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<p>
	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.</p>
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-isolated03188nas 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