02035nas a2200241 4500008004100000245012600041210006900167260000800236300000800244490000700252520115000259653002501409653002901434653002701463653003101490653001401521653002801535100002701563700002101590700002101611700003001632856013101662 2022 eng d00aAssembly, annotation, and comparative whole genome sequence of fusarium verticillioides isolated from stored maize grains0 aAssembly annotation and comparative whole genome sequence of fus cJUL a8100 v113 a

Fusarium verticillioides is a plant pathogenic fungus affecting a wide range of crops worldwide due to its toxigenic properties. F. verticillioides BIONCL4 strain was isolated from stored maize grain samples in India, and produces high amount of fumonisin B1 (FB1). We report a comparative genomic analysis of F. verticillioides, covering the basic genome information, secretome, and proteins involved in host-pathogen interactions and mycotoxin biosynthesis. Whole-genome sequencing (WGS) was performed using the Illumina platform with an assembly size of 42.91 Mb, GC content of 48.24%, and 98.50% coverage with the reference genome (GCA000149555). It encodes 15,053 proteins, including 2058 secretory proteins, 676 classical secretory proteins, and 569 virulence and pathogenicity-related proteins. There were also 1447 genes linked to carbohydrate active enzymes (CaZymes) and 167 genes related to mycotoxin production. Furthermore, F. verticillioides genome comparison revealed information about the species' evolutionary history. The overall study helps in disease prevention and management of mycotoxins to ensure food safety.

10acomparative genomics10aFusarium verticillioides10amycotoxin biosynthesis10aplant-pathogen interaction10aSecretome10awhole-genome sequencing1 aNavale, Vishwambar, D.1 aSawant, Amol, M.1 aGowda, Varun, U.1 aVamkudoth, Koteswara, Rao uhttps://library.ncl.res.in/content/assembly-annotation-and-comparative-whole-genome-sequence-fusarium-verticillioides-isolated02399nas a2200301 4500008004100000245017300041210006900214260000800283300000600291490000700297520134600304653002601650653001101676653002501687653001601712653002801728100001701756700001901773700003301792700002001825700002001845700002301865700001801888700001801906700002201924700002001946856013101966 2023 eng d00aWhole genome sequencing and comparative genomics of Indian isolates of wheat spot blotch pathogen bipolaris sorokiniana reveals expansion of pathogenicity gene clusters0 aWhole genome sequencing and comparative genomics of Indian isola cJAN a10 v123 a

Spot blotch is a highly destructive disease in wheat caused by the fungal pathogen Bipolaris sorokiniana (teleomorph, Cochliobolus sativus). It is prevalent in warm and humid areas, including Africa, Asia, Latin America, and the USA. In the present study, twelve isolates of B. sorokiniana were collected from wheat fields in three different geographical locations in India. The pathogenicity of seven sporulating isolates was assessed on `DDK 1025', a spot blotch-susceptible wheat variety under greenhouse conditions. The isolate `D2' illustrated the highest virulence, followed by `SI' and `BS52'. These three isolates were sequenced using the Illumina HiSeq1000 platform. The estimated genome sizes of the isolates BS52, D2, and SI were 35.19 MB, 39.32 MB, and 32.76 MB, with GC contents of 48.48%, 50.43%, and 49.42%, respectively. The numbers of pathogenicity genes identified in BS52, D2, and SI isolates were 2015, 2476, and 2018, respectively. Notably, the isolate D2 exhibited a relatively larger genome with expanded arsenals of Biosynthetic Gene Clusters (BGCs), CAZymes, secretome, and pathogenicity genes, which could have contributed to its higher virulence among the tested isolates. This study provides the first comparative genome analysis of the Indian isolates of B. sorokiniana using whole genome sequencing.

10aBipolaris sorokiniana10aCAZyme10acomparative genomics10aspot blotch10awhole genome sequencing1 aYadav, Sagar1 aRaazi, Zarrine1 aShivaraj, Sheelavanta, Matha1 aSomani, Deepika1 aPrashant, Ramya1 aKulkarni, Abhijeet1 aKumar, Rajeev1 aBiradar, Suma1 aDesai, Shreenivas1 aKadoo, Narendra uhttps://library.ncl.res.in/content/whole-genome-sequencing-and-comparative-genomics-indian-isolates-wheat-spot-blotch-pathogen03188nas a2200241 4500008004100000022001400041245011800055210006900173260000800242300001400250490000700264520231600271653002502587653002102612653002802633653002302661653002602684653002802710100002102738700002702759700003002786856013002816 2024 eng d a1139-670900aGenome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India0 aGenome sequencing and analysis of penicillin V producing Penicil cOCT a1473-14840 v273 a

Background A filamentous fungus Penicillium rubens is widely recognized for producing industrially important antibiotic, penicillin at industrial scale. Objective To better comprehend, the genetic blueprint of the wild-type P. rubens was isolated from India to identify the genetic/biosynthetic pathways for phenoxymethylpenicillin (penicillin V, PenV) and other secondary metabolites. Method Genomic DNA (gDNA) was isolated, and library was prepared as per Illumina platform. Whole genome sequencing (WGS) was performed according to Illumina NovoSeq platform. Further, SOAPdenovo was used to assemble the short reads validated by Bowtie-2 and SAMtools packages. Glimmer and GeneMark were used to dig out total genes in genome. Functional annotation of predicted proteins was performed by NCBI non-redundant (NR), UniProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Moreover, secretome analysis was performed by SignalP 4.1 and TargetP v1.1 and carbohydrate-active enzymes (CAZymes) and protease families by CAZy database. Comparative genome analysis was performed by Mauve 2.4.0. software to find genomic correlation between P. rubens BIONCL P45 and Penicillium chrysogenum Wisconsin 54-1255; also phylogeny was prepared with known penicillin producing strains by ParSNP tool. Results Penicillium rubens BIONCL P45 strain was isolated from India and is producing excess PenV. The 31.09 Mb genome was assembled with 95.6% coverage of the reference genome P. chrysogenum Wis 54-1255 with 10687 protein coding genes, 3502 genes had homologs in NR, UniProt, KEGG, and GO databases. Additionally, 358 CAZymes and 911 transporter coding genes were found in genome. Genome contains complete pathways for penicillin, homogentisate pathway of phenyl acetic acid (PAA) catabolism, Andrastin A, Sorbicillin, Roquefortine C, and Meleagrin. Comparative genome analysis of BIONCL P45 and Wis 54-1255 revealed 99.89% coverage with 2952 common KEGG orthologous protein-coding genes. Phylogenetic analysis revealed that BIONCL P45 was clustered with Fleming's original isolate P. rubens IMI 15378. Conclusion This genome can be a helpful resource for further research in developing fermentation processes and strain engineering approaches for high titer penicillin production.

10acomparative genomics10aIllumina NovoSeq10aPenicillin biosynthesis10aPenicillium rubens10aSecondary metabolites10awhole genome sequencing1 aSawant, Amol, M.1 aNavale, Vishwambar, D.1 aVamkudoth, Koteswara, Rao uhttps://library.ncl.res.in/content/genome-sequencing-and-analysis-penicillin-v-producing-penicillium-rubens-strain-bioncl-p4502657nas a2200241 4500008004100000022001400041245011900055210006900174260000800243300001400251490000700265520179100272653004202063653002502105653002202130653002502152653002602177653001602203100002502219700002002244700002002264856013102284 2025 eng d a0032-086200aComprehensive genomic analysis of bipolaris sorokiniana strains: insights into genetic diversity and pathogenicity0 aComprehensive genomic analysis of bipolaris sorokiniana strains  cSEP a2054-20730 v743 a

Bipolaris sorokiniana is an important plant-pathogenic fungus that primarily infects cereals, such as wheat and barley, causing diseases such as spot blotch, common root rot and seedling blight. This study presents a comprehensive comparative genomic analysis of nine B. sorokiniana strains based on 16 genomic parameters, including genome completeness, virulence factors, secondary metabolite biosynthesis, effector proteins and CAZymes, to explore their genetic diversity, genome assembly quality and pathogenic potential. Genomic assemblies of the strains LK93 and ND93-1 exhibited higher N50, L50, BUSCO completeness scores and gene annotations, and were designated as high-quality. Similarly, ND90Pr and BS112 demonstrated a rich arsenal of CAZymes and effector proteins, which indicated their greater infection potential. Variability in biosynthetic gene clusters, especially the presence of isocyanide-NRPS and fungal RiPP clusters, highlights the ecological adaptability and metabolic diversity of these strains. The study also revealed distinct protein family distributions and effector protein repertoires, supporting strain-specific pathogenic strategies. Phylogenetic analyses grouped the strains into three clusters, indicating evolutionary divergence and potential ecological specialisation. The findings of the study underscore the importance of high-quality genomic data and propose LK93 and ND93-1 as more reliable reference genomes for B. sorokiniana. Integrating transcriptomics, proteomics and pathogenicity data, along with expanded strain sampling and unified assembly pipelines, can enhance understanding of the molecular basis of pathogenicity and help develop suitable disease management strategies to control this agriculturally important pathogen.

10aCochliobolus sativus10acomparative genomics10aeffector proteins10apathogen variability10aSecondary metabolites10aspot blotch1 aShukla, Anand, Kumar1 aSahoo, Rosaleen1 aKadoo, Narendra uhttps://library.ncl.res.in/content/comprehensive-genomic-analysis-bipolaris-sorokiniana-strains-insights-genetic-diversity-and