Evolutionary Dynamics of the DM Domain Gene Family in Metazoans

2003 ◽  
Vol 57 (0) ◽  
pp. S241-S249 ◽  
Author(s):  
Jean-Nicolas Volff ◽  
David Zarkower ◽  
Vivian J. Bardwell ◽  
Manfred Schartl
Keyword(s):  
Gene Family ◽  
Evolutionary Dynamics ◽  
Dm Domain

scholarly journals Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective

2010 ◽  
Vol 27 (7) ◽  
pp. 1645-1658 ◽  
Author(s):  
S.-J. Cho ◽  
Y. Valles ◽  
V. C. Giani ◽  
E. C. Seaver ◽  
D. A. Weisblat
Keyword(s):  
Gene Family ◽  
Evolutionary Dynamics

Origin and Diversity of Plant Receptor-Like Kinases

2020 ◽  
Vol 71 (1) ◽  
pp. 131-156 ◽  
Author(s):  
Anne Dievart ◽  
Céline Gottin ◽  
Christophe Périn ◽  
Vincent Ranwez ◽  
Nathalie Chantret
Keyword(s):  
Literature Review ◽  
Gene Family ◽  
Genome Sequence ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Land Plants ◽  
Genome Sequence Data ◽  
Receptor Like Kinase ◽  
High Level

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results.

scholarly journals A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants

2014 ◽  
Author(s):  
Johannes A. Hofberger ◽  
Beifei Zhou ◽  
Haibao Tang ◽  
Jonathan DG Jones ◽  
M. Eric Schranz
Keyword(s):  
Gene Family ◽  
Sequence Homology ◽  
Evolutionary Dynamics ◽  
Crop Improvement ◽  
Markov Modelling ◽  
Plant Genomes ◽  
Novel Approach ◽  
Gene Copies ◽  
Ecological Importance ◽  
Species Specific

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection acting on all identified genes and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean=1.59), ohnolog (mean=1.36) and singleton (mean=1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR ?gatekeeper? loci sharing syntelogs across all analyzed genomes. In summary, we designed and implemented an easy-to-follow computational framework for super-gene family identification, and provide the most curated set of NB-LRR genes whose genetic versatility among twelve lineages can underpin crop improvement.

scholarly journals Contraction of the ROS scavenging enzyme glutathioneS-transferase gene family in cetaceans

2019 ◽  
Author(s):  
Ran Tian ◽  
Inge Seim ◽  
Wenhua Ren ◽  
Shixia Xu ◽  
Guang Yang
Keyword(s):  
Gene Family ◽  
Marine Mammals ◽  
Evolutionary Dynamics ◽  
Glutathione Transferase ◽  
Mammalian Species ◽  
Environmental Pollutants ◽  
Evolutionary Model ◽  
Ros Scavenging ◽  
And Function ◽  
Gst Family

ABSTRACTCetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genesGSTA1,GSTA4, andGSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans. Taken together, our results indicate that the cytosolic GST family in cetaceans reflects unique evolutionary dynamics related to oxygen-poor aquatic environments.

scholarly journals Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling

Cells ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 560 ◽  
Author(s):  
Weilong Kong ◽  
Baoguang An ◽  
Yue Zhang ◽  
Jing Yang ◽  
Shuangmiao Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Dynamics ◽  
Brachypodium Distachyon ◽  
Oryza Rufipogon ◽  
Comparative Genomic ◽  
Sugar Transporter ◽  
Transporter Proteins ◽  
Genomic Study ◽  
Duplication Events ◽  
Selective Forces

Sugar transporter proteins (STPs), such as H+/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

Sign in / Sign up

Export Citation Format

Share Document