Mutations in the Promoter and Coding Regions of Avr3a Cause Gain of Virulence of Phytophthora sojae to Rps3a in Soybean

Phytophthora sojae threatens soybean production worldwide, and the cultivation of soybean cultivars carrying Rps genes is the most effective way to control this pathogen. However, DNA mutations in the Avr genes of P. sojae can escape recognization of the corresponding Rps genes, leading to the loss of soybean resistance. In this study, we investigated sequence polymorphism and transcript level of the Avr3a gene in Chinese isolates of P. sojae. Twenty-four mutations resulting in five unique Avr3a alleles were discovered in the Avr3a coding region from 32 P. sojae isolates. The Avr3a transcripts were detectable in the isolates containing Avr3a(I), Avr3a(II), Avr3a(III), and Avr3a(IV) but not in the isolates containing Avr3a(V). Promoter and 5'-UTR sequence analysis revealed eight unique mutations in the promoter region of Avr3a(V), suggesting that the mutations could result in the loss of Avr3a(V) transcription. Virulence tests indicated the isolates containing Avr3a(II) and Avr3a(IV) were virulent, suggesting that the mutations in the coding regions of Avr3a(II) and Avr3a(IV) caused the gain of virulence to Rps3a. Based on DNA mutations of Avr3a in virulent alleles, two SNP markers and one PCR-based marker were developed successfully for detecting the virulence of P. sojae isolates to Rps3a. These findings provide new insights into escape mechanisms of Avr3a and effective support for accurate pathotype identification of P. sojae using molecular methods.

Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation

The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.

Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still adapting to its new human host. Attention has focussed on the viral spike protein, but substantial variation has been seen in the ORF8 gene. Here, we show that SARS-CoV-2 ORF8 protein undergoes signal peptide-mediated processing through the endoplasmic reticulum and is secreted as a glycosylated, disulphide-linked dimer. The secreted protein from the prototype SARS-CoV-2 virus had no major effect on viability of a variety of cell types, or on IFN or NF-κB; signalling. However, it modulated cytokine expression from primary CSF1-derived human macrophages, most notably by decreasing IL-6 and IL-8 secretion. Furthermore, a sequence polymorphism L84S that appeared early in the pandemic associated with the Clade S lineage of virus, showed a markedly different effect, of increasing IL-6 production. We conclude that ORF8 sequence polymorphisms can potentially affect SARS-CoV-2 virulence and should therefore be monitored in sequencing-based surveillance.

Plant HKT Channels: An Updated View on Structure, Function and Gene Regulation

HKT channels are a plant protein family involved in sodium (Na+) and potassium (K+) uptake and Na+-K+ homeostasis. Some HKTs underlie salt tolerance responses in plants, while others provide a mechanism to cope with short-term K+ shortage by allowing increased Na+ uptake under K+ starvation conditions. HKT channels present a functionally versatile family divided into two classes, mainly based on a sequence polymorphism found in the sequences underlying the selectivity filter of the first pore loop. Physiologically, most class I members function as sodium uniporters, and class II members as Na+/K+ symporters. Nevertheless, even within these two classes, there is a high functional diversity that, to date, cannot be explained at the molecular level. The high complexity is also reflected at the regulatory level. HKT expression is modulated at the level of transcription, translation, and functionality of the protein. Here, we summarize and discuss the structure and conservation of the HKT channel family from algae to angiosperms. We also outline the latest findings on gene expression and the regulation of HKT channels.

Der p 1 gene sequence polymorphism in house dust mite Dermatophagoides pteronyssinus

Adji A, Niode NJ, Memah VV, Posangi J, Wahongan GJP, Tallei TE. 2021. Der p 1 gene sequence polymorphism in house dust mite Dermatophagoides pteronyssinus. Biodiversitas 22: 72-78. Gene polymorphisms in Dermatophagoides pteronyssinus (DP) mite can affect the immune response that plays a role in atopic disease. This study aimed to determine the polymorphisms of Der p 1 gene from DP. House dust containing DP was used as a source of DNA containing the Der p 1 gene. The gene was amplified using specific primers DP Der 1 P 108F and DP Der 1 P 1509R. The amplified fragments were cloned using the Toyobo pTA2 vector and sorted then compared with the Gene Bank database. The result shows that there are 8 polymorphism sites in the Der p 1 gene positioned at 190 (GR), 463 (CT), 645 (AR), 751 (CY, CT), 787 (CG), 827 (TA; TW), and 1084 (CG). In the Der p 1 gene, there are 5 silent mutations and 3 nonsynonymous substitutions, resulting in amino acid polymorphisms as follows: Histidine H146 to Tyrosine Y146, Alanine A220 to Valine V220 and amino acid X220, and Tyrosine T232 to Serine S232. Polymorphisms in these amino acids lead to a polarity change, from polar to polar and non-polar to non-polar. These dynamics in polarity does not change the structure or function of the allergen protein. So that they can be used for vaccine design strategies.

Molecular and Pathological Variability Associated with Transposable Elements of Botrytis Cinerea Isolates Infecting Grape and Strawberry in Egypt

Grey mold caused by Botrytis cinerea, is known to cause great losses in most vegetable and fruit crops. Fifty-one isolates of B. cinerea were collected from grape (BCG) and strawberry (BCS) grown in different Egyptian locations. Variation among isolates was demonstrated using fenhexamid resistance and genetic approaches. Isolates were classified into various pathogenic groups depending on their reactions towards lettuce leaves. Genetic variability was identified in all isolates using transposable elements (TEs) analysis which revealed either the presence or absence of boty and flipper transposons. Furthermore, TEs typing of B. cinerea isolates demonstrated four TE types, on the basis of TE distribution in B. cinerea populations, namely, transposa (having both boty and flipper), flipper (possessing only flipper), boty (having only boty), and vacuma (lacking both boty and flipper elements). Transposa type was predominant (43.1%) and both transposa and vacuma isolate types showed no specialization with respect to host plant or plant location, while flipper type revealed a geographical preference in (BCG) isolates. Pathogenicity was also correlated to TE type as isolates containing transposa type revealed some degree of correlation with virulence behaviour, suggesting that transposa populations have higher pathogenic potential as compared to vacuma ones. The sensitivity of sampled isolates was tested against fenhexamid as one of the most important botryticides. Sensitivity to fenhexamid was shown in all isolates from strawberry and grape, grown in different locations, with low EC50 values between 0.012-0.084 μg/ml. This finding provided a cue for effective usage of fenhexamid for grey mold management. The present work demonstrated a correlation between the distribution of TEs and some fungal features such as isolate source and virulence, but no correlation was found between morphological characteristics, TE type, and sensitivity to fenhexamid. Cluster analysis based on phylogenetic tree showed that the Egyptian isolates branched as a separate divergent group from the others retrieved from GenBank, reflecting the presence of sequence polymorphism between the current isolates of B. cinerea and those previously identified.