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      Draft genome sequence of Monascus ruber strain FM39-7

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          ABSTRACT

          In China, certain Monascus ruber strains are traditionally used as edible fungi. We sequenced the genome of M. ruber FM39-7 strain, an isolate from fermented rice. The genome is 25.89 Mb with a G + C content of 48.86%, containing 8485 annotated genes.

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          Most cited references14

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          Tandem repeats finder: a program to analyze DNA sequences.

          G. Benson (1999)
          A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.
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            tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

            Todd Lowe, Sean R. Eddy (1997)
            We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
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              RNAmmer: consistent and rapid annotation of ribosomal RNA genes

              Karin Lagesen, Peter F. Hallin, Einar Andreas Rødland … (2008)
              The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.
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                Author and article information

                Contributors
                Lei Yang: Role: InvestigationRole: ResourcesRole: Writing – original draft
                Yongfeng Jing: Role: InvestigationRole: Methodology
                Zhijun Cheng: Role: MethodologyRole: Software
                Ke Huang: Role: Software
                Xianhai Yang: Role: Data curationRole: Methodology
                Dong Xiang: Role: Software
                LudwigSimaneka Omuwa Hilde: Role: MethodologyRole: Writing – original draft
                Huilin Zhang:
                ORCID: https://orcid.org/0009-0004-3470-4214
                Role: Funding acquisitionRole: InvestigationRole: Project administration
                Yong Liu:
                ORCID: https://orcid.org/0000-0003-1289-7196
                Role: InvestigationRole: Project administrationRole: Writing – review and editing
                Jennifer Geddes-McAlister: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, collection): January 2024
                Publication date (Electronic, pub): 15 December 2023
                Publication date PMC-release: 15 December 2023
                Volume: 13
                Issue: 1
                Electronic Location Identifier: e00805-23
                Affiliations
                [1 ] China Tobacco Hunan Industrial Co. Ltd.; , Changsha, China
                [2 ] School of Biological & Chemical Engineering, Zhejiang University of Science & Technology; , Hangzhou, China
                University of Guelph; , Guelph, Ontario, Canada
                Author notes
                Address correspondence to Huilin Zhang, 3622277@ 123456qq.com
                Address correspondence to Yong Liu, 116047@ 123456zust.edu.cn

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0009-0004-3470-4214
                https://orcid.org/0000-0003-1289-7196
                Article
                Publisher ID: 00805-23 Publisher ID: mra.00805-23
                DOI: 10.1128/mra.00805-23
                PMC ID: 10793298
                PubMed ID: 38099680
                SO-VID: 05ade3cc-7e66-4633-b4dc-a41734b9dcba
                Copyright © Copyright © 2023 Yang et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 30 September 2023
                Date accepted : 18 November 2023
                Page count
                supplementary-material: 0, authors: 9, References: 14, Pages: 3, Words: 1257
                Funding
                Funded by: China Tobacco Hunan Industrial Co. Ltd.;
                Award ID: KY2022JD0002
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Compound subject: food-microbiology, Food Microbiology
                Custom metadata
                cover-date January 2024

                Keywords: draft genome,monascus ruber,edible fungi
                Data availability:
                Keywords: draft genome, monascus ruber, edible fungi

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