The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

A - Papers appearing in refereed journals

King, R., Urban, M., Hammond-Kosack, M. C. U., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum. BMC Genomics. 16, p. 544.

AuthorsKing, R., Urban, M., Hammond-Kosack, M. C. U., Hassani-Pak, K. and Hammond-Kosack, K. E.
Abstract

Background
Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.

Results
We have comprehensively completed the genomic 36,563,796 bp sequence by replacing unknown bases, placing supercontigs within their correct loci, correcting assembly errors, and inserting new sequences which include for the first time complete AT rich sequences such as centromere sequences, subtelomeric regions and the telomeres. Each of the four F. graminearium chromosomes was found to be submetacentric with respect to centromere positioning. The position of a potential neocentromere was also defined. A preferentially higher frequency of genetic recombination was observed at the end of the longer arm of each chromosome. Within the genome 1529 gene models have been modified and 412 new gene models predicted, with a total gene call of 14,164. The re-annotation impacts upon 69 entries held within the Pathogen-Host Interactions database (PHI-base) which stores information on genes for which mutant phenotypes in pathogen-host interactions have been experimentally tested, of which 59 are putative transcription factors, 8 kinases, 1 ATP citrate lyase (ACL1), and 1 syntaxin-like SNARE gene (GzSYN1). Although the completed F. graminearum contains very few transposon sequences, a previously unrecognised and potentially active gypsy-type long-terminal-repeat (LTR) retrotransposon was identified. In addition, each of the sub-telomeres and centromeres contained either a LTR or MarCry-1_FO element. The full content of the proposed ancient chromosome fusion sites has also been revealed and investigated. Regions with high recombination previously noted to be rich in secretome encoding genes were also found to be rich in tRNA sequences. This study has identified 741 F. graminearum species specific genes and provides the first complete genome assembly for a Sordariomycetes species.

Conclusions
This fully completed F. graminearum PH-1 genome and manually curated annotation, available at Ensembl Fungi, provides the optimum resource to perform interspecies comparative analyses and gene function studies.

KeywordsGibberella zeae; Fusarium head blight disease; Fungal centromere sequences; Fungal telomere sequences; Fungal virulence gene hotspots; Completed Sordariomycetes genome
Year of Publication2015
JournalBMC Genomics
Journal citation16, p. 544
Digital Object Identifier (DOI)doi:10.1186/s12864-015-1756-1
PubMed ID26198851
PubMed Central IDPMC4511438
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeWheat
Pathogen-Host Interactions Database: PHI Database [2012-2017]
[20:20 Wheat] Protecting yield potential of wheat
PhytoPath, an infrastructure for hundreds of plant pathogen genomes [2014-2017]
Publisher's version
Output statusPublished
Publication dates
Online22 Jul 2015
Publication process dates
Accepted07 Jul 2015
PublisherBMC
Biomed Central Ltd
Copyright licenseCC BY
ISSN1471-2164

Permalink - https://repository.rothamsted.ac.uk/item/8v0v6/the-completed-genome-sequence-of-the-pathogenic-ascomycete-fungus-fusarium-graminearum

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