Evolution of cow nonstomach lysozyme genes

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1082-1090 ◽  
Author(s):  
David M Irwin
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Adaptive Evolution ◽  
Concerted Evolution ◽  
Gene Evolution ◽  
Gene Duplications ◽  
Cdna Sequences ◽  
Defence Enzymes ◽  
And Function

Expansion of the lysozyme gene family is associated with the evolution of the ruminant lifestyle in ruminant artiodactyls such as the cow. Gene duplications allowed recombination between stomach lysozyme genes that may have assisted in the evolution of an enzyme adapted to survive and function in the stomach environment. Despite amplification of lysozyme genes, cow tears, milk, and blood are considered to be lysozyme deficient. Here we have identified 2 new cow lysozyme cDNA sequences and show that at least 4 different lysozymes are expressed in cows in nonstomach tissues and probably function as antibacterial defence enzymes. These 4 lysozyme genes are in addition to the 4 digestive lysozyme genes expressed in the stomach, yielding a number of expressed lysozyme genes in the cow larger than that found in most nonlysozyme-deficient mammals. In contrast to expectations, evidence for recombination between stomach and nonstomach lysozyme genes was found. Recombination, through concerted evolution, may have allowed some lysozymes to acquire the ability to survive in occasional acidic environments.Key words: molecular evolution, adaptive evolution, lysozyme, ruminants, gene duplication, gene evolution.

scholarly journals Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8813 ◽  
Author(s):  
Kyle T. David ◽  
Jamie R. Oaks ◽  
Kenneth M. Halanych
Keyword(s):  
Gene Duplication ◽  
Gene Evolution ◽  
Strong Support ◽  
Duplication Event ◽  
Gene Trees ◽  
Loss Of Function ◽  
Eukaryotic Genes ◽  
Gene Copies ◽  
Duplication Events ◽  
And Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

scholarly journals Recurrent single-gene duplication drives the expansion and expression diversification of the ADH gene family in pear and other Rosaceae species

2019 ◽  
Author(s):  
Shaoling Zhang ◽  
Weiwei Zeng ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Chunxin Liu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Aromatic Compounds ◽  
Gene Evolution ◽  
Single Gene ◽  
Gene Clusters ◽  
Fruit Species ◽  
Rosaceae Species ◽  
Adh Genes ◽  
Adh Gene

Abstract Background Alcohol dehydrogenases (ADHs) are essential to plant growth and the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Chinese white pear ( Pyrus bretschneideri ) and other fruit species from the family Rosaceae.Results In this study, 464 ADH genes were identified in eight Rosaceae fruit species and 68 of the genes were from pear. Based on the analyses of phylogeny and conserved motifs, the pear ADH genes were classified into four subgroups (I, II, III, and IV). The chromosomal distribution of the genes was found to be uneven and numerous clusters of physically linked ADH genes were detected. Frequent single-gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those that derived from other types of duplication. RNA-sequencing and quantitative-real time-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds that are found during fruit development.Conclusion Comprehensive analyses were conducted in eight Rosaceae species and 464 ADH genes were identified. The results of this study provide new insights into the evolution and expression characteristics of ADH family genes in pear and other Rosaceae species.

scholarly journals RAD51 Gene Family Structure and Function

2020 ◽  
Vol 54 (1) ◽  
pp. 25-46 ◽  
Author(s):  
Braulio Bonilla ◽  
Sarah R. Hengel ◽  
McKenzie K. Grundy ◽  
Kara A. Bernstein
Keyword(s):  
Dna Repair ◽  
Gene Family ◽  
Dna Sequences ◽  
Strand Break ◽  
Structure And Function ◽  
Model Systems ◽  
Gene Duplications ◽  
Rad51 Gene ◽  
Its Gene ◽  
And Function

Accurate DNA repair and replication are critical for genomic stability and cancer prevention. RAD51 and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of RAD51, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the RAD51 gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.

scholarly journals Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples

2018 ◽  
Vol 19 (9) ◽  
pp. 2807 ◽  
Author(s):  
Baiquan Ma ◽  
Yangyang Yuan ◽  
Meng Gao ◽  
Tonghui Qi ◽  
Mingjun Li ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Functional Divergence ◽  
Aluminum Tolerance ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Gene Families ◽  
Biochemical Properties ◽  
Evolutionary Pattern

Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the “Golden Delicious” doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.

scholarly journals Comparative molecular evolution of chitinases in ascomycota with emphasis on mycoparasitism lifestyle

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Chao Wang ◽  
Zhao-Qing Zeng ◽  
Wen-Ying Zhuang
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Pathogenic Fungi ◽  
Scientific Basis ◽  
Acid Sites ◽  
Point Of View ◽  
Fungal Life Cycle ◽  
Group B ◽  
Chitinase Genes ◽  
And Function

Chitinases are involved in multiple aspects of fungal life cycle, such as cell wall remodelling, chitin degradation and mycoparasitism lifestyle. To improve our knowledge of the chitinase molecular evolution of Ascomycota, the gene family of 72 representatives of this phylum was identified and subjected to phylogenetic, evolution trajectory and selective pressure analyses. Phylogenetic analysis showed that the chitinase gene family size and enzyme types varied significantly, along with species evolution, especially for groups B and C. In addition, two new subgroups, C3 and C4, are recognized in group C chitinases. Random birth and death testing indicated that gene expansion and contraction occurred in most of the taxa, particularly for species in the order Hypocreales (class Sordariomycetes). From an enzyme function point of view, we speculate that group A chitinases are mainly involved in species growth and development, while the expansion of genes in group B chitinases is related to fungal mycoparasitic and entomopathogenic abilities, and, to a certain extent, the expansion of genes in group C chitinases seems to be correlated with the host range broadening of some plant-pathogenic fungi in Sordariomycetes. Further selection pressure testing revealed that chitinases and the related amino acid sites were under positive selection in the evolutionary history, especially at the nodes sharing common ancestors and the terminal branches of Hypocreales. These results give a reasonable explanation for the size and function differences of chitinase genes among ascomycetes, and provide a scientific basis for understanding the evolutionary trajectories of chitinases, particularly that towards a mycoparasitic lifestyle.

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