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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #322064

Research Project: Mitigating Alternate Bearing of Pecan

Location: Fruit and Tree Nut Research

Title: Fusicladium effusum draft genome sequence

Author
item Bock, Clive
item Chen, Chunxian
item Yu, Fahong - University Of Florida
item Hotchkiss, Michael - Mike
item Wood, Bruce

Submitted to: Genbank
Publication Type: Other
Publication Acceptance Date: 6/2/2015
Publication Date: 6/2/2015
Citation: Bock, C.H., Chen, C., Yu, F., Hotchkiss, M.W., Wood, B.W. 2015. Fusicladium effusum draft genome sequence. Genbank. GeneBank accession: PRJNA285422.

Interpretive Summary: The pecan scab fungus (Fusicladium effusum [G. Winter]) is an economically important pathogen of pecan (Carya illinoinensis [Wangenh]. K. Koch), on account of its impact on yield and quality of valuable nutmeats. We describe the first draft genome sequence of F. effusum, the characteristics of annotation, and provide a phylogenetic analysis of the taxonomy of the pathogen. The genome sequence will provide an opportunity for new research to gain insight into fundamental aspects of this economically important disease of pecan. The genome was sequenced using 454 GS-FLX Titanium and Illumina Genome Analyzer IIx sequencing platforms. The 454 reads were cleaned and assembled to generate final contigs and scaffolds. The 170× genome coverage indicated that =95% of the genome (42.6 Mb) was covered. Gene prediction was based on FGENESB and reference genes of Phaeosphaeria nodorum, Pyrenophora teres, and Saccharomyces cerevisiae, and three generic genomic databases (NCBI nr, COG and KEGG). The project is deposited in Genbank under Bioproject ID PRJNA285422, BioSample: SAMN03754054, and Sample name: Pecan-scab; SRA: SRS950178 (https://www.ncbi.nlm.nih.gov/genbank/), and the draft assembly and annotation of the isolate of F. effusum described in this article is deposited in the same location with the accession number GDCP00000000.1.

Technical Abstract: The pecan scab fungus (Fusicladium effusum [G. Winter]) is an economically important pathogen of pecan (Carya illinoinensis [Wangenh]. K. Koch), on account of its impact on yield and quality of valuable nutmeats. We describe the first draft genome sequence of F. effusum, the characteristics of annotation, and provide a phylogenetic analysis of the taxonomy of the pathogen. The genome sequence will provide an opportunity for new research to gain insight into fundamental aspects of this economically important disease of pecan. The genome was sequenced using 454 GS-FLX Titanium and Illumina Genome Analyzer IIx sequencing platforms. The 454 reads were cleaned by masking repeats and removing primers and/or adaptors used in library preparation. The Illumina reads were cleaned using ‘cross_match’ in Phrap and the cleanup module in PTA V3.0.0. Assembly was by ABySS, The assembled contigs with =2,000 bp from ABySS were computationally chopped into 800-bp fragments (with 200 bp overlapping between two adjacent fragments) and further assembled with the cleaned 454 reads using Newbler V2.3, to generate the final contigs and scaffolds. A total of 11,959 contigs and 545 scaffolds (average size = 74.4 Kb; total size = 40.6 Mb) were assembled from over 69.2 million clean reads (7.1 Gb). The largest scaffold was >1.1 Mb. There were 3,113 large contigs (=500 bp), totaling >40.1 Mb which is typical for a genome in the Ascomycota. The 170× genome coverage indicated that =95% of the genome (42.6 Mb) was covered. Ab initio gene prediction was with FGENESB and predicted 50,192 ORFs from the 3,113 large contigs. To obtain perspective on functional genes, these ORFs were annotated with the reference genes of Phaeosphaeria nodorum, Pyrenophora teres, and Saccharomyces cerevisiae, and three generic genomic databases (NCBI nr, COG and KEGG). The project is deposited in Genbank under Bioproject ID PRJNA285422, BioSample: SAMN03754054, and Sample name: Pecan-scab; SRA: SRS950178 (https://www.ncbi.nlm.nih.gov/genbank/), and the draft assembly and annotation of the isolate of F. effusum described in this article is deposited in the same location with the accession number GDCP00000000.1.