Peer-reviewed Articles

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Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis...

["Biodiversity","Genomics","Microbiology"]
doi:10.7717/peerj.3837
2 downloads
2 views

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization...

["Agricultural Science","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3747
17 downloads
161 views

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this...

["Evolutionary Studies","Genetics","Genomics"]
doi:10.7717/peerj.3715
20 downloads
263 views

The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis...

["Bioinformatics","Evolutionary Studies","Genetics","Genomics"]
doi:10.7717/peerj.3824
30 downloads
404 views

The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the...

["Animal Behavior","Entomology","Evolutionary Studies","Genomics","Zoology"]
doi:10.7717/peerj.3798
36 downloads
235 views

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3729
31 downloads
257 views

A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases,...

["Evolutionary Studies","Genetics","Genomics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.3790
44 downloads
245 views

MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3776
50 downloads
169 views

Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role...

["Genomics","Microbiology"]
doi:10.7717/peerj.3698
55 downloads
681 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3788
133 downloads
669 views

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents...

["Bioinformatics","Evolutionary Studies","Genomics","Molecular Biology","Zoology"]
doi:10.7717/peerj.3702
60 downloads
261 views

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence...

["Agricultural Science","Genetics","Genomics","Plant Science"]
doi:10.7717/peerj.3731
33 downloads
237 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7717/peerj.3720
100 downloads
537 views

While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography,...

["Genomics","Taxonomy","Zoology"]
doi:10.7717/peerj.3724
77 downloads
498 views

Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.3712

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