Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria ...viridis), a model species for studies of C
grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were ...sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.
Summary
The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM ...habit within the hyperdiverse Russulaceae.
We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales, of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens.
The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell wall‐degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE ‘nests’, or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species‐specific manner. The genome of G. convolvens possesses some characteristics of ECM genomes (e.g. loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters).
Functional specialization in ECM decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.
Background: Medial elbow laxity develops in throwing athletes due to valgus forces. Medial elbow instability in professional, collegiate, and high school athletes is well documented; however, the ...medial elbow of young throwing athletes has received less attention. This study investigated the medial elbow and common flexor tendon during applied elbow valgus stress of youth baseball players. Methods: The study included 15 participants. The medial elbow width and thickness of the common flexor tendon were measured on ultrasound images. Results: No significant side differences in medial elbow width or common flexor tendon were found at rest or under applied valgus stress. At rest, the medial elbow joint width was 3.34±0.94 mm on the dominant side and 3.42±0.86 mm on the non-dominant side. The dominant side increased to 3.83±1.02 mm with applied valgus stress, and the non-dominant side increased to 3.96±1.04 mm. The mean flexor tendon thickness was 3.89±0.63 mm on the dominant side and 4.02±0.70 mm on the non-dominant side. Conclusions: These findings differ from similar studies in older throwing athletes, likely because of the lack of accumulated stress on the medial elbow of youth throwing athletes. Maintaining elbow stability in young throwing athletes is a vital step to preventing injury later in their careers.
Background: Medial elbow laxity develops in throwing athletes due to valgus forces. Medial elbow instability in professional, collegiate, and high school athletes is well documented; however, the ...medial elbow of young throwing athletes has received less attention. This study investigated the medial elbow and common flexor tendon during applied elbow valgus stress of youth baseball players. Methods: The study included 15 participants. The medial elbow width and thickness of the common flexor tendon were measured on ultrasound images. Results: No significant side differences in medial elbow width or common flexor tendon were found at rest or under applied valgus stress. At rest, the medial elbow joint width was 3.34±0.94 mm on the dominant side and 3.42±0.86 mm on the non-dominant side. The dominant side increased to 3.83±1.02 mm with applied valgus stress, and the non-dominant side increased to 3.96±1.04 mm. The mean flexor tendon thickness was 3.89±0.63 mm on the dominant side and 4.02±0.70 mm on the non-dominant side. Conclusions: These findings differ from similar studies in older throwing athletes, likely because of the lack of accumulated stress on the medial elbow of youth throwing athletes. Maintaining elbow stability in young throwing athletes is a vital step to preventing injury later in their careers. KCI Citation Count: 0
This paper presents a complete protection scheme for detecting, classifying and locating the fault in HVDC transmission lines using support vector machines (SVM). SVM has been used for protective ...relaying application in HVAC transmission line, however very limited works have been reported for HVDC transmission line. In this work, a ±500 kV HVDC transmission system is developed in PSCAD/EMTDC and the measurement signals obtained are analyzed in MATLAB. The rectifier side AC RMS voltage, DC voltage and current on both the poles are continuously monitored, and given as input to the SVM binary classifier in order to detect the presence of fault in the line. Once a fault is detected, the SVM multi-class classification module predicts the type of fault and the SVM regression algorithm predicts the location of fault. The feature vector used in the classification and location modules is the standard deviation of the signals over half cycle before and after the occurrence of fault. The method proposed is simple as it requires single-end data and a direct standard deviation of one cycle data gives very accurate results. The detection and classification modules are 100% accurate whereas the fault location module has a mean error of 0.03%.
Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher ...salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na
-H
antiporters and Na
-Pi symporters as salinity decreases, but the K
channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under ...laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species
Smith and Zeller and
Smith and Zeller (Basidiomycota, Boletales)-the first genomes available for Basidiomycota truffles-and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type
-locus as well as pheromone receptor and pheromone precursor homologs at the mating type
-locus. Comparison of
genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the
-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the
-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species.
possesses a greater number of
-locus pheromone receptor and precursor genes than
, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the
-locus compared to a single copy in
Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in
, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with
possessing a
-locus region structure consistent with tetrapolar Boletales and
possessing a
-locus region structure intermediate between bipolar and tetrapolar Boletales.
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