Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-006-035-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2024
End Date: Aug 31, 2028
Objective:
To explore the plant family Malvaceae (mallows), including kenaf and cotton using genomics (including DNA sequencing, transcriptomics, proteomics, and metabolomics) techniques.
Approach:
Malvaceae is a species-rich clade that also includes additional agronomically important species as cacao, okra, and jute, and numerous ornamentals including lindens, mallows, hollyhocks, and hibiscuses. The proposed work will expand on the previous Malvaceae research by the IGBB and GBRU. Goals of the current project include (but are not limited to) [a] generation of de novo genome sequences for kenaf and looking into biological diversity using both genomics and phenotyping; [b] genome sequencing of additional cottons; [c] study of transcriptomes and proteomes of kenaf and cottons including annotation development; and [d] comparative genomic analysis across Malvaceae. All the research will utilize the IGBB’s expertise in computational biology and bioinformatics. The research, which will be conducted in collaboration with several ARS groups and academic scientists, will provide genomic information that can be integrated into breeding programs used in plant improvement, and leveraged to illuminate evolutionary relationships within and among species.
Pacific Bioscience (PacBio, long-read) and/or Oxford Nanopore Technologies (ONT, long-read) sequencing technologies along with HiC will be used for genome sequencing and scaffolding. Illumina (short-read) sequencing as well as Pacific Biosciences IsoSeq will be used for transcriptome sequencing. Genome resequencing will utilize both short-read and long-read technologies. RT-qPCR will be used to validate RNASeq-based differential gene expression results. Proteomics and metabolomics data will be generated using the IGBB’s LTQ Orbitrap Velos mass spectrometer. The IGBB will utilize its supercomputing capacity and expertise to conduct genome assembly, SNP calling, and comparative genomics research.
