The complete genome of “ <i>Candidatus</i> Phytoplasma fraxini” AshY1 from the ash yellows group

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ABSTRACT

The complete genome of “ Candidatus Phytoplasma fraxini” AshY1, originating from Fraxinus americana in North America, was assembled using long reads from single-molecule real-time sequencing technology. The chromosome of 598 kb provides insights into the effector repertoire of a phytopathogenic bacterium from the 16SrVII phytoplasma group.

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Most cited references 11

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Felipe A. Simão, Robert Waterhouse, Panagiotis Ioannidis … (2015)

Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.

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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren, Brian Walenz, Konstantin Berlin … (2017)

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based on tf-idf weighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences (PacBio) or Oxford Nanopore technologies and achieves a contig NG50 of >21 Mbp on both human and Drosophila melanogaster PacBio data sets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

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The RAST Server: Rapid Annotations using Subsystems Technology

Ramy Aziz, Daniela Bartels, Aaron A. Best … (2008)

Background The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. Conclusion By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

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Author and article information

Contributors

Jan W. Böhm:

ORCID: https://orcid.org/0009-0008-2690-5429

David A. Baltrus: 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): July 2024

Publication date (Electronic, pub): 11 June 2024

Publication date PMC-release: 11 June 2024

Volume: 13

Issue: 7

Electronic Location Identifier: e00318-24

Affiliations

[1 ]Integrative Infection Biology Crops-Livestock, University of Hohenheim; , Stuttgart, Germany

[2 ]Max Planck Genome-centre, Max Planck Institute for Plant Breeding; , Köln, Germany

[3 ]Institute for Plant Protection in Fruit Crops and Viticulture, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants; , Dossenheim, Germany

The University of Arizona; , Tucson, Arizona, USA

Author notes

Address correspondence to Jan W. Böhm, jan.boehm@ 123456uni-hohenheim.de

The authors declare no conflict of interest.

Author information

Jan W. Böhm https://orcid.org/0009-0008-2690-5429

Michael Kube https://orcid.org/0000-0001-5962-2259

Article

Publisher ID: 00318-24 Publisher ID: mra.00318-24

DOI: 10.1128/mra.00318-24

PMC ID: 11256861

PubMed ID: 38860808

SO-VID: 843d1830-4d07-4d0b-ace5-c4f6568733e7

License:

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

History

Date received : 09 April 2024

Date accepted : 22 May 2024

Page count

supplementary-material: 0, authors: 4, References: 11, Pages: 2, Words: 1087

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cover-date July 2024

Keywords: 16srvii,fraxinus,genomics

Data availability:

Keywords: 16srvii, fraxinus, genomics

The complete genome of “ Candidatus Phytoplasma fraxini” AshY1 from the ash yellows group

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ABSTRACT

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Genome Integrity

Most cited references 11

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

The RAST Server: Rapid Annotations using Subsystems Technology

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