scholarly journals Functional Divergence of the Glutathione S-Transferase Supergene Family in Physcomitrella patens Reveals Complex Patterns of Large Gene Family Evolution in Land Plants

2012 ◽  
Vol 161 (2) ◽  
pp. 773-786 ◽  
Author(s):  
Yan-Jing Liu ◽  
Xue-Min Han ◽  
Lin-Ling Ren ◽  
Hai-Ling Yang ◽  
Qing-Yin Zeng
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Functional Divergence ◽  
Gene Family Evolution ◽  
Land Plants ◽  
Glutathione S Transferase ◽  
Large Gene Family ◽  
Large Gene ◽  
Complex Patterns ◽  
Supergene Family

Phylogenetics and evolution of Trx SET genes in fully sequenced land plants

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 269-280 ◽  
Author(s):  
Xinyu Zhu ◽  
Caoyi Chen ◽  
Baohua Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Functional Divergence ◽  
Experimental Studies ◽  
Land Plants ◽  
Orthologous Group ◽  
Evolutionary Stage ◽  
Evolutionary Analysis ◽  
Genes Encoding ◽  
Gene Structures

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET–PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

scholarly journals A large gene family in fission yeast encodes spore killers that subvert Mendel’s law

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Wen Hu ◽  
Zhao-Di Jiang ◽  
Fang Suo ◽  
Jin-Xin Zheng ◽  
Wan-Zhong He ◽  
...  
Keyword(s):  
Gene Family ◽  
Fission Yeast ◽  
Reference Genome ◽  
Natural Isolate ◽  
Large Gene Family ◽  
Mendelian Segregation ◽  
Killing Effect ◽  
Selfish Genetic Elements ◽  
Large Gene ◽  
Rapid Divergence

Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.

scholarly journals Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes

2017 ◽  
Author(s):  
Daniel S. Carvalho ◽  
James C. Schnable ◽  
Ana Maria R. Almeida
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Tree ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Phylogenetic Methods ◽  
Combined Use ◽  
Approaches To Study ◽  
Additional Support ◽  
Network Approaches

AbstractThe study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide more robust assessments of gene family evolution.

Production of Polyclonal Antibodies against Pregnancy Associated Glycoprotein in Cattle

2020 ◽  
Keyword(s):  
Gene Family ◽  
False Positive ◽  
Half Life ◽  
Hormone Level ◽  
Polyclonal Antibodies ◽  
Large Gene Family ◽  
Precise Method ◽  
Large Gene ◽  
High Level ◽  
Positive Results

Pregnancy-associated glycoproteins (PAGs) are considered to be a large gene family in the trophoblasts of ruminants. PAGs determination precisely, PAG-1 in serum has been as the solid ground for pregnancy diagnosis in cow. Unluckily the PAG-1 and the antigenically related PAGs show a long half-life in serum less than 8 days and can be assessed 80 to 100 das postpartum, thereafter giving false results in cows bred within 60 days of calving. This study involves using novel polyclonal antibodies after immunizing rabbits and purification of the produced antibodies. The cattle are pregnant when the PAG hormone level is measured in a high level in a serum sample from the animal. It could give a precise method of detecting pregnancy at the early with few false positive results.

The NLR (NBD-LRR containing) Family of Intracellular Sensors in Inflammation and Immune Response.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. SCI-22-SCI-22
Author(s):  
Jenny P-Y. Ting
Keyword(s):  
Immune Response ◽  
Cell Death ◽  
Gene Family ◽  
Conflicts Of Interest ◽  
Type I ◽  
Nucleotide Binding Domain ◽  
Large Gene Family ◽  
Large Gene ◽  
Leucine Rich Repeats ◽  
Production Cell

Abstract Abstract SCI-22 The NLR gene family encodes proteins that are comprised of conserved nucleotide-binding domain (NBD) and leucine rich-repeats (LRR). These genes are conserved from plants, lower animals to mammals. Family members include CIITA, NOD1, NOD2, and NLRP3. Several of these genes are genetically linked to immunodeficiency, inflammatory and immune diseases. This large gene family controls a number of innate responses, including inflammasome function leading to IL-1b/IL-18 production, cell death and type I IFN production. This talk will discuss the broad function of this family of genes, with emphasis on their regulation of inflammation and innate immunity, and their divergent roles in pathogen responses. Disclosures No relevant conflicts of interest to declare.

■ REVIEW : Olfactory Receptors: A Large Gene Family with Broad Affinities and Multiple Functions

1996 ◽  
Vol 2 (5) ◽  
pp. 262-271 ◽  
Author(s):  
Gordon M. Shepherd ◽  
Michael S. Singer ◽  
Charles A. Greer
Keyword(s):  
Gene Family ◽  
Olfactory Receptors ◽  
Large Gene Family ◽  
Multiple Functions ◽  
Large Gene

scholarly journals Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

2019 ◽  
Vol 20 (7) ◽  
pp. 1750 ◽  
Author(s):  
Ghulam Qanmber ◽  
Ji Liu ◽  
Daoqian Yu ◽  
Zhao Liu ◽  
Lili Lu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Plant Species ◽  
Functional Divergence ◽  
Rapid Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Promoter Regions ◽  
Large Gene ◽  
Receptor Kinases

Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.

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