scholarly journals Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life

1996 ◽  
Vol 13 (7) ◽  
pp. 970-977 ◽  
Author(s):  
F. S. Lawson ◽  
R. L. Charlebois ◽  
J. A. Dillon
2001 ◽  
Vol 183 (22) ◽  
pp. 6714-6716 ◽  
Author(s):  
Miklós Müller ◽  
Jennifer A. Lee ◽  
Paul Gordon ◽  
Terry Gaasterland ◽  
Christoph W. Sensen

ABSTRACT Inorganic pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate eukaryoteMastigamoeba balamuthi was sequenced and showed about 60% identity to PPi-PFKs from two eubacteria,Propionibacterium freudenreichii and Sinorhizobium meliloti. These gene products represent a newly recognized lineage of PFKs. All four lineages of group II PFKs, as defined by phylogenetic analysis, contained both prokaryotic and eukaryotic species, underlining the complex evolutionary history of this enzyme.


2017 ◽  
Author(s):  
David M. Unwin

The origin of the pterodactyloid bauplan from that of non-monofenestratan (‘rhamphorhynchoid’) pterosaurs involved extensive anatomical changes and had profound consequences for the evolutionary history of Pterodactyloidea, a clade that dominated the aerial realm throughout the Cretaceous. This important evolutionary transformation, about which almost nothing was known for almost two centuries, is now rapidly coming into focus thanks to a plethora of new pterosaur fossils from the Middle and Upper Jurassic of South America, Europe and China. So far, however, these finds have largely been considered in isolation from each other and few have been thoroughly evaluated. Phylogenetic analysis, combined with improved stratigraphic data for all potentially relevant taxa including putative non-pterodactyloid monofenstratans (NPMs) and the oldest known pterodactyloids (e.g. Liaodactylus) was used to generate a new map of the anatomical transformations and temporal history of the non-monofenestratan–pterodactyloid transition. Evolution of the pterodactyloid skull construction predates the Middle Jurassic, but remains almost completely undocumented by fossils. Liaodactylus reveals that innovation in pterodactyloid skull anatomy and the appearance of derived features was well underway prior to the Upper Jurassic. Douzhanopterus, a derived NPM, demonstrates that elongation of the metacarpus and reduction of the tail and fifth toe (classic pterodactyloid synapomorphies) also predates the Upper Jurassic, but disjunction in the degree of their development across taxa is not consistent with simple explanations such as ‘adaptation for flight’. Overall, late Early to early Late Jurassic pterosaurs were much more diverse and had a far more complex evolutionary history than heretofore recognised.


2017 ◽  
Author(s):  
David M. Unwin

The origin of the pterodactyloid bauplan from that of non-monofenestratan (‘rhamphorhynchoid’) pterosaurs involved extensive anatomical changes and had profound consequences for the evolutionary history of Pterodactyloidea, a clade that dominated the aerial realm throughout the Cretaceous. This important evolutionary transformation, about which almost nothing was known for almost two centuries, is now rapidly coming into focus thanks to a plethora of new pterosaur fossils from the Middle and Upper Jurassic of South America, Europe and China. So far, however, these finds have largely been considered in isolation from each other and few have been thoroughly evaluated. Phylogenetic analysis, combined with improved stratigraphic data for all potentially relevant taxa including putative non-pterodactyloid monofenstratans (NPMs) and the oldest known pterodactyloids (e.g. Liaodactylus) was used to generate a new map of the anatomical transformations and temporal history of the non-monofenestratan–pterodactyloid transition. Evolution of the pterodactyloid skull construction predates the Middle Jurassic, but remains almost completely undocumented by fossils. Liaodactylus reveals that innovation in pterodactyloid skull anatomy and the appearance of derived features was well underway prior to the Upper Jurassic. Douzhanopterus, a derived NPM, demonstrates that elongation of the metacarpus and reduction of the tail and fifth toe (classic pterodactyloid synapomorphies) also predates the Upper Jurassic, but disjunction in the degree of their development across taxa is not consistent with simple explanations such as ‘adaptation for flight’. Overall, late Early to early Late Jurassic pterosaurs were much more diverse and had a far more complex evolutionary history than heretofore recognised.


Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.


Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.


2012 ◽  
Vol 7 (4) ◽  
pp. 571-586 ◽  
Author(s):  
Andrzej Mazur ◽  
Piotr Koper

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.


2009 ◽  
Vol 26 (6) ◽  
pp. 1357-1367 ◽  
Author(s):  
Laura B. Scheinfeldt ◽  
Shameek Biswas ◽  
Jennifer Madeoy ◽  
Caitlin F. Connelly ◽  
Eric E. Schadt ◽  
...  

Taxon ◽  
2012 ◽  
Vol 61 (2) ◽  
pp. 355-367 ◽  
Author(s):  
Steven B. Janssens ◽  
Yi Song Wilson ◽  
Yong-Ming Yuan ◽  
Anne Nagels ◽  
Erik F. Smets ◽  
...  

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