Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: WILDRICE BREEDING, GENETICS, AND GENETIC RESOURCES

Location: Plant Science Research

Title: Assembling and exploring the Cochliobolus miyabeanus genome of a strain pathogenic on wildrice (Zizania palustris)

Authors
item Castell-Miller, Claudia
item Tu, Zheng -
item Vance, Carroll
item Samac, Deborah

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: August 6, 2011
Publication Date: August 6, 2011
Citation: Castell-Miller, C.V., Tu, Z., Vance, C.P., Samac, D.A. 2011. Assembling and exploring the Cochliobolus miyabeanus genome of a strain pathogenic on wildrice (Zizania palustris) [abstract]. 2011 American Phytopathological Society-International Plant Protection Congress Joint Meeting, August 6-10, 2011, Honolulu, Hawaii. Available: http://www.apsnet.org/meetings/Documents/2011_Meeting_Abstracts/a11ma165.htm.

Technical Abstract: The genome of a strain of C. miyabeanus was shotgun sequenced by paired-end reads with Illumina HiSeq 2000 technology. The genome was assembled with AbySS software yielding a total size of 34.96 Mb (114X), with N50 = 99.43 kb contained in the largest 105 scaffolds and a maximum scaffold length of 408.932 kb. The G + C content of the genome was 51%. GeneMark-ES v2.3a detected 12,344 protein-coding genes, with a mean size of 1,537 bp and an average of 2.55 exons per gene. The average size of encoded proteins was 437 aa. Annotation of fungal proteins was done using BLASTP against the protein database of NCBI, and protein functional classification was done with Blast2GO. Complete genome blast searches to the pathogen-host interaction database identified 15% of the genes mostly related to virulence, pathogenicity, and a few effector molecules. Additionally, several genes were associated with transport, resistance, and sensitivity to chemicals. The most abundant repetitive elements identified belong to the LTR/Gypsy retrotransposons. An independent RNA sequencing experiment is being used to validate the genome assembly. DNA genomic sequences from C. miyabeanus were mapped onto a reference genome (C. heterostrophus). Understanding the organization of the C. miyabeanus genome in parallel with the fungal transcriptome can help in developing wildrice varieties that will resist the specific pathogenicity/virulence factors of the fungus.

Last Modified: 9/21/2014
Footer Content Back to Top of Page