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Open AccessA novel approach to exploring the dark genome and its application to map** of the vertebrate virus fossil record
Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (E...
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Article
Open AccessGenomic and common garden data reveal significant genetic differentiation in the endangered San Fernando Valley spineflower Chorizanthe parryi var. fernandina
San Fernando Valley spineflower (Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought to be ex...
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Open AccessBiogeography of Beringian fishes after the molecular revolution and into the post-genomics era
Significant progress in our knowledge of Beringian biodiversity and in the technologies available for biodiversity research has been made in the several decades since a comprehensive biogeographic synthesis of...
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Article
Open AccessWhen nets meet environmental DNA metabarcoding: integrative approach to unveil invertebrate community patterns of hypersaline lakes
Saline and hypersaline wetlands account for almost half of the volume of inland water globally. They provide pivotal habitat for a vast range of species, including crucial ecosystem services for humans such as...
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Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous
Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record...
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Open AccessAuthor Correction: The SEQC2 epigenomics quality control (EpiQC) study
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Open AccessThe SEQC2 epigenomics quality control (EpiQC) study
Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other dis...
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Open AccessPublisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Open AccessSex-dependent dominance maintains migration supergene in rainbow trout
Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict a...
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Open AccessBeringian sub-refugia revealed in blackfish (Dallia): implications for understanding the effects of Pleistocene glaciations on Beringian taxa and other Arctic aquatic fauna
Pleistocene climatic instability had profound and diverse effects on the distribution and abundance of Arctic organisms revealed by variation in phylogeographic patterns documented in extant Arctic populations...
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Open AccessThe transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba
The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. ...
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Open AccessHyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species
Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how express...
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Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)
Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is ...
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Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes. The conversion of these genetic variants (the most prevalent of these being single...
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Open AccessComprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (...
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Article
Engineering Pathogen Resistance in Crop Plants
As the world population continues to increase, food supplies must also grow to meet nutritional requirements. One means of ensuring the stability and plentitude of the food supply is to mitigate crop loss caus...
