Complete Genome Sequence of Strain VNUA116, a Potential Biocontrol Against Phytopathogenic Fusarium Wilt Fungus F. Sp.

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2023 Nov 7

PMID 37933965

Authors

Mai Thi Thanh Nguyen

Son Truong Dinh

Canh Xuan Nguyen

Affiliations

Soon will be listed here.

Abstract

Here, we present the whole-genome sequence of strain VNUA116 was obtained by combining sequencing data from both PacBio RS II and DNBseq platforms. The complete circular genome is 8,306,919 bp with a GC content of 72.49%.

References

Delcher A, Bratke K, Powers E, Salzberg S . Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007; 23(6):673-9. PMC: 2387122. DOI: 10.1093/bioinformatics/btm009. View

Delcher A, Harmon D, Kasif S, White O, Salzberg S . Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999; 27(23):4636-41. PMC: 148753. DOI: 10.1093/nar/27.23.4636. View

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

Akhter S, Aziz R, Edwards R . PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 2012; 40(16):e126. PMC: 3439882. DOI: 10.1093/nar/gks406. View

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Neron B . CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018; 46(W1):W246-W251. PMC: 6030898. DOI: 10.1093/nar/gky425. View

Koren S, Walenz B, Berlin K, Miller J, Bergman N, Phillippy A . Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation. Genome Res. 2017; 27(5):722-736. PMC: 5411767. DOI: 10.1101/gr.215087.116. View

Masoomi-Aladizgeh F, Jabbari L, Khayam Nekouei R, Aalami A, Atwell B, Haynes P . A universal protocol for high-quality DNA and RNA isolation from diverse plant species. PLoS One. 2023; 18(12):e0295852. PMC: 10721051. DOI: 10.1371/journal.pone.0295852. View

Gardner P, Daub J, Tate J, Nawrocki E, Kolbe D, Lindgreen S . Rfam: updates to the RNA families database. Nucleic Acids Res. 2008; 37(Database issue):D136-40. PMC: 2686503. DOI: 10.1093/nar/gkn766. View

Rahman M, Islam M, Islam M . Antibacterial activities of actinomycete isolates collected from soils of rajshahi, bangladesh. Biotechnol Res Int. 2011; 2011:857925. PMC: 3166718. DOI: 10.4061/2011/857925. View

10.

Huang J, Liang X, Xuan Y, Geng C, Li Y, Lu H . A reference human genome dataset of the BGISEQ-500 sequencer. Gigascience. 2017; 6(5):1-9. PMC: 5467036. DOI: 10.1093/gigascience/gix024. View

11.

Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S . SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2017; 7(1):1-6. PMC: 5788068. DOI: 10.1093/gigascience/gix120. View

12.

Hunt M, De Silva N, Otto T, Parkhill J, Keane J, Harris S . Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 2015; 16:294. PMC: 4699355. DOI: 10.1186/s13059-015-0849-0. View