Location: Sustainable Agricultural Systems Laboratory
Project Number: 8042-21220-181-007-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 15, 2018
End Date: Mar 31, 2020
Objective:
Develop the genome and transcriptome maps of two isolates (K-1 and K-4) of Ceratobasidium sp. belonging to Anastomosis Groups AG-K and AG-I, respectively.
(1) Extract the high molecular weight (HMW) genomic DNA and total RNA from the fungal isolates K-1 and K-2 grown in vitro.
(2) Sequence the genomes with Illumina and PacBio sequencing approaches; sequence the transcriptomes (RNA) with Illumina RNAseq approach.
(3) Bioinformatically assemble and annotate the contigs and scaffolds from the genomes and transcriptomes.
(4) Bioinformatically analyze the genomes for:
Chromosome number; gene prediction and annotation; secretome; carbohydrate degrading enzymes; transcription factors; repeat elements (satellites, transposable elements, etc); evolutionary relationships with Rhizoctonia solani (Teleomorph: Thanatephorus cucumeris) genomes.
(5) Creation of a genome and transcriptome database of Ceratobasidium genomes.
Approach:
ARS will develop strategies for genome and transcriptome sequencing in collaboration with the KAUST, in the PI’s laboratory. In this regard, the PI has an ongoing research collaboration with the KAUST, which has resulted in the development of a Rhizoctonia genome databse (http://rsolanidb.kaust.edu.sa/RhDB/).
The cooperator will be using the agency provided Ceratobasidium DNAs and RNAs for genome and transcriptone sequencing, as well as for bioinformatic analyses.
The cooperator and the PI will jointly interpret data and publish in peer-reviewed journals and/or extension notes. This information will be used by both parties to jointly develop tools necessary for assessing and identifying Ceratobasidium pathogens and the respective virulence factors. The information will be useful for developing management strategies for Ceratobasidium pathogens.
