Peer-reviewed Articles

48 downloads
446 views

Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative...

["Ecology","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.2777
60 downloads
264 views

Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the...

["Genomics","Plant Science"]
doi:10.7717/peerj.2734
69 downloads
322 views

Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary...

["Biochemistry","Genomics","Microbiology","Molecular Biology"]
doi:10.7717/peerj.2720
53 downloads
261 views

C-type cytoplasmic male sterility (CMS-C) is widely utilized for hybrid maize seed production. However, genetic mechanisms underlying the fertility restoration are very complicated. At present, there is a divergence on the number of fertility restorer genes in...

["Agricultural Science","Genetics","Genomics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.2719
129 downloads
489 views

Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians...

["Cell Biology","Evolutionary Studies","Genomics","Marine Biology"]
doi:10.7717/peerj.2692
108 downloads
399 views

The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and...

["Biodiversity","Biotechnology","Genetics","Genomics","Plant Science"]
doi:10.7717/peerj.2699
191 downloads
925 views

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology","Soil Science"]
doi:10.7717/peerj.2687
60 downloads
447 views

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.2681
102 downloads
627 views

Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments....

["Bioinformatics","Computational Biology","Genomics","Microbiology","Computational Science"]
doi:10.7717/peerj.2676
60 downloads
203 views

Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the...

["Bioinformatics","Evolutionary Studies","Genetics","Genomics","Zoology"]
doi:10.7717/peerj.2617
67 downloads
229 views

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible...

["Aquaculture, Fisheries and Fish Science","Genomics","Marine Biology","Microbiology"]
doi:10.7717/peerj.2595
65 downloads
456 views

Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is...

["Aquaculture, Fisheries and Fish Science","Conservation Biology","Ecology","Genomics","Molecular Biology"]
doi:10.7717/peerj.2593
82 downloads
325 views

After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably...

["Biochemistry","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7717/peerj.2626
91 downloads
330 views

Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are...

["Evolutionary Studies","Genomics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.2627
2 citations
289 downloads
1,754 views

Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010)...

["Biodiversity","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.2584

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