scholarly journals Comparative Genomics of the Odorant-Binding and Chemosensory Protein Gene Families across the Arthropoda: Origin and Evolutionary History of the Chemosensory System

2011 ◽  
Vol 3 ◽  
pp. 476-490 ◽  
Author(s):  
Filipe G. Vieira ◽  
Julio Rozas
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Protein Gene ◽  
Gene Families ◽  
Chemosensory System ◽  
Chemosensory Protein ◽  
History Of ◽  
Odorant Binding

scholarly journals Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

2018 ◽  
Author(s):  
Mónica Lopes-Marques ◽  
André M. Machado ◽  
Raquel Ruivo ◽  
Elza Fonseca ◽  
Estela Carvalho ◽  
...  
Keyword(s):  
Gene Family ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Gene Families ◽  
Gene Repertoire ◽  
Physiological Processes ◽  
Complex Lipid ◽  
History Of ◽  
Enzyme Families ◽  
Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Determining the evolutionary history of gene families

2011 ◽  
Vol 28 (1) ◽  
pp. 48-55 ◽  
Author(s):  
Ryan M. Ames ◽  
Daniel Money ◽  
Vikramsinh P. Ghatge ◽  
Simon Whelan ◽  
Simon C. Lovell
Keyword(s):  
Evolutionary History ◽  
Gene Families ◽  
History Of

scholarly journals Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda

2017 ◽  
Vol 34 (8) ◽  
pp. 1838-1862 ◽  
Author(s):  
Seong-il Eyun ◽  
Ho Young Soh ◽  
Marijan Posavi ◽  
James B. Munro ◽  
Daniel S.T. Hughes ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Families ◽  
Related Gene ◽  
History Of

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9861
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Marine Bacteria ◽  
Evolutionary History ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene ◽  
Enzymatic Adaptation

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

2018 ◽  
Vol 12 (7) ◽  
pp. 1779-1793 ◽  
Author(s):  
Alejandro Palomo ◽  
Anders G. Pedersen ◽  
S. Jane Fowler ◽  
Arnaud Dechesne ◽  
Thomas Sicheritz-Pontén ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Niche Differentiation ◽  
History Of

scholarly journals RecPD: A Recombination-Aware Measure of Phylogenetic Diversity

2021 ◽  
Author(s):  
Cedoljub Bundalovic-Torma ◽  
Darrell Desveaux ◽  
David S Guttman
Keyword(s):  
Pseudomonas Syringae ◽  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Evolutionary Dynamics ◽  
Gene Families ◽  
Ancestral State ◽  
History Of ◽  
Preliminary Study ◽  
Potential Impact ◽  
Study Type

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) underlying traits or outcomes of interest is assessing their diversity and distribution. Accurate assessments of these patterns are essential for linking features to traits or outcomes and understanding their functional impact. Consequently, it is of crucial importance that the metrics employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard metrics used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity metric for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive a number of related metrics from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably identifies evolutionary histories under diverse recombination and loss scenarios. We then apply RecPD in a real-world scenario in a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and demonstrate that prevalence is an inadequate metric that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.

scholarly journals Structure and evolutionary history of a large family of NLR proteins in the zebrafish

2015 ◽  
Author(s):  
Kerstin Howe ◽  
Philipp H Schiffer ◽  
Julia Zielinski ◽  
Thomas Wiehe ◽  
Gavin K Laird ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Large Family ◽  
Gene Families ◽  
Immune Recognition ◽  
Chromosome 4 ◽  
New Family ◽  
History Of ◽  
Evolutionary Trajectories ◽  
B30.2 Domain

NACHT- and Leucine-Rich-Repeat-containing domain (NLR) proteins act as cytoplasmic sensors for pathogen- and danger-associated molecular patterns and are found throughout the plant and animal kingdoms. In addition to having a small set of conserved NLRs, the genomes in some animal lineages contain massive expansions of this gene family. One of these arose in fishes, after the creation of a gene fusion that combined the core NLR domains with another domain used for immune recognition, the PRY/SPRY or B30.2 domain. We have analysed the expanded NLR gene family in zebrafish, which contains 368 genes, and studied its evolutionary history. The encoded proteins share a defining overall structure, but individual domains show different evolutionary trajectories. Our results suggest gene conversion homogenizes NACHT and B30.2 domain sequences among different gene subfamilies, however, the functional implications of its action remains unclear. The majority of the genes are located on the long arm of chromosome 4, interspersed with several other large multi-gene families, including a new family encoding proteins with multiple tandem arrays of Zinc fingers. This suggests that chromosome 4 may be a hotspot for rapid evolutionary change in zebrafish.

scholarly journals The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms

2019 ◽  
Vol 37 (2) ◽  
pp. 379-394
Author(s):  
Aida Arcas ◽  
David G Wilkinson ◽  
M Ángela Nieto
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Gene Families ◽  
Cell Contact ◽  
Eph Receptors ◽  
Origin And Evolution ◽  
Downstream Signaling ◽  
Ancestral Function ◽  
History Of ◽  
Cell Cell

Abstract Eph receptor (Eph) and ephrin signaling regulate fundamental developmental processes through both forward and reverse signaling triggered upon cell–cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that 1) premetazoan choanoflagellates may already have rudimental Eph/ephrin signaling as they have an Eph-/ephrin-like pair and homologs of downstream-signaling genes; 2) both forward- and reverse-downstream signaling might already occur in Porifera since sponges have most genes involved in these types of signaling; 3) the nonvertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane-anchoring structure, glycosylphosphatidylinositol, or transmembrane; 4) Eph/ephrin cross-class binding is specific to Gnathostomata; and 5) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signaling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream-signaling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell–cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.

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