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Zachary L. Fuller Elina L. Ni?o Harland M. Patch Oscar C. Bedoya-Reina Tracey Baumgarten Elliud Muli Fiona Mumoki Aakrosh Ratan John McGraw Maryann Frazier Daniel Masiga Stephen Schuster Christina M. Grozinger Webb Miller 《BMC genomics》2015,16(1)
Background
With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including FST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.Results
We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.Conclusions
These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1712-0) contains supplementary material, which is available to authorized users. 相似文献2.
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Daniel I Speiser M Sabrina Pankey Alexander K Zaharoff Barbara A Battelle Heather D Bracken-Grissom Jesse W Breinholt Seth M Bybee Thomas W Cronin Anders Garm Annie R Lindgren Nipam H Patel Megan L Porter Meredith E Protas Ajna S Rivera Jeanne M Serb Kirk S Zigler Keith A Crandall Todd H Oakley 《BMC bioinformatics》2014,15(1)
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《基因组蛋白质组与生物信息学报(英文版)》2022,20(3):557-567
MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA prediction tools. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users in selecting promising miRNA candidates in an interactive mode, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We also illustrate the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity. The source codes and web server of iwa-miRNA are freely accessible at http://iwa-miRNA.omicstudio.cloud/. 相似文献
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ABSTRACT: A report on the Galaxy Community Conference at the University of Illinois, Chicago, July 25-27, 2012. 相似文献
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Milan M. Ćirković Branislav Vukotić 《Origins of life and evolution of the biosphere》2008,38(6):535-547
Can astrophysics explain Fermi’s paradox or the “Great Silence” problem? If available, such explanation would be advantageous over most of those suggested in literature which rely on unverifiable cultural and/or sociological assumptions. We suggest, instead, a general astrobiological paradigm which might offer a physical and empirically testable paradox resolution. Based on the idea of James Annis, we develop a model of an astrobiological phase transition of the Milky Way, based on the concept of the global regulation mechanism(s). The dominant regulation mechanisms, arguably, are γ-ray bursts, whose properties and cosmological evolution are becoming well-understood. Secular evolution of regulation mechanisms leads to the brief epoch of phase transition: from an essentially dead place, with pockets of low-complexity life restricted to planetary surfaces, it will, on a short (Fermi–Hart) timescale, become filled with high-complexity life. An observation selection effect explains why we are not, in spite of the very small prior probability, to be surprised at being located in that brief phase of disequilibrium. In addition, we show that, although the phase-transition model may explain the “Great Silence”, it is not supportive of the “contact pessimist” position. To the contrary, the phase-transition model offers a rational motivation for continuation and extension of our present-day Search for ExtraTerrestrial Intelligence (SETI) endeavours. Some of the unequivocal and testable predictions of our model include the decrease of extinction risk in the history of terrestrial life, the absence of any traces of Galactic societies significantly older than human society, complete lack of any extragalactic intelligent signals or phenomena, and the presence of ubiquitous low-complexity life in the Milky Way. 相似文献
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