Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.

Tran TKP, Pham MH, Trinh TH, Widiarsih S, Ho VT. 2022. Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers. Biodiversitas 23: 4816-4825. Jewel orchid is a general name for several genera belonging to the Orchidaceae family, namely Anoectochilus, Doddinia, Goodyera, Ludisia, and Macodes. These plants are generally used as medicinal herbal for common diseases in Vietnam. Due to over-exploitation, the natural resources of jewel orchids are gradually depleted. Therefore, genetic resource research for proper development of this medicinal plant is necessary. This study aimed to investigate the genetic diversity of jewel orchids in Vietnam using RAPD and ISSR markers to provide basic data conservation of genetic resources and the development of this medicinal plant. A total of 20 jewel orchid samples were genetically characterized by using 10 RAPD and 10 ISSR primers. The amplified bands were binary coded and used to construct phylogenetic trees with NTSYSpc 2.1 software. Each RAPD primer produced 5-11 bands with an average of 8.0, and similarity coefficients ranged from 0.52 to 0.81. Each ISSR primer produced 5-10 bands with an average of 7.6, and the similarity coefficients ranged from 0.54 to 0.87. Combined RAPD and ISSR markers produced similarity coefficients ranging from 0.53 to 0.83. Based on the PIC values, the primers used by both markers are highly informative. However, the topology of cluster analysis of 20 jewel orchid accessions does not correspond to the taxa studied. The findings could be potential to employ in future classification, conservation, and development of this plant.

Ho VT, Nguyen MP. 2020. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas 21: 3879-3885. DNA barcodes have been used intensively to discriminate different species in Cucurbitaceae family. The main of this study is to evaluate the effectiveness of rbcL and matK loci for 16 species of Cucurbitaceae family by using in silico approach. For analysis, sequences were firstly retrieved from NCBI and then calculated for sequence parameters. Sequences were then aligned and constructed phylogenetic try and examined for species resolution ability. The obtained data show the variability of resolving capacity among species. rbcL region is suitable for distinguishing five species namely S. edule, M. cochinchinensis, L. aegyptiaca, C. melo, and C. pepo, whereas matK locus is more proper for different five species consisting of M. balsamina, M. cochinchinensis, M. charantia, S. edule, and C. sativus. The resolving power is improved sharply by analyzing the rbcL + matK combination with up to nine species consisting of C. lanatus, B. hispida, C. melo, C. sativus, C. pepo, C. agryrosperma, L. aegyptiaca, S. edule, and M. cochinchinensis. Therefore, the integration of rbcL and matK loci may improve the competence of assessing genetic relatedness at species level of members in Cucurbitaceae family. The obtained information could be important for choosing proper DNA barcode loci for phylogenetic study of this crop family.

Nguyen MP, Trinh TH, Ngo TKA, Widiarsih S, Ho VT. 2023. In silico comparative analysis of the complete chloroplast genome sequences in different jewel orchid species. Nusantara Bioscience 15: 12-21. Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics but variable in medicinal properties. As these plants are utilized to treat several diseases, their natural existence in the wild habitat is rapidly diminished. Therefore, a better understanding of the genetic information of this plant for better genetic conservation and development of these plants is necessary. In this study, a total of 18 published chloroplast genomes of 18 jewel orchid species determined by the next-generation sequencing method were retrieved from NCBI GenBank and targeted for genomic characterization and phylogenetic analyses. Different bioinformatics tools were utilized to characterize these genomes’ genomic structure, repetitive sequences, interspecific variation, divergence, and phylogenetic relationships. The obtained data revealed that the chloroplast genomes of different jewel orchid species varied in length between 151,414 (Anoectochilus formosanus MN880624.1) and 154,375 (Goodyera biflora OM314910.1). Each species contains 34-87 SSR loci which could be useful as molecular markers for further genetic diversity study of this plant. Structural variations in the expansion and contraction of inverted repeat regions were also considered. Phylogenetic analysis identified a close relationship among species belonging to the Goodyera genus, and this genus is distinctive from other genera such as Anoectochilus, Cystorchis, Dossinia, Ludisia, and Macodes. The obtained results show a high potential of deeper characterizing the chloroplast genome of jewel orchids for species classification, identification, molecular breeding, and evolutionary exploration of these important herbal plants.

The mulberry family (Moraceae) encompasses a wide range of angiosperms and includes several important fruit plants, such as jackfruit, breadfruit, and figs, among others. While there have been multiple published complete chloroplast (cp) genomes within this family, there has been no comprehensive study that summarizes the characteristics of these sequences. In the current study, a comprehensive analysis was conducted using a dataset consisting of 32 cp genomes obtained from NCBI GenBank. These genomes belong to 32 species, encompassing 12 genera within the mulberry family. The collected data were used to conduct genomic comparisons and phylogenetic analyses, employing a range of bioinformatics tools. The findings revealed length variations among the cp genomes of different species, ranging from 158,459 bp in Morus mongolica to 162,594 bp in Broussonetia luzonica. Additionally, the study detected structural variations in simple sequence repeat motifs including gene losses. Overall, the phylogenetic results in this study generally supported the existing taxonomy of species within this family, with the exception that Malaisia scandens and Trophis scandens are clustered in the clade of the Broussonetia genus. This investigation provides further evidence of the effectiveness of characterizing the entire cp genome when classifying species and genera within the mulberry family.

Camellia tienii, an indigenous plant species in Vietnam, is renowned for its remarkable medicinal properties. However, the current methods for plant identification are not reliable due to shared characteristics with other species in Camellia genus. To address this, the present study aimed to sequence and characterize the complete chloroplast (cp) genome of C. tienii. The resulting cp genome is 162,167 bp in size and encompasses 154 genes, including 98 protein-coding genes, 8 rRNA genes, and 48 tRNA genes. Notably, this genome contains 55 simple sequence repeats, specifically type A and T motifs. It is worth mentioning that the ndhF gene was not detected in this genome, while the trnL gene was present. Phylogenetic analysis revealed that C. tienii shares a close relationship with C. tamdaoensis. These significant findings contribute with valuable insights that can aid in the accurate taxonomy, plant identification, and conservation efforts concerning this herb in Vietnam.