02399nas 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<p>
	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.</p>
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<p>
	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.</p>
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-p45