Complete genome sequence of lovastatin producer  Aspergillus terreus  ATCC 20542 and evaluation of genomic diversity among  A. terreus  strains

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Abstract

In the present study, the complete genome of a filamentous fungus Aspergillus terreus ATCC 20542 was sequenced, assembled, and annotated. This strain is mainly recognized for being a model wild-type lovastatin producer and a parental strain of high-yielding industrial mutants. It is also a microorganism with a rich repertoire of secondary metabolites that has been a subject of numerous bioprocess-related studies. In terms of continuity, the genomic sequence provided in this work is of the highest quality among all the publicly available genomes of A. terreus strains. The comparative analysis revealed considerable diversity with regard to the catalog of biosynthetic gene clusters found in A. terreus. Even though the cluster of lovastatin biosynthesis was found to be well-conserved at the species level, several unique genes putatively associated with metabolic functions were detected in A. terreus ATCC 20542 that were not detected in other investigated genomes. The analysis was conducted also in the context of the primary metabolic pathways (sugar catabolism, biomass degradation potential, organic acid production), where the visible differences in gene copy numbers were detected. However, the species-level genomic diversity of A. terreus was more evident for secondary metabolism than for the well-conserved primary metabolic pathways. The newly sequenced genome of A. terreus ATCC 20542 was found to harbor several unique sequences, which can be regarded as interesting subjects for future experimental efforts on A. terreus metabolism and fungal biosynthetic capabilities.

Key points

• The high-quality genome of Aspergillus terreus ATCC 20542 has been assembled and annotated.

• Comparative analysis with other sequenced Aspergillus terreus strains has revealed considerable diversity in biosynthetic gene repertoire, especially related to secondary metabolism.

• The unique genomic features of A. terreus ATCC 20542 are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11133-0.

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BLAST+: architecture and applications

Christiam Camacho, George Coulouris, Vahram Avagyan … (2009)

Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.

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InterProScan 5: genome-scale protein function classification

Philip Jones, David Binns, Hsin-Yu Chang … (2014)

Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk

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Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin … (2019)

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.

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Author and article information

Contributors

Małgorzata Ryngajłło:

ORCID: http://orcid.org/0000-0002-0430-0102

malgorzata.ryngajllo@p.lodz.pl

Journal

Journal ID (nlm-ta): Appl Microbiol Biotechnol

Journal ID (iso-abbrev): Appl Microbiol Biotechnol

Title: Applied Microbiology and Biotechnology

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0175-7598

ISSN (Electronic): 1432-0614

Publication date (Electronic): 30 January 2021

Publication date PMC-release: 30 January 2021

Publication date (Print): 2021

Volume: 105

Issue: 4

Pages: 1615-1627

Affiliations

[1 ]GRID grid.412284.9, ISNI 0000 0004 0620 0652, Institute of Molecular and Industrial Biotechnology, , Lodz University of Technology, ; B. Stefanowskiego 4/10, 90-924 Lodz, Poland

[2 ]GRID grid.412284.9, ISNI 0000 0004 0620 0652, Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, , Lodz University of Technology, ; ul. Wolczanska 213, 90-924 Lodz, Poland

Author information

Małgorzata Ryngajłło http://orcid.org/0000-0002-0430-0102

Tomasz Boruta https://orcid.org/0000-0002-8807-878X

Marcin Bizukojć https://orcid.org/0000-0003-1641-9917

Article

Publisher ID: 11133

DOI: 10.1007/s00253-021-11133-0

PMC ID: 7880949

PubMed ID: 33515286

SO-VID: 591af65e-0f1d-4a48-a56d-45e10e8daa31

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 13 November 2020

Date revision received : 30 December 2020

Date accepted : 20 January 2021

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100004281, Narodowe Centrum Nauki;

Award ID: 2017/27/B/NZ9/00534

Award Recipient : Marcin Bizukojć

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ScienceOpen disciplines: Biotechnology

Keywords: aspergillus terreus,genome,comparative genomics,secondary metabolites

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ScienceOpen disciplines: Biotechnology

Keywords: aspergillus terreus, genome, comparative genomics, secondary metabolites

Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains

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Supplementary Information

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Most cited references 54

BLAST+: architecture and applications

InterProScan 5: genome-scale protein function classification

Assembly of long, error-prone reads using repeat graphs

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