P-274 - CUCP Platform: Accurate Identification of Cuscuta Species Through Chloroplast Genome Analysis

Tuesday, July 15, 2025

09:55 - 11:30

Location: Confex Hall 3

Population Biology, Ecology & Genomics

Presenting Author(s)

YK

Yang Jae Kang

Gyeongsang National University
Jinju, Kyongsang-namdo, Republic of Korea

Author(s)

SP

Soyon Park, Assistant Professor

Assistant Professor
University of Missouri-Columbia
COLUMBIA, Missouri, Nepal
Cd

Claude dePamphilis

The Pennsylvania State University
University Park, Pennsylvania, United States
JC

Juan Daniel Cerda

The Pennsylvania State University
University Park, Pennsylvania, United States
JP

Joo-Seok Park

Gyeongsang National University
Jinju, Kyongsang-namdo, Republic of Korea
SH

Suyeon Ha

Gyeongsang National University
Jinju, Kyongsang-namdo, Republic of Korea
JP

Jin Hwa Park

DEEVO Inc.
Jinju, Kyongsang-namdo, Republic of Korea
HP

Halim Park

Gyeongsang National University
Jinju, Kyongsang-namdo, Republic of Korea

Dodder plants (Cuscuta species) threaten global agriculture by parasitizing crops and reducing yields. Accurate identification of these species is challenging due to morphological similarities, limited reference specimens, and their adaptability to different hosts. Even experts struggle with identification as host-parasite molecular exchanges alter their characteristics. While next-generation sequencing enables chloroplast genome analysis from short reads, converting this data to species identification remains complex. Traditional approaches using genetic markers or phylogenetic analyses require expertise and significant manual effort. We developed CUCP, a web platform leveraging 33 Cuscuta chloroplast genomes through a genotype matrix that matches unknown samples against reference sequences. This platform delivers accurate results within 20 seconds, significantly faster than conventional methods while maintaining comparable accuracy. CUCP's interface and regular database updates make it suitable for routine screening and large-scale projects. The platform transforms species identification from a laborious, error-prone process to a rapid, reliable solution, though its effectiveness depends on quality input sequences and comprehensive reference data. Future improvements require expanding the reference database beyond the current 33 species, which represent only a fraction of Cuscuta diversity, to better address agricultural challenges posed by these parasitic plants.