scholarly journals Applying comparative genomics to plant disease epidemiology

2004 ◽  
Vol 85 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Linda M. Kohn
Keyword(s):  
Magnaporthe Grisea ◽  
Sequence Data ◽  
Population Level ◽  
Avirulence Genes ◽  
Genome Database ◽  
Disease Epidemiology ◽  
Dna Sequence Data ◽  
Specific Pathogen ◽  
Pathogen Populations ◽  
Genomic Regions

Astract Phylogenetic or genealogical interpretation of DNA sequence data from multiple genomic regions has become the gold standard for species delimitation and population genetics. Precise species concepts can inform quarantine decisions but are likely to reflect evolutionary events too far in the past to impact disease management. On the other hand, multilocus approaches at the population level can identify patterns of endemism or migration directly associated with episodes of disease, including host shifts and associated changes in determinants of pathogenicity and avirulence. We used the genome database of Magnaporthe grisea to frame a comparative, multilocus genomics approach from which we demonstrate a single origin for rice infecting genotypes with concomitant loss of sex in pandemic clonal lineages, and patterns of gain and loss of avirulence genes. In the Sclerotinia sclerotiorum pathosystem, we identified significant associations of multilocus haplotypes with specific pathogen populations in North America. Following the introduction of a new crop, endemic pathogen genotypes and newly evolved migrant genotypes caused novel, early-season symptoms.

scholarly journals Biogeographic evidence supports the Old Amazon hypothesis for the formation of the Amazon fluvial system

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12533
Author(s):  
Karen Méndez-Camacho ◽  
Omar Leon-Alvarado ◽  
Daniel R. Miranda-Esquivel
Keyword(s):  
Amazon Basin ◽  
Sequence Data ◽  
Population Level ◽  
Ancestral Reconstruction ◽  
Fluvial System ◽  
Dna Sequence Data ◽  
Molecular Phylogenetic ◽  
Log Normal ◽  
Log Normal Distribution ◽  
Relaxed Clock

The Amazon has high biodiversity, which has been attributed to different geological events such as the formation of rivers. The Old and Young Amazon hypotheses have been proposed regarding the date of the formation of the Amazon basin. Different studies of historical biogeography support the Young Amazon model, however, most studies use secondary calibrations or are performed at the population level, preventing evaluation of a possible older formation of the Amazon basin. Here, we evaluated the fit of molecular phylogenetic and biogeographic data to previous models regarding the age of formation of the Amazon fluvial system. We reconstructed time-calibrated molecular phylogenies through Bayesian inference for six taxa belonging to Amphibia, Aves, Insecta and Mammalia, using both, nuclear and mitochondrial DNA sequence data and fossils as calibration points, and explored priors for both data sources. We detected the most plausible vicariant barriers for each phylogeny and performed an ancestral reconstruction analysis using areas bounded by major Amazonian rivers, and therefore, evaluated the effect of different dispersal rates over time based on geological and biogeographical information. The majority of the genes analyzed fit a relaxed clock model. The log normal distribution fits better and leads to more precise age estimations than the exponential distribution. The data suggested that the first dispersals to the Amazon basin occurred to Western Amazonia from 16.2–10.4 Ma, and the taxa covered most of the areas of the Amazon basin between 12.2–6.2 Ma. Additionally, regardless of the method, we obtained evidence for two rivers: Tocantins and Madeira, acting as vicariant barriers. Given the molecular and biogeographical analyses, we found that some taxa were fitted to the “Old Amazon” model.

scholarly journals Variation in Akt protein kinases in human populations

2017 ◽  
Vol 313 (6) ◽  
pp. R687-R692 ◽  
Author(s):  
Peter Rotwein
Keyword(s):  
Human Physiology ◽  
Metabolic Regulation ◽  
Hormone Receptors ◽  
Sequence Data ◽  
Normal Growth ◽  
Population Level ◽  
Human Populations ◽  
Dna Sequence Data ◽  
Disease Predisposition ◽  
Biochemical Signals

The three Akt kinases are related proteins that are essential for normal growth and metabolic regulation and are implicated as key signaling mediators in many physiological and pathophysiological processes. Each Akt is activated by common biochemical signals that act downstream of growth factor and hormone receptors via phosphatidylinositol-3 kinase, and each controls several downstream pathways. The importance of Akt actions in human physiology is strengthened by the rarity of modifying mutations in their genes and by the devastating impact caused by these mutations on growth and development and in disorders such as cancer. Recent advances in genomics present unique opportunities for enhancing our understanding of human physiology and disease predisposition through the lens of population genetics, and the availability of DNA sequence data from 60,706 people in the Exome Aggregation Consortium has prompted this analysis. Results reveal a cohort of potential missense and other alterations in the coding regions of each AKT gene, but with nearly all changes being uncommon. The total number of different alleles per gene varied over an approximately threefold range, from 52 for AKT3 to 158 for AKT2, with variants distributed throughout all Akt protein domains. Previously characterized disease-causing mutations were found rarely in the general population. In contrast, a fairly prevalent amino acid substitution in AKT2 appears to be linked to increased predisposition for type 2 diabetes. Further analysis of variant Akt molecules as identified here will provide opportunities to understand the intricacies of Akt signaling and actions at a population level in human physiology and pathology.

scholarly journals A hybrid capture RNA bait set for resolving genetic and evolutionary relationships in angiosperms from deep phylogeny to intraspecific lineage hybridization

2021 ◽  
Author(s):  
Michelle Waycott ◽  
Jent Kornelis van Dijk ◽  
Ed Biffin
Keyword(s):  
Sequence Data ◽  
Evolutionary Relationships ◽  
Plastid Gene ◽  
High Quality ◽  
Transcriptomic Data ◽  
Dna Sequence Data ◽  
Evolutionary Studies ◽  
High Quality Sequence ◽  
Targeted Capture ◽  
Genomic Regions

Novel multi-gene targeted capture probes have been developed with the objective of obtaining multi-locus high quality sequence reads across any angiosperm lineage. Using existing genomic and transcriptomic data, two independent single assay probe/bait sets have been developed, the first targeting conserved exons from 20 low copy nuclear genes (OzBaits_NR V1.0) and the second, 19 plastid gene regions (OZBaits_CP V1.0). These universal bait sets can efficiently generate DNA sequence data that are suitable for systematics and evolutionary studies of flowering plants. The bait sets can be ordered as Daicel-Arbor Sciences custom myBaits. We demonstrate the utility of the bait set in consistently recovering the targeted genomic regions across an evolutionarily broad range of angiosperm taxa.

scholarly journals Utility of Population-Level DNA Sequence Data in the Diagnosis of Hereditary Endocrine Disease

2017 ◽  
Vol 1 (12) ◽  
pp. 1507-1526 ◽  
Author(s):  
Paul J Newey ◽  
Jonathan N Berg ◽  
Kaixin Zhou ◽  
Colin N A Palmer ◽  
Rajesh V Thakker
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Population Level ◽  
Endocrine Disease ◽  
Dna Sequence Data

Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams

2003 ◽  
Vol 54 (7) ◽  
pp. 807 ◽  
Author(s):  
Stephen F. Chenoweth ◽  
Jane M.Hughes
Keyword(s):  
Sequence Data ◽  
Sequence Divergence ◽  
Population Level ◽  
Specific Rate ◽  
Dna Sequence Data ◽  
Freshwater Streams ◽  
Freshwater Shrimps ◽  
Eastern Australia ◽  
North Eastern ◽  
Mtdna Lineages

The Caridina indistincta complex is a group of closely related atyid shrimps that inhabit coastal freshwater streams throughout north-eastern Australia. Using mitochondrial DNA sequence data (cytochrome oxidase 1, CO1), we (1) inferred the timing of speciation in the C. indistincta group and (2) examined the intraspecific phylogeographic patterns within the group. Assuming a shrimp-specific rate of CO1 evolution, the level of sequence divergence among species suggests that speciation took place during the Miocene epoch. Within one widespread mainland species, phylogeographic patterns suggest strong geographic 'regionalisation' of mtDNA lineages that are most likely of Pleistocene origin. By contrast, another species comprises two highly divergent mtDNA lineages that occur in sympatry. We suggest that although Pleistocene sea-level regressions appear important in generating population-level phylogeographic patterns, these events were largely unimportant in the formation of species in this group.

scholarly journals IGD: high-performance search for large-scale genomic interval datasets

2020 ◽  
Author(s):  
Jianglin Feng ◽  
Nathan C Sheffield
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Interval Data ◽  
Scale Analysis ◽  
Genome Database ◽  
Genomic Interval ◽  
Critical Resource ◽  
Genomic Regions ◽  
Genome Projects

Abstract Summary Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions. Availability https://github.com/databio/IGD

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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