scholarly journals Shedding new light on opsin evolution

2011 ◽  
Vol 279 (1726) ◽  
pp. 3-14 ◽  
Author(s):  
Megan L. Porter ◽  
Joseph R. Blasic ◽  
Michael J. Bok ◽  
Evan G. Cameron ◽  
Thomas Pringle ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Current Model ◽  
Expression Patterns ◽  
Model Organisms ◽  
Biological Functions ◽  
Site Specific ◽  
History Of ◽  
Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

scholarly journals ­­Building a reference Transcriptome for Juniperus squamata (Cupressaceae) based on Single-molecule real-time sequencing

2021 ◽  
Author(s):  
Yufei Wang ◽  
Siyu Xie ◽  
Jialiang Li ◽  
Jieshi Tang ◽  
Tsam Ju ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Evolutionary History ◽  
Full Length ◽  
Model Organisms ◽  
Rna Seq ◽  
Data Description ◽  
History Of ◽  
Simple Sequence

Abstract Objectives Cupressaceae is the second largest family of coniferous trees (Coniferopsida) with important economic and ecological values. However, like other conifers, the members of Cupressaceae have extremely large genome (>8 gigabytes), which limited the researches of these taxa. A high-quality transcriptome is an important resource for gene discovery and annotation for non-model organisms. Data descriptionJuniperus squamata, a tetraploid species which is widely distributed in Asian mountains, represents the largest genus, Juniperus, in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of Juniperus squamata. The full-length transcriptome was corrected with Illumina RNA-seq data from the same individual. A total of 47, 860 non-redundant full-length transcripts, N50 of which was 2, 839, were obtained. Simple sequence repeats for Juniperus squamata were also identified. This data presents the first comprehensive transcriptome characterization of Cupressaceae species, and provides an important reference for researches on the genomic evolutionary history of Cupressaceae plants and even conifers in the future.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals Identification and Characterization of a Novel clcn7 Variant Associated With Osteopetrosis

2020 ◽  
Author(s):  
Dmitrii S. Bug ◽  
Ildar M. Barkhatov ◽  
Yana V. Gudozhnikova ◽  
Artem V. Tishkov ◽  
Natalia V. Petukhova ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Evolutionary History ◽  
Hot Spot ◽  
Phylogenetic Reconstruction ◽  
Novel Variant ◽  
Uncertain Significance ◽  
Precise Diagnosis ◽  
History Of ◽  
Identification And Characterization

Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same “hot spot” as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps predicting phenotypical consequences of variants of uncertain significance.

scholarly journals Defaunation precipitates the extinction of evolutionarily distinct interactions in the Anthropocene

2019 ◽  
Vol 5 (6) ◽  
pp. eaav6699 ◽  
Author(s):  
Carine Emer ◽  
Mauro Galetti ◽  
Marco A. Pizo ◽  
Pedro Jordano ◽  
Miguel Verdú
Keyword(s):  
Seed Dispersal ◽  
Evolutionary History ◽  
Bird Species ◽  
Forest Fragments ◽  
Ecological Interactions ◽  
Rescue Effect ◽  
History Of ◽  
Local Extinctions ◽  
Functional Features ◽  
Avian Seed Dispersal

Species on Earth are interconnected with each other through ecological interactions. Defaunation can erode those connections, yet we lack evolutionary predictions about the consequences of losing interactions in human-modified ecosystems. We quantified the fate of the evolutionary history of avian–seed dispersal interactions across tropical forest fragments by combining the evolutionary distinctness of the pairwise-partner species, a proxy to their unique functional features. Both large-seeded plant and large-bodied bird species showed the highest evolutionary distinctness. We estimate a loss of 3.5 to 4.7 × 104 million years of cumulative evolutionary history of interactions due to defaunation. Bird-driven local extinctions mainly erode the most evolutionarily distinct interactions. However, the persistence of less evolutionarily distinct bird species in defaunated areas exerts a phylogenetic rescue effect through seed dispersal of evolutionarily distinct plant species.

scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

scholarly journals Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i516-i524
Author(s):  
Midori Iida ◽  
Michio Iwata ◽  
Yoshihiro Yamanishi
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Therapeutic Targets ◽  
Molecular Networks ◽  
Supplementary Information ◽  
New Associations ◽  
Disease States ◽  
Molecular Features ◽  
Novel Approach

Abstract Motivation Disease states are distinguished from each other in terms of differing clinical phenotypes, but characteristic molecular features are often common to various diseases. Similarities between diseases can be explained by characteristic gene expression patterns. However, most disease–disease relationships remain uncharacterized. Results In this study, we proposed a novel approach for network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets. We performed large-scale analyses of omics data and molecular interaction networks for 79 diseases, including adrenoleukodystrophy, leukaemia, Alzheimer's disease, asthma, atopic dermatitis, breast cancer, cystic fibrosis and inflammatory bowel disease. We quantified disease–disease similarities based on proximities of abnormally expressed genes in various molecular networks, and showed that similarities between diseases could be explained by characteristic molecular network topologies. Furthermore, we developed a kernel matrix regression algorithm to predict the commonalities of drugs and therapeutic targets among diseases. Our comprehensive prediction strategy indicated many new associations among phenotypically diverse diseases. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Development and characterization of twelve new polymorphic microsatellite loci in the Iberian ribbed newt, Pleurodeles waltl (Caudata: Salamandridae), with data on cross-amplification in P. nebulosus

2014 ◽  
Vol 35 (1) ◽  
pp. 129-134 ◽  
Author(s):  
Jorge Gutiérrez-Rodríguez ◽  
Elena G. Gonzalez ◽  
Íñigo Martínez-Solano
Keyword(s):  
Population Dynamics ◽  
Microsatellite Loci ◽  
Evolutionary History ◽  
The Novel ◽  
Expected Heterozygosity ◽  
History Of ◽  
Southern Iberia ◽  
Polymorphic Microsatellite ◽  
Pleurodeles Waltl

Twelve novel polymorphic microsatellite loci were isolated and characterized for the Iberian ribbed newt, Pleurodeles waltl (Caudata, Salamandridae). The distribution of this newt ranges from central and southern Iberia to northwestern Morocco. Polymorphism of these novel loci was tested in 40 individuals from two Iberian populations and compared with previously published markers. The number of alleles per locus ranged from two to eight. Observed and expected heterozygosity ranged from 0.13 to 0.57 and from 0.21 to 0.64, respectively. Cross-species amplification was tested in Pleurodeles nebulosus, which is listed as Vulnerable by the IUCN. Eight new and seven previously published loci amplified successfully in that species and thus represent a valuable conservation tool. The novel microsatellites will be useful for a better understanding of the population dynamics, demography, genetic structure, and evolutionary history of Pleurodeles waltl and P. nebulosus.

The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

2019 ◽  
Vol 94 (2) ◽  
pp. 366-377 ◽  
Author(s):  
Bryan M. Gee ◽  
Robert R. Reisz
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Phylogenetic Position ◽  
Early Permian ◽  
Larval Form ◽  
Terrestrial Environments ◽  
History Of ◽  
Insight Into

AbstractNanobamus macrorhinus Schoch and Milner, 2014 is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon's autapomorphies. Our analysis of the taxon's phylogenetic position within Amphibamiformes shows that N. macrorhinus was recovered as diverging after basal amphibamiforms, e.g., the micropholids, and before derived amphibamiforms, e.g., the amphibamids. This is supported by the unique mixture of retained plesiomorphies, e.g., nonforeshortened postparietals and an oval choana, and apomorphies, e.g., a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.

scholarly journals RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Li ◽  
Lan Jiang ◽  
Ke Wang ◽  
Hai-Jun Wu ◽  
Rui-Heng Yang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Its Region ◽  
Wide Distribution ◽  
Specific Primers ◽  
Ophiocordyceps Sinensis ◽  
Single Genome ◽  
History Of ◽  
Geographic Populations ◽  
Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

scholarly journals Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140806 ◽  
Author(s):  
Daniel B. Thomas ◽  
Kevin J. McGraw ◽  
Michael W. Butler ◽  
Matthew T. Carrano ◽  
Odile Madden ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
High Performance ◽  
Evolutionary History ◽  
Carotenoid Pigments ◽  
Biological Functions ◽  
The Family ◽  
Family Level ◽  
History Of ◽  
Living Species ◽  
Insight Into

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66–56 Myr), and not at the base of crown-lineage birds.

Sign in / Sign up

Export Citation Format

Share Document