"Генетика", 2025 г., № 7

Статьи, опубликованные только в Russian J. of Genetics, № 7 – 2025 г.

Different Expression of Three WRKY Genes under Simultaneous Biotic and Abiotic Stresses in the Root of Wheat

N. Mirakhorli¹, M. Ahmadi¹, M. Arkan¹, L. Shabani², O. Ansari³, A. A. Dababat⁴

¹ Department of Plant Breeding and Biotechnology, Shahrekord University, Shahrekord, Chaharmahal and Bakhtiari province, Iran
² Department of Biology, Shahrekord University, Shahrekord, Chaharmahal and Bakhtiari province, Iran
³ HempGenTech, Brisbane Qld 4069, Brisbane, Australia
⁴ Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
Correspondence to N. Mirakhorli

Wheat (Triticum aestivum L.) is the most widely grown crop in the world. It grows under different climatic and agronomic conditions and faces various biotic and abiotic stresses. To cope and survive under these conditions, wheat uses a variety of defense and tolerance mechanisms. These mechanisms involve many genes and regulatory factors related to a network that causes different expression patterns of genes under different conditions. This study investigated the expression pattern of three transcription factor genes, WRKY29, WRKY53, and WRKY71, under both biotic and abiotic stress conditions. These genes were identified as stress-responsive genes by meta-analysis studies. Stresses include Heterodera filipjevi, Fusarium culmorum, and drought which were applied individually, double, and triple simultaneously. The expression of these genes under the introduced stress conditions was compared with the levels of antioxidant enzymes and traits of yield components in the two-wheat accession, 2–49 (resistant to Fusarium), “Silverstar” (resistant to Heterodera). It was found that drought as abiotic stress is the main factor in increasing the expression level of the three WRKY genes. One week after double simultaneous stress drought plus Heterodera in “Silverstar” (resistant to Heterodera) accession, the highest gene expression was obtained. But the level of expression decreased in triple simultaneous stress (drought + Heterodera + Fusarium) which caused damage and reduced the yield components traits. The level of gene expression was reduced under triple stress because of the antagonistic effect of fungus on nematodes and different pathways of fungal resistance and drought tolerance in wheat. This accession was susceptible to fungal stress and had the lowest gene expression under this stress. Accession 2–49 (resistant to Fusarium), the highest gene expression was in fungal stress. Since 2–49 was known as a drought-resistant accession, the WRKY gene expression was also high in drought stress. However, different stress combinations cause unpredictable plant responses, by studying the pattern expression of genes involved in resistance pathways, the potential of the plant can be understood generally.

DOI: 10.1134/S1022795425700334
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Identification of Reliable Reference Genes for Gene Expression Analysis in Saposhnikovia divaricata (Turcz.) Schischk under Salt and Drought Stress

Yue Pan, Zun Lv, Yukun Ma, Yanshi Ma, Ying Cui, Yang Liu, Hui Li, Ming Jiang

Qiqihar Medical University, 161006, Qiqihar, Heilongjiang, China
Correspondence to Hui Li or Ming Jiang

The Quantitative Real-time PCR (qRT-PCR) technique enables exact estimate of target gene expression, careful selection of appropriate reference genes is required. In this study, we evaluated eight candidate reference genes (GAPDH-1, GAPDH-2, EF1A-1, EF1A-2, 18SrRNA-1, 18SrRNA-2, 18SrRNA-3, UBQ) using root tissues from Saposhnikovia divaricata (Turcz.) Schischk under two different abiotic stress conditions. Quantification of expression levels was carried through qRT-PCR analysis and stability was assessed using geNorm, NormFinder and BestKeeper algorithms as well as RefFinder software. Validation was performed by analyzing ABF gene expression. Our findings showed that the expression stability of GAPDH-2 was the highest, while 18SrRNA-3 was the lowest. This study provides valuable insights for standardized selection of reference genes and accurate transcript quantification in SD gene expression and functional analysis.

DOI: 10.1134/S1022795425700346
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The First Analysis of the Complete Mitochondrial Genome of the Chinese Endemic Species, Micromys pygmaeus, and Determination of Phylogenetic Relationships of the Genus Micromys within the Subfamily Murinae

Chengxin Zhou¹, Siyu Yang¹, Zongyun Zhang¹, Qiong Wang¹, Abu ul Hassan Faiz², Shunde Chen¹

¹ Ministry of Education, Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), 610101, Chengdu, Sichuan, China
² Department of Zoology, Women University of Azad Jammu and Kashmir, Bagh, Pakistan
Correspondence to Shunde Chen

Recent integrative studies combining morphological, taxonomic, and molecular evidence have proposed the recognition of Micromys pygmaeus as a new species within the genus Micromys (Rodentia: Muridae). To investigate the evolutionary implications of this taxonomic proposal, we assembled the complete mitogenome of M. pygmaeus and generated an additional mitochondrial genome sequence for M. minutus. Comparative mitogenomic analysis revealed conserved genomic architecture across the genus, with total lengths ranging from 16 232 to 16 243 bp, maintaining consistent gene order, nucleotide composition trends (A + T conet), and codon usage patterns. Notably, M. pygmaeus exhibited a unique 35 bp incomplete repeat motif in its nad6 gene (period size: 15 bp; copy number: 2.3; sequence similarity: 90%), representing the first documented structural variation in Micromys mitogenomes. Phylogenomic reconstruction using concatenated mitochondrial protein-coding genes via Bayesian inference and maximum likelihood consistently resolved three well-supported clades within Micromys, with strong nodal support (posterior probability >0.98, bootstrap >95%). Topological analyses further confirmed the genus’ sister relationship to the tribe Rattini, providing a robust framework for understanding murine radiation patterns.

DOI: 10.1134/S102279542570036X
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Analysis of Genomic Characteristics and Genome-Wide Microsatellite Distribution Pattern of the Blue Shark (Prionace glauca)

M. S. Li, Z. Y. Qiu, T. Wang, Y. Y. Sun, C. C. Hu, S. Y. Xu

School of Fisheries, Zhejiang Ocean University, 316022, Zhoushan, Zhejiang, China
Correspondence to S. Y. Xu

The blue shark (Prionace glauca) is one of the main targets in the global shark fin trade. In recent years, the resources of P. glauca have declined dramatically, and it has been listed as a “Near Threatened” species by the IUCN Red List. Till now, limited studies related to the genomics of P. glauca have been reported, which should constrain conservation genetics studies of this species. In this study, we collected the sample of P. glauca off Zhoushan, China, and carried out genome-wide investigations to evaluate the fundamental genomic characteristics and analyze the genome-wide distribution pattern of microsatellites. The results showed that the genome size of P. glauca was about 3 Gb, the heterozygosity rate was 0.54%, and the proportion of repeat sequences was 65.06%. The preliminary assembly results of the genome showed that the Contig N50 was 2357 bp and the Scaffold N50 was 3917 bp. A total of 444 196 microsatellite loci were screened from the preliminary assembly of P. glauca, with a relative abundance of 172.23 loci/Mb. Among them, the number of dinucleotide microsatellites was the largest, accounting for 50.34% of the total microsatellites. The C/G and AC/GT types were dominant in mononucleotide and dinucleotide repeats, accounting for 27.57 and 26.22%, respectively. The results of this study can provide basic data for high-quality genome sequencing of P. glauca, and the detected microsatellite loci can provide molecular markers for further conservation genetics and evolutionary biology studies of P. glauca.

DOI: 10.1134/S1022795425700371
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Identification of Gene Expression Profile in Inflammatory Breast Cancer Patients Using Machine Learning Method

N. Rabiei¹, F. Bahreini², S. Moslehi³

¹ Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
² Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
³ Department of Biostatistics, School of Public Healthand Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
Correspondence to S. Moslehi

Inflammatory Breast Cancer (IBC) is a rare subtype of locally advanced breast cancer, and caused 7% of breast cancer deaths. Studying the function of gene expression profile is one of the strategies that can help to identify and monitor this malignancy. This study aimed to determine the important genes expression and their function in the classification of the IBC patients. Based on microarray dataset with accession number GSE5847, the most important genes among 22 283 genes associated with IBC (n = 13) and non-IBC (n = 34) patients were selected using the eXtreme Gradient Boosting (XGBoost) and Random Forest (RF) method. Then, the relationship between the expression levels of the selected genes in the two groups, an independent sample t-test and Mann–Whitney U test were used. Finally, using decision tree algorithm, performance evaluation of the developed decision tree (DDT) such as F1-score and AUC indices of 3-fold cross-validation were reported. The rules extracted from the DDT were also interpreted. EDN1, NUCB2, REST, CCL5, UBE3A, ARMCX3, ITGBL1, AR, DZIP3, SLC2A10, FOSB, BLNK, IL6, PSD3, ABAT, LIMCH1, STS, ANGPTL4, and ZIC1 were selected using random forest. Statistical tests revealed differences in the expression levels of all genes except CCL5, DZIP3, FOSB, and ANGPTL4. The mean of the 3-fold cross-validation F1-score, and AUC indices of the DDT were 71.1, and 73.73, respectively. This study demonstrated the effectiveness of the decision tree in classifying IBC. It also highlighted the contributions of the AR, REST, UBE3A, STS, and NUCB2 genes to the classification of IBC and non-IBC patients.

DOI: 10.1134/S1022795425700383
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