Biology subjects

Tongyoo, P.

Publications and source records attributed to Tongyoo, P..

3 recordsLinked to original sources

bioRxiv2026

AI in Practice: A Multilingual Survey of 2025 BioHackathon Participants

This dataset arises from a multilingual survey of AI use among participants and community members in the DBCLS BioHackathon 2025 in Japan. The questionnaire, offered in English, Japanese, and Thai, asked about how often respondents use AI tools, what they use them for, obstacles they encounter, institutional support, satisfaction, and concerns. Additional items captured role, institution type, work country, and other demographics, totaling 105 responses. The dataset includes both raw anonymized responses and a cleaned, standardized English-only version suitable for quantitative analysis, along with the full questionnaire, a data dictionary for cleaned dataset, and a translation lookup table. Free-text answers were screened and redacted to remove URLs, names, and other potentially identifiable information. Together, these materials provide a community-level view of AI practice in genomics, bioinformatics, software development, and related areas, and can support work on AI adoption, policy, and methods for analyzing survey data on AI use in science.

scientific communication and education↗

bioRxiv2025

Pathogenicity and genome assembly of a Pythium aphanidermatum isolate causing damping-off in amaranth in controlled environment agriculture

Several species of Pythium are destructive soilborne pathogens, causing root rot and damping-off of seedlings and posing significant challenges in controlled environment agriculture (CEA). In this study, four isolates (PT2-1-1, PT2-1-2, PT5, and PT6) were obtained from infected amaranth seedlings and confirmed as P. aphanidermatum through morphology and ITS rDNA sequencing. These isolates dramatically reduced the root length of amaranth seedlings in plate-based pathogenicity assays. In soil-based post-emergence assays, damping-off symptoms were prevalent, with disease incidence reaching up to 100% in susceptible amaranth genotypes. Genome sequencing of isolate PT2-1-1 yielded a 51.55 Mb assembly consisting of 120 contigs, with 14,453 predicted protein-coding genes, including a diverse set of plant cell wall-degrading enzymes with a likely role in host invasion. Analysis of the predicted P. aphanidermatum secretome revealed potential intracellular and apoplastic effectors, including Crinkler and YxSL[RK] effectors; no RxLR effectors were detected. This work provides a second genome assembly for P. aphanidermatum as well as demonstrating variation in pathogenicity of this isolate on different amaranth accessions. Together these pave the way for investigation of pathogen-host interaction and identification of key virulence and defence strategies.

plant biology↗

bioRxiv2020

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Tropical Asian collection using DArTseq based SNP markers

This study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. STRUCTURE analysis ({Delta}K at K=6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (-10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

genomics↗