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© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies.

Details

Title
Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids
Author
Chittavichai, Thanyaporn 1   VIAFID ORCID Logo  ; Sathitnaitham, Sukhita 1 ; Utthiya, Supanut 1 ; Prompichai, Wanasilp 1 ; Prommarit, Kamonchat 1   VIAFID ORCID Logo  ; Vuttipongchaikij, Supachai 2   VIAFID ORCID Logo  ; Wonnapinij, Passorn 2   VIAFID ORCID Logo 

 Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; [email protected] (T.C.); [email protected] (S.S.); [email protected] (S.U.); [email protected] (W.P.); [email protected] (K.P.); [email protected] (S.V.) 
 Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; [email protected] (T.C.); [email protected] (S.S.); [email protected] (S.U.); [email protected] (W.P.); [email protected] (K.P.); [email protected] (S.V.); Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok 10900, Thailand 
First page
275
Publication year
2025
Publication date
2025
Publisher
MDPI AG
e-ISSN
20762607
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3171078101
Copyright
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.