Location: Vegetable Research
Project Number: 6080-22000-032-004-I
Project Type: Interagency Reimbursable Agreement
Start Date: Oct 1, 2015
End Date: Sep 30, 2022
Objective:
Comparative genomics to identify genetic factors making East African cassava-adapted whiteflies super-abundant and invasive.
Approach:
Collection of male populations of super-abundant whiteflies: Field samples of super-abundant whiteflies will be collected in north-western Tanzania, shipped to the ARS lab in Charleston to isolate males (> 12,000 individuals) for genomic DNA isolation. With the availability of a draft whitefly genome for the Bemisia tabaci B-biotype, we can now use a reference-guided method to assemble the genome sequence for the super-abundant cassava-colonizing whitefly. Sampling locations for cassava-colonizing whiteflies from north-western Tanzania will be determined based on previous geo-referenced sequence datasets to have the greatest genetic homogeneity. It is likely that the genetic homogeneity in a male-only (haploid) population from a major cassava plantation could be satisfactory for a reference-guided genome assembly.
Library preparation, sequencing and assembly: To achieve a full genomic sequence for the super-abundant whitefly on cassava, three paired-end (300 bp, 500 bp and 1 Kb) and 3 mate-pair libraries (with insert sizes of 3-5 Kb, 8-10 Kb and 15-20 Kb) will be prepared and sequenced using an Illumina platform. After cleaning, a reference-guided assembly will be carried out to assemble the genome for the super-abundant whitefly.
Annotation of genome sequence: Annotation of genome sequence will be conducted initially through gene prediction software by integrating evidences from ab initio predictions, homologous proteins, and transcriptome sequences, followed by manual curation of important gene families by scientists in the whitefly research community.
Comparative genomic analysis: B biotype vs super-abundant cassava biotype. Through comparative genome sequence analysis between a cassava-feeding whitefly and a non-cassava feeding whitefly (B biotype, U.S. colony), sequences or genes unique to the super-abundant cassava-feeding biotype/variant will be identified and their expression profiles evaluated through transcriptome analysis. Functional genes uniquely responding to cassava virus infection and transmission will be selected as target RNAi initiator sequences for RNA interference (RNAi) manipulation.
Submit data to public databases to promote cross-commodity product development by the wider research community: These include developing a database to provide access to sequence data, applying knowledge to inform the RNAi product development pipeline, identifying and publishing valuable non-whitefly supplementary sequence data, and building sequencing and bioinformatics capacity for Africa while promoting women in science. We will develop a whitefly genomics database for technology transfer, similar to the one for the International Cucurbit Genomics Initiative (http://www.icugi.org). The knowledge through comparative genomics and functional genomics analyses between the cassava-feeding and non-cassava feeding whiteflies will help to identify genes that are responsible for host plant adaptation and virus transmission in cassava. Such genes or RNAi initiator sequences could be exploited for whitefly control using the RNAi strategy.
