Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products

Hishamuddin, Muhammad Syahmi; Lee, Shiou Yih; Syazwan, Samsuddin Ahmad; Ramlee, Shairul Izan; Lamasudin, Dhilia Udie; Mohamed, Rozi

doi:10.1007/s13205-023-03479-1

Cited by 3 publications

(4 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is because the gene markers derived from the highly variable regions identified from the sliding window analysis could provide a better resolution in species delimitation for closely related species when compared to the universal DNA barcoding loci 59 . While it is recommended to have at least five to seven closely related chloroplast genome sequences from different species to identify such barcodes 60 , our study has utilized 31 chloroplast genomes derived from 30 different Ipomoea taxa, making the finding highly reliable when compared to other published works (i.e. Park et al 23 , Wang et al 61 ).…”

Section: Discussionmentioning

confidence: 99%

“…When reconstructing the phylogenetic tree of closely related species, the complete chloroplast genome sequence data could be superior to the chloroplast CDS data because the former contains a significant amount of genetic information, as demonstrated in Ref. 60 . These informative sites will contribute to a better resolution in delimiting closely related species, revealing well-resolved phylogenetic relationships in complicated genera or families 63 .…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

Sudmoon,

Kaewdaungdee,

et al. 2024

Sci Rep

Self Cite

View full text Add to dashboard Cite

Ipomoea species have diverse uses as ornamentals, food, and medicine. However, their genomic information is limited; I. alba and I. obscura were sequenced and assembled. Their chloroplast genomes were 161,353 bp and 159,691 bp, respectively. Both genomes exhibited a quadripartite structure, consisting of a pair of inverted repeat (IR) regions, which are separated by the large single-copy (LSC) and small single-copy (SSC) regions. The overall GC content was 37.5% for both genomes. A total of 104 and 93 simple sequence repeats, 50 large repeats, and 30 and 22 short tandem repeats were identified in the two chloroplast genomes, respectively. G and T were more preferred than C and A at the third base position based on the Parity Rule 2 plot analysis, and the neutrality plot revealed correlation coefficients of 0.126 and 0.105, indicating the influence of natural selection in shaping the codon usage bias in most protein-coding genes (CDS). Genome comparative analyses using 31 selected Ipomoea taxa from Thailand showed that their chloroplast genomes are rather conserved, but the presence of expansion or contraction of the IR region was identified in some of these Ipomoea taxa. A total of five highly divergent regions were identified, including the CDS genes accD, ndhA, and ndhF, as well as the intergenic spacer regions psbI-atpA and rpl32-ccsA. Phylogenetic analysis based on both the complete chloroplast genome sequence and CDS datasets of 31 Ipomoea taxa showed that I. alba is resolved as a group member for series (ser.) Quamoclit, which contains seven other taxa, including I. hederacea, I. imperati, I. indica, I. nil, I. purpurea, I. quamoclit, and I. × sloteri, while I. obscura is grouped with I. tiliifolia, both of which are under ser. Obscura, and is closely related to I. biflora of ser. Pes-tigridis. Divergence time estimation using the complete chloroplast genome sequence dataset indicated that the mean age of the divergence for Ipomoeeae, Argyreiinae, and Astripomoeinae, was approximately 29.99 Mya, 19.81 Mya, and 13.40 Mya, respectively. The node indicating the divergence of I. alba from the other members of Ipomoea was around 10.06 Mya, and the split between I. obscura and I. tiliifolia is thought to have happened around 17.13 Mya. The split between the I. obscura accessions from Thailand and Taiwan is thought to have taken place around 0.86 Mya.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

Sudmoon,

Kaewdaungdee,

et al. 2024

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Until now, molecular identification methods for agarwood have mainly focused on DNA barcode screening and its combinations, such as ITS2+trnL-trnF , ITS2+matK (Kang et al, 2018), ITS+matK, ITS+rbcL, ITS+trnL-trnF (Li et al, 2018;Lin et al, 2023), and psbJ-petA+trnT-trnL (Hishamuddin et al, 2023).…”

Section: Importance Of Traditional Chinese Medicinal Agarwood Species...mentioning

confidence: 99%

“…Therefore, it is of great importance to identify medicinal agarwood species from large amounts of agarwood. Some scholars have suggested ITS2+trnL-trnF , ITS2+matK (Kang et al, 2019), ITS+matK, ITS+rbcL, ITS+trnL-trnF (Li et al, 2019;Lin et al, 2023), and psbJ-petA+trnT-trnL (Hishamuddin et al, 2023) for the molecular identification of agarwood. However, the actual situation is not working well.…”

Section: Introductionmentioning

confidence: 99%

Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome

Feng,

Liu,

Xie

et al. 2024

Front. Plant Sci.

View full text Add to dashboard Cite

Agarwood is a valuable traditional medicine and fragrance. The production process is a typical injury-induced defense response. Currently, there are approximately 22 known species in the genus Aquilaria Lam., all of which can produce agarwood, whereas there are only two legal species of traditional Chinese medicinal agarwood, Aquilaria sinensis (Lour.) Spreng. and Aquilaria agallocha (Lour.) Roxb. The Taiwan herbal Pharmacopoeia of China stipulates that the medicinal agarwood species are A. sinensis and its relatives in the same genus. Moreover, there are five species of agarwood available for clinical medicinal use in Japan, including A. agallocha and A. sinensis, which are often confused with each other or used in a mixed way in the trade process. Therefore, accurate identification of traditional Chinese medicinal agarwood species is important to ensure the authenticity of traditional medicines and to guide the safety of clinical medication. In this study, 59 specific single-nucleotide polymorphism loci were screened and obtained from the chloroplast genomes of 12 species of the genus Aquilaria Lam. We established an identification method for traditional Chinese medicinal agarwood using mini-barcoding combined with high-resolution melting (HRM) and designed and validated 10 pairs of primers from the psbM-trnD, psbA, rps16, petN, ndhE-psaC, rps4, atpE, ycf1, rps15-trnN, and matK regions. The amplification products were all less than 200 bp, with a high success rate of amplification. The method was applied to successfully identify traditional Chinese medicinal agarwood species from commercial agarwood samples. Overall, the sensitivity of this method was sufficient to detect 1% of adulterants in medicinal agarwood products, proving that mini-barcoding HRM is a powerful and flexible tool. This method can be used as a fast and effective high-throughput method for authenticity testing of traditional Chinese medicinal agarwood and its raw materials containing agarwood-containing proprietary Chinese medicines and is recommended for industrial applications.

show abstract

Conservation Strategies for Aquilaria sinensis: Insights from DNA Barcoding and ISSR Markers

Zhang,

Luo,

Guan

et al. 2024

Plant Foods Hum Nutr

View full text Add to dashboard Cite

Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products

Cited by 3 publications

References 45 publications

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome

Conservation Strategies for Aquilaria sinensis: Insights from DNA Barcoding and ISSR Markers

Contact Info

Product

Resources

About