• The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and ...divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
• We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world’s oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.
• Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
• The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
Summary
Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new ...cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance.
A nanopore‐based assembly anchored to a high‐resolution linkage map provided a chromosome‐resolved genome for CBDRx, a potent CBD‐type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed.
Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD‐type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio.
Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.
Families of Dothideomycetes Hyde, Kevin D; Jones, Gareth E B; Liu, Jian-Kui ...
Fungal diversity,
11/2013, Letnik:
63, Številka:
1
Journal Article
Recenzirano
Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with ...many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.
Technological advances have yielded new molecular biology-based methods for the diagnosis of infectious diseases. The newest and most powerful molecular diagnostic tests are available at regional ...and national reference laboratories, as well as at specialized centers that are certified to conduct metagenomic testing. Metagenomic assays utilize advances in DNA extraction technology, DNA sequence library construction, high throughput DNA sequencing and automated data analysis to identify millions of individual strands of DNA extracted from clinical samples. At present, metagenomic assays are only possible at a small number of special research, academic and commercial laboratories. Continued research in human and pathogen genomic organization and host-pathogen interactions, represent important future goals that will maximize the information obtained from metagenomic assays. To illustrate the power and limitations of metagenomics, we report on a previously healthy 27 year old woman with work related exposure to ill animals, and who developed a rapidly progressive, severe diffuse interstitial pneumonitis that ultimately ended in the need for a double lung transplant. Metagenomic testing on DNA extracted from pleural fluid and nasopharyngeal swabs demonstrated the presence of expected normal bacterial flora along with some unexpected herpesvirus and non-HIV retroviral elements integrated into the patients DNA. Although no specific pathogen was ultimately identified to explain this patient’s severe disease, the sample preparation and data analysis methods detailed herein illustrate the powerful benefits and limitations of metagenomic testing.
• Understanding the genetic basis of natural variation in grain size among diverse rice varieties can help breeders develop high-yielding rice cultivars.
• Here, we report the discovery of qTGW2, a ...new semidominant quantitative trait locus for grain width and weight. The corresponding gene, TGW2, encodes CELL NUMBER REGULATOR 1 (OsCNR1) localized to the plasma membrane.
• A single nucleotide polymorphism (SNP) variation 1818 bp upstream of TGW2 is responsible for its different expression, leading to alteration in grain width and weight by influencing cell proliferation and expansion in glumes. TGW2 interacts with KRP1, a regulator of cell cycle in plants, to negatively regulate grain width and weight. Genetic diversity analysis of TGW2 in 141 rice accessions revealed it as a breeding target in a selective sweep region.
• Our findings provide new insights into the genetic mechanism underlying grain morphology and grain weight, and uncover a promising gene for improving rice yield.
DNA visibility graphs Kosmidis, Kosmas; Hütt, Marc-Thorsten
Physica A,
09/2023, Letnik:
626
Journal Article
Recenzirano
DNA walks are mathematical representations of DNA sequences that have been used to study the long-range organization of DNA. Visibility graphs are network representations of time series that give ...access to features usually difficult to analyze on the time series level alone. Here we combine the two approaches and introduce the concept of DNA visibility graphs. The main goal of our investigation is to calibrate this new tool by analyzing DNA visibility graphs for various random DNA sequences.
Our results show that the method is robust with respect to the arbitrary choice of step up for pyrimidine (C or T) and step down for purine (A or G), and varies predictably with respect to sequence composition (notably the pyrimidine content, pC+pT). Short range correlations cause changes in the topology of the visibility graphs, with more profound changes occurring near a balanced composition point pC+pT∼0.5.
As a first illustration of the applicability of DNA visibility graphs, we study the full genome of the bacterium Escherichia coli and compare DNA visibility graphs for short DNA sequences from different domains of life. These initial results show an approximate power law for the degree distribution of the E. coli DNA visibility graph and systematic differences in the clustering coefficients and other topological quantities of DNA visibility graphs between bacteria and eukaryotic species.
Our findings suggest that DNA Visibility Graphs can be a powerful tool for studying the properties of DNA and may provide new insights into its structure and function.
•DNA visibility graphs combine visibility graphs and DNA walks.•Focus on synthetic sequences to establish this new method of studying DNA sequences.•Two applications of the method to real DNA sequences are shown.•DNA visibility graph for E. coli has a power law degree distribution.•Topological properties differ between bacterial and eukaryotic sequences.
Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated ...91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial β-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
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•Proposed model combines baseline predictions for enhancer accuracy.•Uses physiochemical descriptors for sequence and epigenetic data.•Outperforms existing techniques in accuracy and ...specificity.•Important for genetics, genomics, and biomedical research.
Enhancers are DNA regions that are responsible for controlling the expression of genes. Enhancers are usually found upstream or downstream of a gene, or even inside a gene’s intron region, but are normally located at a distant location from the genes they control. By integrating experimental and computational approaches, it is possible to uncover enhancers within DNA sequences, which possess regulatory properties. Experimental techniques such as ChIP-seq and ATAC-seq can identify genomic regions that are associated with transcription factors or accessible to regulatory proteins. On the other hand, computational techniques can predict enhancers based on sequence features and epigenetic modifications. In our study, we have developed a multi-classifier stacked ensemble (MCSE-enhancer) model that can accurately identify enhancers. We utilized feature descriptors from various physiochemical properties as input for our six baseline classifiers and built a stacked classifier, which outperformed previous enhancer classification techniques in terms of accuracy, specificity, sensitivity, and Mathew’s correlation coefficient. Our model achieved an accuracy of 81.5%, representing a 2–3% improvement over existing models.
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough ...research on practical and efficient coding schemes to enable accurate recovery of stored data. To this end, we consider a simplified model of a nanopore sequencer inspired by Mao et al ., incorporating intersymbol interference and measurement noise. Essentially, our channel model passes a sliding window of length l over a q -ary input sequence that outputs the composition of the enclosed l bits, and shifts by δ positions with each time step. In this context, the composition of a q -ary vector x specifies the number of occurrences in x of each symbol in {0,1,..., q - 1}. The resulting compositions vector, termed the read vector , may also be corrupted by t substitution errors. By employing graph-theoretic techniques, we deduce that for δ = 1, at least log log n symbols of redundancy are required to correct a single ( t = 1) substitution. Finally, for l ≥ 3, we exploit some inherent characteristics of read vectors to arrive at an error-correcting code that is of optimal redundancy up to a (small) additive constant for this setting. This construction is also found to be optimal for the case of reconstruction from two noisy read vectors.
Abstract A special‐purpose Committee on DNA Sequences as Types was established at the XIX International Botanical Congress (IBC) in Shenzhen, China, in 2017, with a mandate to report to the XX IBC in ...Madrid in 2024 with recommendations on a preferred course of action with respect to potential amendments of the International Code of Nomenclature for algae, fungi, and plants to allow DNA sequences as types. This is the first in an expected series of papers from the Special‐purpose Committee on this issue. We set out the background to the establishment of the Committee, explore key issues around typification that are pertinent to the question of DNA sequences as types, enumerate pros and cons of allowing DNA sequences as types, and foreshadow options for future discussion and potential recommendations.
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