4 downloads
112 views

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.2388v1
45 downloads
374 views

Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual...

["Ecology","Genomics","Microbiology","Plant Science"]
doi:10.7717/peerj.2367
34 downloads
245 views

Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Virology"]
doi:10.7717/peerj.2326
34 downloads
362 views

Background Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however,...

["Conservation Biology","Ecology","Genetics","Genomics","Marine Biology"]
doi:10.7717/peerj.2366
44 downloads
489 views

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.2359
6 downloads
52 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:10.7287/peerj.preprints.2381v1
53 downloads
83 views

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes...

["Bioinformatics","Genomics","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2379v1
28 downloads
97 views

Identification and quantification of microorganisms is an important step in studying the alpha and beta diversities within and between microbial communities respectively. Both, identification and quantification of a given microbial community can be carried out...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.2378v1
37 downloads
297 views

Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric...

["Agricultural Science","Genomics","Plant Science"]
doi:10.7717/peerj.2334
45 downloads
442 views

The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus...

["Ecology","Entomology","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.2324
66 downloads
522 views

To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using...

["Bioinformatics","Developmental Biology","Genomics","Respiratory Medicine"]
doi:10.7717/peerj.2318
46 downloads
360 views

Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches...

["Biotechnology","Genetics","Genomics"]
doi:10.7717/peerj.2281
34 downloads
198 views

Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA-sequencing (RNA-seq) to analyse the transcriptome of a panel of...

["Genomics","Molecular Biology","Dermatology","Oncology","Medical Genetics"]
doi:10.7287/peerj.preprints.2331v1
35 downloads
268 views

The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.2272
83 downloads
112 views

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms...

["Ecology","Environmental Sciences","Genomics","Marine Biology","Microbiology"]
doi:10.7287/peerj.preprints.2315v1

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