Sequence Analyses to Study the Evolutionary History and Cis-Regulatory Elements of Hedgehog Genes

Abstract The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5′ exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage.

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Insulinlike Growth Factor 1 Gene Variation in Vertebrates

Endocrinology ◽

10.1210/en.2018-00259 ◽

2018 ◽

Vol 159 (6) ◽

pp. 2288-2305 ◽

Cited By ~ 9

Author(s):

Peter Rotwein

Keyword(s):

Evolutionary History ◽

Somatic Growth ◽

Regulatory Elements ◽

Single Chain ◽

Exon 2 ◽

Gene Variation ◽

Large Intron ◽

Different Types ◽

Transcriptional Pathway ◽

Igf1 Expression

Abstract IGF1—a small, single-chain, secreted peptide in mammals—is essential for normal somatic growth and is involved in a variety of other physiological and pathophysiological processes. IGF1 expression appears to be controlled by several different signaling mechanisms in mammals, with GH playing a key role by activating an inducible transcriptional pathway via the Jak2 protein kinase and the Stat5b transcription factor. Here, to understand aspects of Igf1 gene regulation over a substantially longer timeline than is discernible in mammals, Igf1 genes have been examined in 21 different nonmammalian vertebrates representing five different classes and ranging over ∼500 million years of evolutionary history. Parts of vertebrate Igf1 genes resemble components found in mammals. Conserved exons encoding the mature IGF1 protein are detected in all 21 species studied and are separated by a large intron, as seen in mammals; the single promoter contains putative regulatory elements that are similar to those functionally mapped in human IGF1 promoter 1. In contrast, GH-activated Stat5b-binding enhancers found in mammalian IGF1 loci are completely absent, there is no homolog of promoter 2 or exon 2 in any nonmammalian vertebrate, and different types of “extra” exons not present in mammals are found in birds, reptiles, and teleosts. These data collectively define properties of Igf1 genes and IGF1 proteins that were likely present in the earliest vertebrates and support the contention that common structural and regulatory features in Igf1 genes have a long evolutionary history.

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Tissue-specific ramp sequences correspond with increased gene expression in humans and SARS-CoV-2

10.21203/rs.3.rs-738082/v1 ◽

2021 ◽

Author(s):

Justin Miller ◽

Taylor Meurs ◽

Matthew Hodgman ◽

Benjamin Song ◽

Mark Ebbert ◽

...

Keyword(s):

Gene Expression ◽

Cell Types ◽

Regulatory Elements ◽

Targeted Therapeutics ◽

Cell Type ◽

Sequence Analyses ◽

Tissue Specific ◽

Cell Type Specific ◽

Viral Proliferation ◽

Increase Gene Expression

Abstract Translational ramp sequences are essential regulatory elements that have yet to be characterized in specific tissues. Ramp sequences increase gene expression by evenly spacing ribosomes and slowing initial translation. Therefore, the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. Here, we present the first comprehensive analysis of tissue and cell type-specific ramp sequences, and report 3,108 genes with ramp sequences that change between tissues and cell types. The Ramp Atlas (https://ramps.byu.edu/) is an accompanying web portal that allows researchers to query ramp sequences in 18,388 genes across 62 tissues and 66 cell types. We also identified seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate future tissue-specific ramp sequence analyses to develop targeted therapeutics for human disease.

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Ensembl 2021

Nucleic Acids Research ◽

10.1093/nar/gkaa942 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D884-D891 ◽

Cited By ~ 1

Author(s):

Kevin L Howe ◽

Premanand Achuthan ◽

James Allen ◽

Jamie Allen ◽

Jorge Alvarez-Jarreta ◽

...

Keyword(s):

Comparative Genomics ◽

Evolutionary History ◽

Genomic Data ◽

Regulatory Elements ◽

Vertebrate Species ◽

Variant Effect Predictor ◽

Rapid Release ◽

History Of ◽

Genome Browsers ◽

Gene Structures

Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

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Detection of natural hybridization and delimitation of two closely related operational taxonomic units of the Astyanax fasciatus (Teleostei: Characidae) complex through integrative approaches

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz199 ◽

2020 ◽

Vol 129 (3) ◽

pp. 687-700

Author(s):

Mariane Gavazzoni ◽

Carla S Pavanelli ◽

Weferson J Graça ◽

Bruno F Melo ◽

Éder André Gubiani ◽

...

Keyword(s):

South America ◽

Evolutionary History ◽

Natural Hybridization ◽

Secondary Contact ◽

Sequence Analyses ◽

Southern South America ◽

Operational Taxonomic Units ◽

Astyanax Fasciatus ◽

History Of ◽

Uruguay River

Abstract Astyanax is a species-rich, non-monophyletic genus composed of several supraspecific taxa that are poorly delimited. The Astyanax fasciatus complex is one of these taxa and shows high taxonomic complexity. To elucidate the evolutionary history of the A. fasciatus complex from southern South America, we conducted cytogenetic, molecular and morphological analyses in specimens from the Uruguay River basin. Cytogenetic characters demonstrated two closely related operational taxonomic units: Astyanax sp. 1 (8m+22sm+10st+6a), Astyanax sp. 2 (8m+24sm+10st+4a) and natural hybrids (8m+23sm+8st+5a). 5S ribosomal DNA sites were found in two pairs of m chromosomes and one pair of a chromosomes in Astyanax sp. 1, two pairs of a chromosomes and one pair of m chromosomes in Astyanax sp. 2, and three m chromosomes and three a chromosomes in hybrids. As51 sites were found in three chromosomes in Astyanax sp. 1 and in five chromosomes in Astyanax sp. 2 and hybrids. Mitochondrial sequence analyses did not separate the two units and hybrids. Morphological analyses revealed differences between Astyanax sp. 2 and hybrids. This secondary contact with gene flow between lineages that diverged long ago might slow or reverse the differentiation/speciation process. These results help us to understand the evolutionary history of this highly complex clade of Astyanax in southern South America.

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Stress-Free Evolution: The Nrf-Coordinated Oxidative Stress Response in Early Diverging Metazoans

Integrative and Comparative Biology ◽

10.1093/icb/icz055 ◽

2019 ◽

Vol 59 (4) ◽

pp. 799-810 ◽

Cited By ~ 6

Author(s):

Liam B Doonan ◽

Ashlie Hartigan ◽

Beth Okamura ◽

Paul F Long

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Evolutionary History ◽

Regulatory Elements ◽

Oxidative Stress Response ◽

Last Common Ancestor ◽

Redox Control ◽

Functional Responses ◽

Regulatory Pathways ◽

History Of

Abstract Environmental stress from ultraviolet radiation, elevated temperatures or metal toxicity can lead to reactive oxygen species in cells, leading to oxidative DNA damage, premature aging, neurodegenerative diseases, and cancer. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) activates many cytoprotective proteins within the nucleus to maintain homeostasis during oxidative stress. In vertebrates, Nrf2 levels are regulated by the Kelch-family protein Keap1 (Kelch-like ECH-associated protein 1) in the absence of stress according to a canonical redox control pathway. Little, however, is known about the redox control pathway used in early diverging metazoans. Our study examines the presence of known oxidative stress regulatory elements within non-bilaterian metazoans including free living and parasitic cnidarians, ctenophores, placozoans, and sponges. Cnidarians, with their pivotal position as the sister phylum to bilaterians, play an important role in understanding the evolutionary history of response to oxidative stress. Through comparative genomic and transcriptomic analysis our results show that Nrf homologs evolved early in metazoans, whereas Keap1 appeared later in the last common ancestor of cnidarians and bilaterians. However, key Nrf–Keap1 interacting domains are not conserved within the cnidarian lineage, suggesting this important pathway evolved with the radiation of bilaterians. Several known downstream Nrf targets are present in cnidarians suggesting that cnidarian Nrf plays an important role in oxidative stress response even in the absence of Keap1. Comparative analyses of key oxidative stress sensing and response proteins in early diverging metazoans thus provide important insights into the molecular basis of how these lineages interact with their environment and suggest a shared evolutionary history of regulatory pathways. Exploration of these pathways may prove important for the study of cancer therapeutics and broader research in oxidative stress, senescence, and the functional responses of early diverging metazoans to environmental change.

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New insights into the evolutionary history ofPlasmodium falciparumfrom mitochondrial genome sequence analyses of Indian isolates

Molecular Ecology ◽

10.1111/mec.12800 ◽

2014 ◽

Vol 23 (12) ◽

pp. 2975-2987 ◽

Cited By ~ 11

Author(s):

Suchi Tyagi ◽

Veena Pande ◽

Aparup Das

Keyword(s):

Mitochondrial Genome ◽

Genome Sequence ◽

Evolutionary History ◽

Sequence Analyses ◽

Mitochondrial Genome Sequence ◽

Indian Isolates

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Going Forward and Back: The Complex Evolutionary History of the GPx

Biology ◽

10.3390/biology10111165 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1165

Author(s):

Thomaz Stumpf Trenz ◽

Camila Luiza Delaix ◽

Andreia Carina Turchetto-Zolet ◽

Marcel Zamocky ◽

Fernanda Lazzarotto ◽

...

Keyword(s):

Amino Acid ◽

Glutathione Peroxidase ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Common Ancestor ◽

Sequence Analyses ◽

History Of ◽

Substrate Usage ◽

Encoding Genes ◽

Complex Evolutionary History

There is large diversity among glutathione peroxidase (GPx) enzymes regarding their function, structure, presence of the highly reactive selenocysteine (SeCys) residue, substrate usage, and reducing agent preference. Moreover, most vertebrate GPxs are very distinct from non-animal GPxs, and it is still unclear if they came from a common GPx ancestor. In this study, we aimed to unveil how GPx evolved throughout different phyla. Based on our phylogenetic trees and sequence analyses, we propose that all GPx encoding genes share a monomeric common ancestor and that the SeCys amino acid was incorporated early in the evolution of the metazoan kingdom. In addition, classical GPx and the cysteine-exclusive GPx07 have been present since non-bilaterian animals, but they seem to have been lost throughout evolution in different phyla. Therefore, the birth-and-death of GPx family members (like in other oxidoreductase families) seems to be an ongoing process, occurring independently across different kingdoms and phyla.

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Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews)

Molecular Biology and Evolution ◽

10.1093/molbev/msaa137 ◽

2020 ◽

Vol 37 (10) ◽

pp. 2931-2943 ◽

Cited By ~ 1

Author(s):

Michael Buckley ◽

Virginia L Harvey ◽

Johanset Orihuela ◽

Alexis M Mychajliw ◽

Joseph N Keating ◽

...

Keyword(s):

Evolutionary History ◽

Greater Antilles ◽

Cayman Islands ◽

Geographical Isolation ◽

Sequence Analyses ◽

Evolutionary Patterns ◽

Caribbean Islands ◽

The Past ◽

History Of ◽

The Caribbean

Abstract Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

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