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To better understand the structure and evolution of the genomes of four plant pathogenic species of Zymoseptoria, we analyzed the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in their whole genome and transcriptome sequences. In this study, SSRs are defined as repeats of more than 12 bases in length. The genome and transcriptome sequences of Zymoseptoria ardabiliae show the highest RA (201.1 and 129.9) and RD (3229.4 and 1928.2) of SSRs, while those of Zymoseptoria pseudotritici show the lowest RA (167.2 and 118.5) and RD (2482.2 and 1687.0). The majority of SSRs in the genomic and transcriptome sequences of species were trinucleotide SSRs, while dinucleotide SSRs were the least common. The most common trinucleotide motifs in the transcriptomic sequences across all species were those that encoded the amino acid arginine. As per our motif conservation study, Zymoseptoria tritici (12.4%) possessed the most unique motifs, while Z. pseudotritici (3.9%) had the fewest. Overall, only 38.1% of the motifs were found to be conserved among the species. Gene enrichment studies reveal that three of the species, Z. ardabiliae, Zymoseptoria brevis, and Z. pseudotritici, have SSRs in their genes related to cellular metabolism, while the remaining Z. tritici harbors SSRs in genes related to DNA synthesis and gene expression. In an effort to improve the genetic resources for the orphan species of pathogenic Zymoseptoria, a total of 73,134 primers were created. The genomic resources developed in this study could help with analyses of genetic relatedness within the population and the development of species-specific markers. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the alterations in physiological, biochemical, and transcriptional reactions in the flag leaf of rice following the application of Trichoderma as a biofertilizer (BF) at both ambient (aCO2; 395 ppm) and enhanced (eCO2; 550 ppm) carbon dioxide levels. A comparatively smaller percentage change was observed in the photosynthetic parameters, including photosynthetic rate, respiration, and stomatal conductance, subsequent to the introduction of BF in the elevated carbon dioxide (eCO2) environment. Furthermore, biochemical analysis revealed a noteworthy elevation in photosynthetic pigments, total sugar, proline, and ascorbate peroxidase concentration levels in plants treated with BF under ambient and increased carbon dioxide conditions. The buildup of indole‐3‐acetic acid (IAA) was shown to be increased in rice treated with BF under both conditions. Moreover, ICP‐MS analysis demonstrated an augmentation in the levels of vital micronutrients in the experimental group while observing no alterations in the carbon‐to‐nitrogen ratio within the flag leaf. The examination of transcriptional responses in the flag leaf demonstrated an increase in the expression of genes associated with the photosynthetic system, amino acid metabolism, several transporters, including aquaporin, and the phosphate pathway, as well as carbon and nitrogen metabolism. Hence, our work elucidates the effective role of Trichoderma in mitigating the adverse consequences associated with elevated levels of atmospheric carbon dioxide (eCO2). [ABSTRACT FROM AUTHOR]

The present study aims to explore the alternative way to improve the quality and productivity of rice grown under CO2 stress through an external supplement of Trichoderma as a biofertilizer (BF). The impact of BF-treated rice under elevated CO2 (eCO2) was examined by different plant growth parameters, physiological observations, scanning electron microscopy, microbial community profiling and expression levels of stress-related genes. The effect of eCO2 on percent change in yielding attributes of rice (Heena and Kiran) was found higher in control, whereas it was reduced in the presence of BF. Photosynthetic rate, stomatal conductance and transpiration rate were higher in BF-treated rice under eCO2 condition. SEM analysis of BF-treated roots exhibits an increase in the number of metaxylem along with its diameter with thicker and rigid sclerenchymatous cells. Expression analysis of stress-related genes showed an increase in their mRNA transcripts under eCO2 condition. A significant change in the microbial community was found in the rhizospheric region of Heena treated with BF under eCO2. The current study demonstrates the potential of BF in ameliorating the stress generated as a result of CO2 enrichment. [ABSTRACT FROM AUTHOR]

We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents <1%. Among all classes of repeats, 36.5% motifs were found conserved within Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium. [ABSTRACT FROM AUTHOR]

Monkeypox (MPOX), a zoonotic disease originating in Western and Central Africa in 1970, has seen a recent surge in outbreaks across 100+ countries. A comparative analysis of 404 Monkeypox virus (MPXV) genomes revealed notable changes in microsatellite abundance and density, especially within Clades I, IIa, and IIb. Each clade exhibited unique microsatellite motifs, with twenty-six conserved loci specific to MPXV, suggesting their potential as molecular markers in diagnostics. Additionally, nine genes in the MPXV genome featured ten variable hotspot microsatellite regions associated with surface protein synthesis and host control. Notably, gene OPG153, especially at the SSR locus '(ATC)n', exhibited the most pronounced variations among lineages over time and plays a role in virus pathogenesis within the host cell. These findings not only enhance our understanding of MPXV unique molecular profile but also offer valuable insights into potential pathogenic and evolutionary implications., Competing Interests: The authors wish to state that they possess no conflicts of interest pertaining to this study, and there exists no substantial financial backing that might have impacted the results of this research., (© The Author(s) 2024. Published by Oxford University Press.)

The frequency and distribution of microsatellites were analyzed in the 19 mitogenomes of phytopathogenic fungi covering five phyla. Our analysis revealed that in all the mitogenomes studied, the frequency and relative abundance varied, and it was neither influenced by genome size nor by GC content. SSRs were found to be differential distributed in genic and intergenic regions. An average of 5.14 (23.6%) SSRs were present in genic sequences and 21.7 (76.4%) SSRs were located in the intergenic sequences. Relative abundance of SSRs in mitogenomes was the highest in Aspergillus tubigensis, whereas, it was the least in Phaeosphaeria nodurum, the average being 0.45. Trinucleotide repeats were the most abundant motifs in the genic and intergenic regions of the mitogenomes of the phytopathogenic fungi. Among the genes, cox1 harbors the maximum SSRs, whereas cox3 and nad 7 contain the least. Based on the presence of SSRs in a particular gene, genetic relationships among individual organisms were also established.