Genome Biology最新文献

{"title":"The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.","authors":"Oksung Chung,&nbsp;Seondeok Jin,&nbsp;Yun Sung Cho,&nbsp;Jeongheui Lim,&nbsp;Hyunho Kim,&nbsp;Sungwoong Jho,&nbsp;Hak-Min Kim,&nbsp;JeHoon Jun,&nbsp;HyeJin Lee,&nbsp;Alvin Chon,&nbsp;Junsu Ko,&nbsp;Jeremy Edwards,&nbsp;Jessica A Weber,&nbsp;Kyudong Han,&nbsp;Stephen J O'Brien,&nbsp;Andrea Manica,&nbsp;Jong Bhak,&nbsp;Woon Kee Paek","doi":"10.1186/s13059-015-0780-4","DOIUrl":"https://doi.org/10.1186/s13059-015-0780-4","url":null,"abstract":"<p><strong>Background: </strong>The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.</p><p><strong>Results: </strong>We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.</p><p><strong>Conclusions: </strong>We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"215"},"PeriodicalIF":12.3,"publicationDate":"2015-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0780-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34102743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The utility of transposon mutagenesis for cancer studies in the era of genome editing.","authors":"Gina M DeNicola,&nbsp;Florian A Karreth,&nbsp;David J Adams,&nbsp;Chi C Wong","doi":"10.1186/s13059-015-0794-y","DOIUrl":"https://doi.org/10.1186/s13059-015-0794-y","url":null,"abstract":"<p><p>The use of transposons as insertional mutagens to identify cancer genes in mice has generated a wealth of information over the past decade. Here, we discuss recent major advances in transposon-mediated insertional mutagenesis screens and compare this technology with other screening strategies. </p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"229"},"PeriodicalIF":12.3,"publicationDate":"2015-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0794-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34167722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.","authors":"Catarina A Marques, Nicholas J Dickens, Daniel Paape, Samantha J Campbell, Richard McCulloch","doi":"10.1186/s13059-015-0788-9","DOIUrl":"10.1186/s13059-015-0788-9","url":null,"abstract":"<p><strong>Background: </strong>DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania.</p><p><strong>Results: </strong>Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins.</p><p><strong>Conclusions: </strong>The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"230"},"PeriodicalIF":12.3,"publicationDate":"2015-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34099797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens.","authors":"Jian Feng,&nbsp;Matthew Wilkinson,&nbsp;Xiaochuan Liu,&nbsp;Immanuel Purushothaman,&nbsp;Deveroux Ferguson,&nbsp;Vincent Vialou,&nbsp;Ian Maze,&nbsp;Ningyi Shao,&nbsp;Pamela Kennedy,&nbsp;JaWook Koo,&nbsp;Caroline Dias,&nbsp;Benjamin Laitman,&nbsp;Victoria Stockman,&nbsp;Quincey LaPlant,&nbsp;Michael E Cahill,&nbsp;Eric J Nestler,&nbsp;Li Shen","doi":"10.1186/s13059-015-0789-8","DOIUrl":"https://doi.org/10.1186/s13059-015-0789-8","url":null,"abstract":"","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"227"},"PeriodicalIF":12.3,"publicationDate":"2015-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0789-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34088520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to: Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases.","authors":"","doi":"10.1186/s13059-015-0798-7","DOIUrl":"https://doi.org/10.1186/s13059-015-0798-7","url":null,"abstract":"","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"226"},"PeriodicalIF":12.3,"publicationDate":"2015-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0798-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34084806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.","authors":"Gabriel Renaud,&nbsp;Viviane Slon,&nbsp;Ana T Duggan,&nbsp;Janet Kelso","doi":"10.1186/s13059-015-0776-0","DOIUrl":"https://doi.org/10.1186/s13059-015-0776-0","url":null,"abstract":"<p><strong>Unlabelled: </strong>Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.</p><p><strong>Availability: </strong>https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"224"},"PeriodicalIF":12.3,"publicationDate":"2015-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0776-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34080304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Do count-based differential expression methods perform poorly when genes are expressed in only one condition?","authors":"Xiaobei Zhou,&nbsp;Mark D Robinson","doi":"10.1186/s13059-015-0781-3","DOIUrl":"https://doi.org/10.1186/s13059-015-0781-3","url":null,"abstract":"<p><p>A response to 'Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data' by Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND and Betel D in Genome Biology, 2013, 14:R95. </p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"222"},"PeriodicalIF":12.3,"publicationDate":"2015-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0781-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34073017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PfAlba1: master regulator of translation in the malaria parasite.","authors":"Evelien M Bunnik,&nbsp;Karine G Le Roch","doi":"10.1186/s13059-015-0795-x","DOIUrl":"https://doi.org/10.1186/s13059-015-0795-x","url":null,"abstract":"<p><p>During the asexual replication cycle of the malaria parasite Plasmodium falciparum, the RNA-binding protein PfAlba1 binds and stabilizes a subset of transcripts for translation at a later time point.Please see related Research article: http://www.genomebiology.com/2015/16/1/212. </p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"221"},"PeriodicalIF":12.3,"publicationDate":"2015-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0795-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34073537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response to Zhou and Robinson.","authors":"Doron Betel,&nbsp;Nicholas D Socci,&nbsp;Raya Khanin,&nbsp;Christopher E Mason,&nbsp;Franck Rapaport","doi":"10.1186/s13059-015-0782-2","DOIUrl":"https://doi.org/10.1186/s13059-015-0782-2","url":null,"abstract":"","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"223"},"PeriodicalIF":12.3,"publicationDate":"2015-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0782-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34140324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.","authors":"Fabian Schmich,&nbsp;Ewa Szczurek,&nbsp;Saskia Kreibich,&nbsp;Sabrina Dilling,&nbsp;Daniel Andritschke,&nbsp;Alain Casanova,&nbsp;Shyan Huey Low,&nbsp;Simone Eicher,&nbsp;Simone Muntwiler,&nbsp;Mario Emmenlauer,&nbsp;Pauli Rämö,&nbsp;Raquel Conde-Alvarez,&nbsp;Christian von Mering,&nbsp;Wolf-Dietrich Hardt,&nbsp;Christoph Dehio,&nbsp;Niko Beerenwinkel","doi":"10.1186/s13059-015-0783-1","DOIUrl":"https://doi.org/10.1186/s13059-015-0783-1","url":null,"abstract":"<p><p>Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package. </p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"220"},"PeriodicalIF":12.3,"publicationDate":"2015-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0783-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34069744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}