Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest

2016 ◽  
pp. 273-284 ◽  
Author(s):  
Lorenzo Carretero-Paulet ◽  
Victor A. Albert
Keyword(s):  
Evolutionary Dynamics ◽  
Gene Families

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families inAegilops tauschii

2016 ◽  
Vol 87 (5) ◽  
pp. 495-506 ◽  
Author(s):  
Lingli Dong ◽  
Naxin Huo ◽  
Yi Wang ◽  
Karin Deal ◽  
Daowen Wang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Evolutionary Dynamics ◽  
Chromosomal Region ◽  
Gene Families

scholarly journals Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes

2018 ◽  
Vol 28 (11) ◽  
pp. 1664-1674 ◽  
Author(s):  
Neel Prabh ◽  
Waltraud Roeseler ◽  
Hanh Witte ◽  
Gabi Eberhardt ◽  
Ralf J. Sommer ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Gene Families ◽  
Taxon Sampling ◽  
Novel Gene

scholarly journals Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Yocelyn T Gutiérrez-Guerrero ◽  
Enrique Ibarra-Laclette ◽  
Carlos Martínez del Río ◽  
Josué Barrera-Redondo ◽  
Eria A Rebollar ◽  
...  
Keyword(s):  
Positive Selection ◽  
Evolutionary Dynamics ◽  
Feeding Habits ◽  
Parallel Evolution ◽  
Gene Families ◽  
Feeding Strategies ◽  
Phylogenomic Analysis ◽  
Glucose Content ◽  
Nectar Feeding ◽  
Dietary Diversification

Abstract Background The New World leaf-nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown. Results We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled, and annotated the genomes of five Phyllostomid species: one insect feeder (Macrotus waterhousii), one fruit feeder (Artibeus jamaicensis), and three nectar feeders from the Glossophaginae subfamily (Leptonycteris yerbabuenae, Leptonycteris nivalis, and Musonycteris harrisoni), also including the previously sequenced vampire Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar–feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids. Conclusions Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content.

scholarly journals Differential Evolutionary Constraints in the Evolution of Chemoreceptors: A Murine and Human Case Study

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Ricardo D’Oliveira Albanus ◽  
Rodrigo Juliani Siqueira Dalmolin ◽  
José Luiz Rybarczyk-Filho ◽  
Mauro Antônio Alves Castro ◽  
José Cláudio Fonseca Moreira
Keyword(s):  
Evolutionary Dynamics ◽  
Homo Sapiens ◽  
Phylogenetic Analyses ◽  
Gene Families ◽  
Human Case ◽  
Evolutionary Constraints ◽  
Copy Numbers ◽  
Vomeronasal Receptors ◽  
Processing Pathways ◽  
Network Topologies

Chemoreception is among the most important sensory modalities in animals. Organisms use the ability to perceive chemical compounds in all major ecological activities. Recent studies have allowed the characterization of chemoreceptor gene families. These genes present strikingly high variability in copy numbers and pseudogenization degrees among different species, but the mechanisms underlying their evolution are not fully understood. We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes inMus musculus,Homo sapiens, andRattus norvegicus. We have observed significant differences regarding the constraints on the orthologous groups and network topologies of chemoreceptors and signal transduction machinery. Our findings suggest that chemosensory receptor genes are less constrained than their signal transducing machinery, resulting in greater receptor diversity and conservation of information processing pathways. More importantly, we have observed significant differences among the receptors themselves, suggesting that olfactory and bitter taste receptors are more conserved than vomeronasal receptors.

scholarly journals The Ecology of Bacterial Genes and the Survival of the New

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
M. Pilar Francino
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Gene Families ◽  
Relative Importance ◽  
Gene Duplications ◽  
Bacterial Genomes ◽  
Selective Pressures ◽  
Different Types ◽  
Bacterial Genes ◽  
Gains And Losses

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

scholarly journals Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species

2019 ◽  
Author(s):  
Kyungyong Seong ◽  
Eunyoung Seo ◽  
Meng Li ◽  
Brian Staskawicz
Keyword(s):  
Single Molecule ◽  
Evolutionary Dynamics ◽  
Plant Immunity ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Wild Tomato Species ◽  
Most Recent Common Ancestor ◽  
Tomato Species ◽  
Large Gene ◽  
And Function

AbstractBackgroundNucleotide-binding and leucine-rich repeat immune receptors (NLRs) are an important component of plant immunity that provides resistance against diverse pathogens. NLRs often exist as large gene families, the members of which display diverse multi-domain architectures (MDAs) and evolve through various mechanisms of duplications and selections.ResultsWe conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real time (SMRT) sequencing of PacBio for 18 accessions in Solanaceae including 15 wild tomatoes. We demonstrate what was previously known as Solanaceae Domain (SD) not only is more diverse in structure and function but also far anciently originated from the most recent common ancestor (MRCA) between Asterids and Amaranthaceae. In tomato, NLRs with the extended N-terminus displayed distinct patterns of evolution based on phylogenetic clades by proliferation, continuous elongation and domain losses.ConclusionsOur study provides high quality gene models of NLRs that can serve as resources for future studies for crop engineering and elucidates greater evolutionary dynamics of the extended NLRs than previously assumed.

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 Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

2021 ◽  
Author(s):  
Maxime Policarpo ◽  
Katherine E Bemis ◽  
Patrick Laurenti ◽  
Laurent Legendre ◽  
Jean-Christophe Sandoz ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Evolutionary Dynamics ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Olfactory Organ ◽  
Functional Link ◽  
Receptor Repertoire ◽  
Mola Mola ◽  
Main Gene ◽  
Olfactory Receptor Genes

Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.

scholarly journals Rapid expansion of immune-related gene families in the house fly, Musca domestica

2016 ◽  
Author(s):  
Timothy B. Sackton ◽  
Brian P. Lazzaro ◽  
Andrew G. Clark
Keyword(s):  
Bacterial Infection ◽  
Musca Domestica ◽  
Evolutionary Dynamics ◽  
Gene Families ◽  
House Fly ◽  
Gene Family Evolution ◽  
Rapid Expansion ◽  
Whole Transcriptome Sequencing ◽  
Gene Duplication And Loss ◽  
Immune Related Genes

AbstractThe house fly, Musca domestica, occupies an unusual diversity of potentially septic niches among sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies by bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes. Genes up-regulated after bacterial infection are biased toward being evolutionarily recent innovations, suggesting the recruitment of novel immune components in the M. domestica or ancestral Dipteran lineages. In addition, using new models of gene family evolution, we show that several different classes of immune-related genes, particularly those involved in either pathogen recognition or pathogen killing, are duplicating at a significantly accelerated rate on the M. domestica lineage relative to other Dipterans. Taken together, these results suggest that the M. domestica immune response includes an unusual diversity of genes, perhaps as a consequence of its lifestyle in septic environments.

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