scholarly journals Assigning confidence scores to homoeologs using fuzzy logic

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6231 ◽  
Author(s):  
Natasha M. Glover ◽  
Adrian Altenhoff ◽  
Christophe Dessimoz
Keyword(s):  
Triticum Aestivum ◽  
Fuzzy Logic ◽  
Brassica Napus ◽  
Gossypium Hirsutum ◽  
Bread Wheat ◽  
Plant Species ◽  
Upland Cotton ◽  
Previous Method ◽  
Improved Method ◽  
Polyploid Plant

In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.

scholarly journals Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 246 ◽  
Author(s):  
Jadwiga Wyszkowska ◽  
Agata Borowik ◽  
Jacek Olszewski ◽  
Jan Kucharski
Keyword(s):  
Triticum Aestivum ◽  
Alkaline Phosphatase ◽  
Brassica Napus ◽  
Pisum Sativum ◽  
Plant Species ◽  
Field Experiments ◽  
Diversity Index ◽  
Size Fraction ◽  
Soil Microbiome ◽  
Colony Development

This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

scholarly journals GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

2021 ◽  
Vol 22 (14) ◽  
pp. 7328
Author(s):  
Yang Chen ◽  
Mi Zhang ◽  
Lei Wang ◽  
Xiaohan Yu ◽  
Xianbi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Plants ◽  
Gossypium Hirsutum ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Defense Response ◽  
Upland Cotton ◽  
Effector Protein ◽  
Positive Regulator ◽  
Its Gene

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

Effect of Cold Pretreatment and Incubation Temperature on Bread Wheat (Triticum aestivum L.) Anther Culture

2001 ◽  
Vol 29 (3-4) ◽  
pp. 331-338 ◽  
Author(s):  
I. N. Xynias ◽  
I. A. Zamani ◽  
E. Gouli-Vavdinoudi ◽  
D. G. Roupakias
Keyword(s):  
Triticum Aestivum ◽  
Anther Culture ◽  
Bread Wheat ◽  
Incubation Temperature ◽  
Triticum Aestivum L ◽  
Cold Pretreatment
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