Transcriptome characterization and population genetics of Ludisia discolor (Ker Gawl.) A.Rich (Orchidaceae):...

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.