Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes ( > 0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assemblyThis work was supported by projects MEDIMAX BFPU2013-48007-P, VIREVO CGL2016- 76273-P [AEI/FEDER, EU], (cofunded with FEDER funds) and Acciones de dinaminación REDES DE EXCELENCIA CONSOLIDER CGL2015-71523- REDC, from the Spanish Ministerio de Economía y Competitividad; and project AQUAMET PROMETEOII/2014/012 from Generalitat Valenciana. JMHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). MLP was supported with a Postdoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (APOSTD/2016/051). RGS was supported with a Predoctoral fellowship from the Valencian Consellería de Educació Investigació, Cultura i Esport (ACIF/2016/050

Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.[Background]: Most proteins have evolved in specific cellular compartments that limit their functions and potential interactions. On the other hand, motifs define amino acid arrangements conserved between protein family members and represent powerful tools for assigning function to protein sequences. The ideal motif would identify all members of a protein family but in practice many motifs identify both family members and unrelated proteins, referred to as True Positive (TP) and False Positive (FP) sequences, respectively. [Results]: To address the relationship between protein motifs, protein function and cellular localization, we systematically assigned subcellular localization data to motif sequences from the comprehensive PROSITE sequence motif database. Using this data we analyzed relationships between localization and function. We find that TPs and FPs have a strong tendency to localize in different compartments. When multiple localizations are considered, TPs are usually distributed between related cellular compartments. We also identified cases where FPs are concentrated in particular subcellular regions, indicating possible functional or evolutionary relationships with TP sequences of the same motif. [Conclusions]: Our findings suggest that the systematic examination of subcellular localization has the potential to uncover evolutionary and functional relationships between motif-containing sequences. We believe that this type of analysis complements existing motif annotations and could aid in their interpretation. Our results shed light on the evolution of cellular organelles and potentially establish the basis for new subcellular localization and function prediction algorithms.We acknowledge institutional support from the Junta de Andalucía to the CABD, and to the Unit of Information Resources for Research at the “Consejo Superior de Investigaciones Científicas” (CSIC) for the article-processing charge contribution.Peer Reviewe

Recombination events and variability among full-length genomes of co-circulating molluscum contagiosum virus subtypes 1 and 2

Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and causes a highly prevalent human disease of the skin characterized by the formation of a variable number of lesions that can persist for prolonged periods of time. Two major genotypes, subtype 1 and subtype 2, are recognized, although currently only a single complete genomic sequence corresponding to MCV subtype 1 is available. Using next-generation sequencing techniques, we report the complete genomic sequence of four new MCV isolates, including the first one derived from a subtype 2. Comparisons suggest a relatively distant evolutionary split between both MCV subtypes. Further, our data illustrate concurrent circulation of distinct viruses within a population and reveal the existence of recombination events among them. These results help identify a set of MCV genes with potentially relevant roles in molluscum contagiosum epidemiology and pathogenesis. © 2017 The Authors

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assemblySpanish Ministerio de Economía y Competitividad; and project AQUAMET PROMETEOII/2014/012 from Generalitat Valenciana. JMHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828).Peer Reviewe

General features of complete genomes and putative host assignment.

<p>General features of complete genomes and putative host assignment.</p

Reconstruction of Metagenome-Assembled Viral Genomes (MAVGs) using sequences belonging to Cluster-2.

<p>A nucleotide comparison of several highly related contigs coming from different metagenomic samples is shown. Selected genes are labeled and colored uniformly.</p

Distribution of metagenomic viral contigs by length (Kb) and GC content (%).

<p>Bacterial phages are open circles and colored according to the host assigned.</p

Recruitment of the Viral clusters (VCs) and singletons that recruits more than 10 RPKG (Reads per Kilobase of genome and Gigabase of metagenome) in at least two stations of the <i>Tara</i> Oceans viromes.

<p>Left axis and dotted line indicates depth of sample. Upper panel shows the normalized value of total VCs by the number of stations belonging to SRF (surface) DCM (deep chlorophyll maximum) and DEEP (deep). Region abbreviations are as follows: ANTA, Antarctic Province; ARAB, Northwest Arabian Sea Upwelling Province; BENG, Benguela Current Coastal Province; CHIL, Chile-Peru Current Coastal Province; EAFR, Eastern Africa Coastal Province; FKLD, Southwest Atlantic Shelves Province; ISSG, Indian South Subtropical Gyre Province; MEDI, Mediterranean Sea Black Sea Province; MONS, Indian Monsoon Gyres Province; REDS, Red Sea; SATL, South Atlantic Gyral Province.</p