Transcriptome characterization and population genetics of Ludisia discolor (Ker Gawl.) A.Rich (Orchidaceae): implication for its conservation in Vietnam

Phan, Huan; Thi-Lan, Nguyen; Le, Oanh; Nguyen, Cuong; Trinh, Chung; Ha, Yen; Shah, Syed Noor Muhammad; Vu, Duy

doi:10.3897/BDJ.14.e173579

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Article: Transcriptome characterization and population genetics of Ludisia discolor (Ker Gawl.) A.Rich (Orchidaceae): implication for its conservation in Vietnam

Title

Transcriptome characterization and population genetics of Ludisia discolor (Ker Gawl.) A.Rich (Orchidaceae): implication for its conservation in Vietnam

By

Phan, Huan
Thi-Lan, Nguyen
Le, Oanh
Nguyen, Cuong
Trinh, Chung
Ha, Yen
Shah, Syed Noor Muhammad
Vu, Duy

Type

Article

Date of Publication

2026-1-8

Original Publication

Biodiversity data journal

Volume

Pages

1--26

Subjects

Conservation , EST-SSR , genetic diversity , Illumina HiSeq™ 4000 , Ludisia discolor , transcriptome

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia Pensoft Publishers [2013]-

Identifiers

DOI: https://doi.org/10.3897/BDJ.14.e173579

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License Type URL: https://creativecommons.org/licenses/by/4.0/
Rights: https://biodiversitylibrary.org/permissions
Copyright Status: In copyright. Digitized with the permission of the rights holder.
Rights Holder: Copyright held by individual article author(s).

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The combined pressures of overharvesting for ornamental and medicinal markets, along with pervasive habitat degradation, have precipitated a critical threat to wild populations of the jewel orchid, Ludisia discolor , within the biodiversity hotspots of Vietnam. The development of robust molecular tools is therefore essential to inform effective conservation strategies. This study established a suite of polymorphic Expressed Sequence Tag-derived Simple Sequence Repeat (EST-SSR) markers for L. discolor and applied them to assess genetic diversity and population structure. Transcriptome sequencing on the Illumina HiSeq™ 4000 platform yielded 44,764,702 high-quality reads. De novo assembly generated 26,271 unigenes (N50 = 2,160 bp; Q30 = 96.3%), which were comprehensively annotated against public databases (Nr, Swiss-Prot) and classified into Gene Ontology, KOG, and KEGG pathways. From 9,495 identified EST-SSR loci, 15 highly polymorphic markers were validated. Analysis of Vietnamese populations revealed moderate genetic diversity (Na = 3.17; He = 0.54; PIC = 0.59). Analysis of molecular variance (AMOVA) indicated significant genetic differentiation, with 23% of variation partitioned among populations. Bayesian clustering, Principal Coordinates Analysis (PCoA), and Neighbor-Joining (NJ) tree reconstruction consistently identified two distinct genetic clusters correlated with geography, suggesting restricted gene flow. These transcriptome-derived EST-SSR markers have proven effective for population genetic studies in L. discolor . The genomic resources and findings presented here provide a critical foundation for genetic monitoring and support the integration of molecular data into conservation and restoration programs for this ecologically and culturally significant orchid.