Pacific ◽  
Genome Content

ABSTRACT Information on the genome content of deeply branching phyla with very few cultured members is invaluable for expanding understanding of microbial evolution. Lentisphaera araneosa HTCC2155T was isolated from the Oregon coast using dilution-to-extinction culturing. It is a marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic oceans and has the unusual property of producing a net-like matrix of secreted exopolysaccharide. Here we present the genome sequence of L. araneosa HTCC2155T, importantly, one of only two sequenced members of the phylum Lentisphaerae.

Sign in / Sign up

Export Citation Format

Share Document