Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

AbstractWhen and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

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Structure and Characterization of Crimean-Congo Hemorrhagic Fever Virus GP38

Journal of Virology ◽

10.1128/jvi.02005-19 ◽

2020 ◽

Vol 94 (8) ◽

Author(s):

Akaash K. Mishra ◽

Crystal L. Moyer ◽

Dafna M. Abelson ◽

Daniel J. Deer ◽

Kamel El Omari ◽

...

Keyword(s):

Crystal Structure ◽

Gene Duplication ◽

Mouse Model ◽

Hemorrhagic Fever ◽

Duplication Event ◽

Fever Virus ◽

Gene Duplication Event ◽

Protective Antibody ◽

Crimean Congo Hemorrhagic Fever ◽

Hemorrhagic Fever Virus

ABSTRACT Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of the most widespread tick-borne viral infection in humans. CCHFV encodes a secreted glycoprotein (GP38) of unknown function that is the target of a protective antibody. Here, we present the crystal structure of GP38 at a resolution of 2.5 Å, which revealed a novel fold primarily consisting of a 3-helix bundle and a β-sandwich. Sequence alignment and homology modeling showed distant homology between GP38 and the ectodomain of Gn (a structural glycoprotein in CCHFV), suggestive of a gene duplication event. Analysis of convalescent-phase sera showed high titers of GP38 antibodies indicating immunogenicity in humans during natural CCHFV infection. The only protective antibody for CCHFV in an adult mouse model reported to date, 13G8, bound GP38 with subnanomolar affinity and protected against heterologous CCHFV challenge in a STAT1-knockout mouse model. Our data strongly suggest that GP38 should be evaluated as a vaccine antigen and that its structure provides a foundation to investigate functions of this protein in the viral life cycle. IMPORTANCE Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen that poses a high risk to public health. Due to the high morbidity and mortality rates associated with CCHFV infection, there is an urgent need to develop medical countermeasures for disease prevention and treatment. CCHFV GP38, a secreted glycoprotein of unknown function unique to the Nairoviridae family, was recently shown to be the target of a protective antibody against CCHFV. Here, we present the crystal structure of GP38, which revealed a novel fold with distant homology to another CCHFV glycoprotein that is suggestive of a gene duplication event. We also demonstrate that antibody 13G8 protects STAT1-knockout mice against heterologous CCHFV challenge using a clinical isolate from regions where CCHFV is endemic. Collectively, these data advance our understanding of GP38 structure and antigenicity and should facilitate future studies investigating its function.

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Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates

Scientific Reports ◽

10.1038/srep42571 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 19

Author(s):

Madhuri A. Inupakutika ◽

Soham Sengupta ◽

Rachel Nechushtai ◽

Patricia A. Jennings ◽

Jose’ N. Onuchic ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Duplication ◽

Duplication Event ◽

Gene Duplication Event

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Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

Molecular Biology and Evolution ◽

10.1093/molbev/msz261 ◽

2019 ◽

Vol 37 (3) ◽

pp. 730-756 ◽

Cited By ~ 10

Author(s):

Irene Julca ◽

Marina Marcet-Houben ◽

Fernando Cruz ◽

Carlos Vargas-Chavez ◽

John Spencer Johnston ◽

...

Keyword(s):

Gene Duplication ◽

Large Scale ◽

Duplication Event ◽

Aphid Species ◽

Common Finding ◽

Segmental Duplications ◽

Genome Duplication Event ◽

Phloem Sap ◽

Recent Species ◽

Species Specific

Abstract Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

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Sequences encoding two trypsin inhibitors occur in strikingly similar genomic environments

Biochemical Journal ◽

10.1042/bj2330443 ◽

1986 ◽

Vol 233 (2) ◽

pp. 443-450 ◽

Cited By ~ 24

Author(s):

I B Kingston ◽

S Anderson

Keyword(s):

Gene Duplication ◽

Trypsin Inhibitor ◽

Bovine Genome ◽

Duplication Event ◽

The Other ◽

Bovine Pancreatic Trypsin Inhibitor ◽

Gene Duplication Event ◽

Coding Region ◽

Pancreatic Trypsin Inhibitor ◽

Putative Intron

The nucleotide sequences of two approx. 4 kilobase pair segments of the bovine genome are presented. One segment contains a coding region for bovine pancreatic trypsin inhibitor (BPTI) and the other segment contains a coding region for a BPTI homologue. The two 4 kilobase pair sequences are strikingly similar over approx. 3.4 kilobase pairs of their sequence, including putative intron sequences, suggesting that they have evolved from a gene duplication event.

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Mutually Exclusive Expression of Closely Related Odorant-Binding Proteins 9A and 9B in the Antenna of the Red Flour Beetle Tribolium castaneum

Biomolecules ◽

10.3390/biom11101502 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1502

Author(s):

Alice Montino ◽

Karthi Balakrishnan ◽

Stefan Dippel ◽

Björn Trebels ◽

Piotr Neumann ◽

...

Keyword(s):

Gene Duplication ◽

Tribolium Castaneum ◽

Gene Pair ◽

Binding Proteins ◽

Duplication Event ◽

Food Sources ◽

Gene Duplication Event ◽

Odorant Binding Proteins ◽

Receptor Complexes ◽

Odorant Binding

Olfaction is crucial for insects to find food sources, mates, and oviposition sites. One of the initial steps in olfaction is facilitated by odorant-binding proteins (OBPs) that translocate hydrophobic odorants through the aqueous olfactory sensilla lymph to the odorant receptor complexes embedded in the dendritic membrane of olfactory sensory neurons. The Tribolium castaneum (Coleoptera, Tenebrionidae) OBPs encoded by the gene pair TcasOBP9A and TcasOBP9B represent the closest homologs to the well-studied Drosophila melanogaster OBP Lush (DmelOBP76a), which mediates pheromone reception. By an electroantennographic analysis, we can show that these two OBPs are not pheromone-specific but rather enhance the detection of a broad spectrum of organic volatiles. Both OBPs are expressed in the antenna but in a mutually exclusive pattern, despite their homology and gene pair character by chromosomal location. A phylogenetic analysis indicates that this gene pair arose at the base of the Cucujiformia, which dates the gene duplication event to about 200 Mio years ago. Therefore, this gene pair is not the result of a recent gene duplication event and the high sequence conservation in spite of their expression in different sensilla is potentially the result of a common function as co-OBPs.

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APT1, but Not APT2, Codes for a Functional Adenine Phosphoribosyltransferase inSaccharomyces cerevisiae

Journal of Bacteriology ◽

10.1128/jb.181.1.347-352.1999 ◽

1999 ◽

Vol 181 (1) ◽

pp. 347-352 ◽

Cited By ~ 13

Author(s):

Juan D. Alfonzo ◽

Timothy R. Crother ◽

Maria L. Guetsova ◽

Bertrand Daignan-Fornier ◽

Milton W. Taylor

Keyword(s):

Escherichia Coli ◽

Saccharomyces Cerevisiae ◽

Phylogenetic Analysis ◽

Gene Duplication ◽

Genetic Analysis ◽

Duplication Event ◽

Cloning And Expression ◽

Gene Duplication Event ◽

Adenine Phosphoribosyltransferase ◽

Physiological Conditions

ABSTRACT The yeast Saccharomyces cerevisiae has two separate genes (APT1 and APT2) that encode two potentially different forms of adenine phosphoribosyltransferase (APRT). However, genetic analysis indicated that only APT1could code for a complementing activity. Cloning and expression of both the APT1 and APT2 genes in Escherichia coli showed that although discrete proteins (APRT1 and APRT2) were made by these genes, only APRT1 had detectable APRT activity. Northern and Western blot analyses demonstrated that onlyAPT1 was transcribed and translated under normal physiological conditions in yeast. Phylogenetic analysis revealed that APRT1 and APRT2 are evolutionary closely related and that they arise from a gene duplication event. We conclude that APT1 is the functional gene in S. cerevisiae and that APT2is a pseudogene.

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Conservation and divergence of ancestral AGAMOUS/SEEDSTICK subfamily genes from the basal angiosperm Magnolia wufengensis

Tree Physiology ◽

10.1093/treephys/tpz091 ◽

2019 ◽

Vol 40 (1) ◽

pp. 90-107 ◽

Cited By ~ 1

Author(s):

Jiang Ma ◽

Shixin Deng ◽

Zhongkui Jia ◽

Ziyang Sang ◽

Zhonglong Zhu ◽

...

Keyword(s):

Gene Duplication ◽

Current Knowledge ◽

Expression Profiles ◽

Expression Patterns ◽

Duplication Event ◽

Basal Angiosperm ◽

Interaction Patterns ◽

Gene Duplication Event ◽

Core Eudicots ◽

Magnolia Wufengensis

Abstract AGAMOUS/SEEDSTICK (AG/STK) subfamily genes play crucial roles in the reproductive development of plants. However, most of our current knowledge of AG/STK subfamily genes is restricted to core eudicots and grasses, and the knowledge of ancestral exon–intron structures, expression patterns, protein–protein interaction patterns and functions of AG/STK subfamily genes remains unclear. To determine these, we isolated AG/STK subfamily genes (MawuAG1, MawuAG2 and MawuSTK) from a woody basal angiosperm Magnolia wufengensis (Magnoliaceae). MawuSTK arose from the gene duplication event occurring before the diversification of extant angiosperms, and MawuAG1 and MawuAG2 may result from a gene duplication event occurring before the divergence of Magnoliaceae and Lauraceae. Gene duplication led to apparent diversification in their expression and interaction patterns. It revealed that expression in both stamens and carpels likely represents the ancestral expression profiles of AG lineage genes, and expression of STK-like genes in stamens may have been lost soon after the appearance of the STK lineage. Moreover, AG/STK subfamily proteins may have immediately established interactions with the SEPALLATA (SEP) subfamily proteins following the emergence of the SEP subfamily; however, their interactions with the APETALA1/FRUITFULL subfamily proteins or themselves differ from those found in monocots and basal and core eudicots. MawuAG1 plays highly conserved roles in the determinacy of stamen, carpel and ovule identity, while gene duplication contributed to the functional diversification of MawuAG2 and MawuSTK. In addition, we investigated the evolutionary history of exon–intron structural changes of the AG/STK subfamily, and a novel splice-acceptor mode (GUU-AU) and the convergent evolution of N-terminal extension in the euAG and PLE subclades were revealed for the first time. These results further advance our understanding of ancestral AG/STK subfamily genes in terms of phylogeny, exon–intron structures, expression and interaction patterns, and functions, and provide strong evidence for the significance of gene duplication in the expansion and evolution of the AG/STK subfamily.

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Sequence of Sockeye Salmon Type 1 and 2 Growth Hormone Genes and the Relationship of Rainbow Trout with Atlantic and Pacific Salmon

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f93-195 ◽

1993 ◽

Vol 50 (8) ◽

pp. 1738-1748 ◽

Cited By ~ 73

Author(s):

Robert H. Devlin

Keyword(s):

Growth Hormone ◽

Rainbow Trout ◽

Gene Duplication ◽

Atlantic Salmon ◽

Sockeye Salmon ◽

Pacific Salmon ◽

Duplication Event ◽

Breeding Population ◽

Gene Duplication Event ◽

Relationship Of

Two types of growth hormone genes have been isolated from sockeye salmon (Oncorhynchus nerka) and their complete nucleotide sequence determined. The genes encode proteins of 210 amino acids and show considerable similarity to growth hormones characterized in other salmonids and fishes. The two genes presumably arose from a gene duplication event that generated the tetraploid condition in salmonids and are highly conserved in their coding regions. The sequences have diverged approximately 18% in noncoding regions since the gene duplication event and show numerous deletions and/or insertions. Isolation of these two genes from a Pacific salmon allows comparison of their sequences to growth hormone genes characterized from rainbow trout and from Atlantic salmon. The results indicate that rainbow trout is more similar to Pacific than to Atlantic salmon and suggest that Atlantic salmon diverged from Pacific salmonids at a time when sockeye and rainbow trout were part of a common breeding population. These results support the recent reclassification of rainbow trout from the genus Salmo to Oncorhynchus.

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