Preprints (not yet peer-reviewed)

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms,...

["Bioinformatics","Genomics","Molecular Biology","Plant Science"]
doi:10.7287/peerj.preprints.26545v1
44 downloads
322 views

Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional...

["Biodiversity","Evolutionary Studies","Genomics","Plant Science","Taxonomy"]
doi:10.7287/peerj.preprints.26530v1
32 downloads
82 views

Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.26515v1
18 downloads
51 views

Background: Identifying and characterizing genetic variation can clarify the molecular basis of biological phenomena in plants. In particular, related or morphologically similar species can be distinguished by molecular markers. Pinus densiflora Siebold & Zucc....

["Genomics","Plant Science"]
doi:10.7287/peerj.preprints.26506v1
66 downloads
98 views

Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present the first nuclear genome and transcriptome...

["Evolutionary Studies","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.26488v1
115 downloads
459 views

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3266v4
654 downloads
1,772 views

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging...

["Biodiversity","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.26449v3
93 downloads
214 views

The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and its order as in other known bryophyte chondriomes. The genome contains...

["Biodiversity","Evolutionary Studies","Genomics","Plant Science","Taxonomy"]
doi:10.7287/peerj.preprints.3465v2
100 downloads
149 views

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem...

["Genetics","Genomics","Taxonomy","Zoology"]
doi:10.7287/peerj.preprints.26466v1
112 downloads
192 views

Background. Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, which often is associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. The CMS phenomenon...

["Agricultural Science","Genetics","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.26438v1
78 downloads
366 views

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric...

["Evolutionary Studies","Genetics","Genomics"]
doi:10.7287/peerj.preprints.4043v1
78 downloads
436 views

Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines...

["Bioinformatics","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7287/peerj.preprints.3525v1
379 downloads
513 views

Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics...

["Bioinformatics","Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2961v2
190 downloads
499 views

Although recent advances in molecular methods have facilitated understanding the evolution of fungal symbiosis, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae...

["Biodiversity","Ecology","Genomics","Microbiology","Mycology"]
doi:10.7287/peerj.preprints.3408v3
123 downloads
259 views

Unknown sequences, or gaps, are largely present in most published genomes across public databases. Gap filling is an important finishing step in de novo genome assembly, especially in large genomes. The gap filling problem is nontrivial and while many computational...

["Bioinformatics","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3467v1
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