RESUMEN
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
Asunto(s)
Regulación de la Expresión Génica , Metagenoma , Océanos y Mares , Transcriptoma/genética , Geografía , Microbiota/genética , Anotación de Secuencia Molecular , ARN Mensajero/genética , ARN Mensajero/metabolismo , Agua de Mar/microbiología , TemperaturaRESUMEN
MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.
Asunto(s)
Genoma , Metagenoma , Aminoácidos/química , Automatización , Biología Computacional , Bases de Datos de Proteínas , Conjuntos de Datos como Asunto , Programas InformáticosRESUMEN
SUMMARY: ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes. AVAILABILITY AND IMPLEMENTATION: ViPTree is freely available at: http://www.genome.jp/viptree . CONTACT: goto@kuicr.kyoto-u.ac.jp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Genoma Viral , Anotación de Secuencia Molecular/métodos , Proteómica/métodos , Programas Informáticos , Proteínas Virales/genética , Virus/clasificación , Genómica/métodos , Metagenoma , Metagenómica/métodos , Proteínas Virales/clasificación , Virus/genéticaRESUMEN
Environmental genomics can describe all forms of organisms--cellular and viral--present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts.