Elevated Evolutionary Rates among Functionally Diverged Reproductive Genes across Deep Vertebrate Lineages

Among closely related taxa, proteins involved in reproduction generally evolve more rapidly than other proteins. Here, we apply a functional and comparative genomics approach to compare functional divergence across a deep phylogenetic array of egg-laying and live-bearing vertebrate taxa. We aligned and annotated a set of 4,986 1 : 1 : 1 : 1 : 1 orthologs in Anolis carolinensis (green lizard), Danio rerio (zebrafish), Xenopus tropicalis (frog), Gallus gallus (chicken), and Mus musculus (mouse) according to function using ESTs from available reproductive (including testis and ovary) and non-reproductive tissues as well as Gene Ontology. For each species lineage, genes were further classified as tissue-specific (found in a single tissue) or tissue-expressed (found in multiple tissues). Within independent vertebrate lineages, we generally find that gonadal-specific genes evolve at a faster rate than gonadal-expressed genes and significantly faster than non-reproductive genes. Among the gonadal set, testis genes are generally more diverged than ovary genes. Surprisingly, an opposite but nonsignificant pattern is found among the subset of orthologs that remained functionally conserved across all five lineages. These contrasting evolutionary patterns found between functionally diverged and functionally conserved reproductive orthologs provide evidence for pervasive and potentially cryptic lineage-specific selective processes on ancestral reproductive systems in vertebrates.

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Faculty Opinions recommendation of Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1128831.585916 ◽

2009 ◽

Author(s):

Vitaly Citovsky

Keyword(s):

Evolutionary History ◽

Functional Divergence ◽

Histone Demethylase ◽

Evolutionary Patterns ◽

History Of

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Fluorescent Light Incites a Conserved Immune and Inflammatory Genetic Response within Vertebrate Organs (Danio Rerio, Oryzias Latipes and Mus Musculus)

Genes ◽

10.3390/genes10040271 ◽

2019 ◽

Vol 10 (4) ◽

pp. 271 ◽

Cited By ~ 2

Author(s):

Boswell ◽

Lu ◽

Boswell ◽

Savage ◽

Hildreth ◽

...

Keyword(s):

Immune Responses ◽

Danio Rerio ◽

Mus Musculus ◽

Expression Patterns ◽

Solar Spectrum ◽

Oryzias Latipes ◽

Hairless Mouse ◽

Gene Clustering ◽

Fluorescent Light ◽

Evolutionary Divergence

Fluorescent light (FL) has been utilized for ≈60 years and has become a common artificial light source under which animals, including humans, spend increasing amounts of time. Although the solar spectrum is quite dissimilar in both wavelengths and intensities, the genetic consequences of FL exposure have not been investigated. Herein, we present comparative RNA-Seq results that establish expression patterns within skin, brain, and liver for Danio rerio, Oryzias latipes, and the hairless mouse (Mus musculus) after exposure to FL. These animals represent diurnal and nocturnal lifestyles, and ≈450 million years of evolutionary divergence. In all three organisms, FL induced transcriptional changes of the acute phase response signaling pathway and modulated inflammation and innate immune responses. Our pathway and gene clustering analyses suggest cellular perception of oxidative stress is promoting induction of primary up-stream regulators IL1B and TNF. The skin and brain of the three animals as well as the liver of both fish models all exhibit increased inflammation and immune responses; however, the mouse liver suppressed the same pathways. Overall, the conserved nature of the genetic responses observed after FL exposure, among fishes and a mammal, suggest the presence of light responsive genetic circuitry deeply embedded in the vertebrate genome.

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Bioinformatics of Metalloproteins and Metalloproteomes

Molecules ◽

10.3390/molecules25153366 ◽

2020 ◽

Vol 25 (15) ◽

pp. 3366

Author(s):

Yan Zhang ◽

Junge Zheng

Keyword(s):

Comparative Genomics ◽

Metal Binding ◽

Computational Prediction ◽

Bioinformatic Analysis ◽

Research Progress ◽

Evolutionary Patterns ◽

Cellular Processes ◽

Metal Binding Sites ◽

Domains Of Life ◽

Systematic Understanding

Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.

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Identification of FDA-Approved Drugs and Bioactives that Protect Hair Cells in the Zebrafish (Danio rerio) Lateral Line and Mouse (Mus musculus) Utricle

Journal of the Association for Research in Otolaryngology ◽

10.1007/s10162-009-0158-y ◽

2009 ◽

Vol 10 (2) ◽

pp. 191-203 ◽

Cited By ~ 73

Author(s):

Henry C. Ou ◽

Lisa L. Cunningham ◽

Shimon P. Francis ◽

Carlene S. Brandon ◽

Julian A. Simon ◽

...

Keyword(s):

Lateral Line ◽

Danio Rerio ◽

Hair Cells ◽

Mus Musculus ◽

Approved Drugs ◽

Fda Approved Drugs

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Comparative genomics of duplicate γ-glutamyl transferase genes in teleosts: medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), green spotted pufferfish (Tetraodon nigroviridis), fugu (Takifugu rubripes), and zebrafish (Danio rerio)

Journal of Experimental Zoology Part B Molecular and Developmental Evolution ◽

10.1002/jez.b.21439 ◽

2011 ◽

Vol 318B (1) ◽

pp. 35-49 ◽

Cited By ~ 4

Author(s):

Sheran Hiu Wan Law ◽

Benjamin David Redelings ◽

Seth William Kullman

Keyword(s):

Comparative Genomics ◽

Danio Rerio ◽

Gasterosteus Aculeatus ◽

Oryzias Latipes ◽

Takifugu Rubripes ◽

Tetraodon Nigroviridis ◽

Glutamyl Transferase

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Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

PLoS ONE ◽

10.1371/journal.pone.0011257 ◽

2010 ◽

Vol 5 (6) ◽

pp. e11257 ◽

Cited By ~ 58

Author(s):

Jonathan L. Klassen

Keyword(s):

Comparative Genomics ◽

Carotenoid Biosynthesis ◽

Evolutionary Patterns

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Different evolutionary patterns of classical swine fever virus envelope proteins

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0709 ◽

2016 ◽

Vol 62 (3) ◽

pp. 210-219 ◽

Cited By ~ 1

Author(s):

Yan Li ◽

Zexiao Yang ◽

Mingwang Zhang

Keyword(s):

Classical Swine Fever Virus ◽

Functional Divergence ◽

Classical Swine Fever ◽

Acid Sites ◽

Envelope Proteins ◽

Viral Envelope ◽

Fever Virus ◽

Host Cells ◽

Virus Envelope ◽

Evolutionary Patterns

Classical swine fever virus (CSFV) is the causative agent of classical swine fever, which is a highly contagious disease of the domestic pig as well as wild boar. The proteins Erns, E1, and E2 are components of the viral envelope membrane. They are also implicated in virus attachment and entry, replication, and (or) anti-immune response. Here, we studied the genetic variations of these envelope proteins in the evolution of CSFV. The results reveal that the envelope proteins underwent different evolutionary fates. In Ernsand E1, but not E2, a number of amino acid sites experienced functional divergence. Furthermore, the diversification in Ernsand E1 was generally episodic because the divergence-related changes of E1 only occurred with the separation of 2 major groups of CSFV and that of Ernstook place with the division of 1 major group. The major divergence-related sites of Ernsare located on one of the substrate-binding regions of the RNase domain and C-terminal extension. These functional domains have been reported to block activation of the innate immune system and attachment and entry into host cells, respectively. Our results may shed some light on the divergent roles of the envelope proteins.

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