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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Research Project #444539

Research Project: Whole Genome Sequencing of a Solanum Brevicaule Clone

Location: Emerging Pests and Pathogens Research

Project Number: 8062-22000-023-012-A
Project Type: Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2024

Wild potato species offer novel resistance against potato cyst nematodes, pests of regulatory concern. The objective of this project is to obtain a high-quality whole genome sequence of a Solanum brevicaule clone (Y1-5) that confers broad-spectrum resistance to potato cyst nematodes.

Obtaining a high-quality whole genome sequence of a S. brevicaule clone that confers novel resistance to potato cyst nematodes is needed for a quick discovery of novel nematode resistance genes expressed in wild potato clones. High quality genome assembly of the clone will be carried out using PacBio HiFi long read sequencing technology and will be assembled using Hifiasm and HiCanu. The assembled genome will be remapped to the potato reference genome for chromosome level assembly. The genome will be subjected to gene prediction and functional annotation using available Solanum sp annotations using pipelines like Maker, BRAKER and eggNOG-mapper. Furthermore, potential resistance genes will be identified from the predicted genes based on their domain structures (LRR, Kinase, NBS and TIR domains) using Drago2 pipeline. Genes encoding LRR and NBS domains are of particular interest, since the majority of R-genes encode a LRR and NBS domain.