Aug 2026· Journal of Advanced Research· 0 citations· 59 references
Medicine
TL;DR
This study provides new insights into the pangenome of Magnaporthe oryzae and introduces a method for the identification of functionally important genes in fungal species.
Abstract
INTRODUCTION
Magnaporthe oryzaeis a model pathogenic fungus that causes serious disease in the two most important staple crops, rice and wheat. Elucidating the genetic variation within natural populations ofM. oryzaeand identifying genes involved in pathogenicity and environmental adaptation are essential for sustainable disease control.
Objectives
This study aimed to elucidate the mechanisms underlying genomic variation within the M. oryzae population and to develop a novel GWAS method specifically tailored to this species.
Methods
The genomes ofM. oryzaediversity population 1 (MDP1), comprising 118 strains, were sequenced andde novoassembled. In addition, a novel gene-unit GWAS (GU-GWAS) method was developed to identify associated loci.
Results
Phylogenetic analyses revealed three subgroups among the sequenced strains, which were associated with indica and japonica rice differentiation. We also characterized core and accessory genes in theM. oryzaepopulation through pan-genome analysis. Using GU-GWAS followed by functional validation, we cloned three new genes associated with pathogenesis (SPP1), fungicide tolerance (MoFCS1), and heavy metal tolerance (MoHMT1).
Conclusion
This study provides new insights into the pangenome ofM. oryzaeand introduces a method for the identification of functionally important genes in fungal species.
Moruga Hill Rice (MHR) is an African rice (Oryza glaberrima Steud.) brought to Trinidad by formerly enslaved African Americans and has been grown for many generations in Trinidad at subsistence and commercial scale. Despite its historical and agricultural significance, genomic resources specific to MHR remain unexplored, and its genetic composition, evolutionary history, and potential agronomic traits have not been characterized. This current study presents the first draft genome assembly of the MHR genome using a hybrid sequencing approach. The MHR genome size was found to be ~372.9 Mb with 56,073 predicted genes. Variant analysis revealed a total of 3,318,242 variants, of which 2,440,476 were SNPs, and 877,766 were InDels. Several candidate genes encoding proteins with orthology to previously characterized biotic resistance and abiotic stress-responsive genes in rice were identified. Potential gene families identified prompt further investigation of their roles in MHR drought and salt stress responses. Phylogenomic analysis of O. glaberrima landraces suggests that MHR shares close genetic affinity with the IRGC−104595 Malian landrace, consistent with historical records. This assembly thus expands the African rice genomic repository, providing a foundation to understand the genetic architecture underlying key phenotypic traits and identifying potential novel gene sources in MHR for rice improvement in the Caribbean region.
Uddesh M. Sahadeo, Omar Ali, A. Ramsubhag et al.· BioTech· 0 citations
Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding.
Yang Lv, Hao Wu, M. Asad et al.· Plants· 0 citations
Background: Traditional rice landraces represent valuable reservoirs of genetic diversity associated with agronomically important traits, stress adaptation, nutritional quality and regional adaptation. Iluppai Poo Samba (Oryza sativa L.) is a traditional South Indian rice landrace cultivated in Tamil Nadu, India, valued for its characteristic aroma, grain quality and adaptation to local agroecological conditions. However, genomic information for this cultivar remains limited. The present study aimed to characterize genome-wide sequence variation in Iluppai Poo Samba through whole-genome sequencing (WGS). Methods: High-quality paired-end sequencing libraries were prepared using the NEXTflex Rapid DNA Sequencing platform and sequenced using Illumina chemistry. Sequence reads were subjected to quality assessment, genome alignment, variant calling, genome-wide SNP density analysis and functional annotation of genomic variants. Result: Sequencing quality assessment demonstrated high-quality reads with Q20 values exceeding 97% and Q30 values exceeding 94%, with an average GC content of approximately 45%. A total of 1,410,690 SNPs and 138,431 InDels were observed across the genome. Genome-wide SNP analysis revealed extensive chromosomal variation, heterogeneous SNP distribution patterns and distinct polymorphic hotspot regions. Functional annotation detected widespread intergenic, intronic and coding-region polymorphisms, including 44,070 synonymous and 51,380 non-synonymous SNPs. Transition/transversion (Ts/Tv) ratios ranging from 2.24 to 2.50 supported the reliability of variant identification. Variants associated with stress-responsive transporters, kinase signalling proteins, transcription factors and regulatory genes were also detected, indicating potentially important adaptive genomic signatures within the Iluppai Poo Samba genome.
Einstein Mariya David, Theivasigamani Parthasarathi· Agricultural Science Digest...· 0 citations
A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning all 10 recognized tetraploid wheat subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
BACKGROUND
ESKAPE pathogens are major causes of hospital-acquired infections and are characterized by extensive antimicrobial resistance (AMR) and diverse virulence mechanisms. Although species-specific pan-genome studies have revealed substantial genomic diversity, the relationships among genome plasticity, resistance burden, and virulence remain incompletely understood across the ESKAPE complex.
METHODS
We analyzed 120 high-quality genomes representing six single-species ESKAPE groups (20 genomes per species). Genome quality was assessed using CheckM2. Species-specific pan-genomes were constructed with Roary, AMR genes were identified using AMRFinderPlus, and virulence factors were detected against the VFDB database using DIAMOND. AMR genes were mapped to core and accessory genome compartments through integration of Prokka annotations and Roary outputs. Statistical associations were evaluated using Fisher's exact tests and correlation analyses, with false discovery rate correction applied within each test family. Core-genome maximum-likelihood phylogenies were reconstructed to provide an evolutionary framework.
RESULTS
Pan-genome sizes ranged from 4720 to 17,272 genes, with Enterobacter and Pseudomonas possessing the largest accessory genomes. Multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) was detected in 93.3% of strains. After false discovery rate correction, AMR genes remained significantly enriched in the accessory genomes of Enterobacter, Enterococcus, Klebsiella, and Staphylococcus, whereas Acinetobacter and Pseudomonas did not show significant enrichment in either genome compartment. Within-species analyses identified significant positive associations between accessory genome size and AMR class burden in Staphylococcus, Enterococcus, and Enterobacter, whereas the moderate Pearson correlation observed in Pseudomonas was not significant after FDR correction. Virulence factor repertoires varied markedly among species, with Pseudomonas exhibiting the highest burden and Enterococcus the lowest.
CONCLUSIONS
ESKAPE pathogens display distinct patterns of resistance and virulence. Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.
Srishti Singh, Pankaj Kumar· Computational biology and ch...· 0 citations
Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication. Silphium species native to North American prairies show strong drought tolerance. This study presents a haplotype-phased genome of a hybrid between S. integrifolium (oilseed crop) and S. perfoliatum (biomass/fiber crop), identifying loci linked to environmental adaptation and domestication.
Renan Souza, J. Clevenger, Jerry W. Jenkins et al.· Nature Communications· 0 citations