The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

Abstract

Abstract:The genus Dalbergia contains approximately 250 species with many valuable trees being destroyed by targeted and illegal logging. DNA barcoding is a reliable method for the molecular identification of different species and resources conservation. In the present study, the specimen discrimination ability of internal transcribed spacer (ITS), matK, rbcL and psbA-trnH barcoding were tested on Dalbergia sequences, downloaded from the National Center for Biotechnology Information (NCBI), and the combined barcoding ITS + matK + rbcL was used to identify unknown specimens. It was found that ITS + matK + rbcL have good discrimination rates based on the analysis methods best match (BM) and best close match (BCM). These barcodes also have the best performance concerning barcode gap distribution, and are able to discriminate unknown specimens from South-China. Furthermore, it was demonstrated that D. tamarindifolia and D. rubiginosa are also relatively close to sister-species D. pinnata and D. candenatensis within the phylogenetic Dalbergia tree. Considering the overall performance of these barcodes, we suggest that the ITS + matK + rbcL region is a suitable barcode for identifying Dalbergia species.

Molecular Identification of Three <i>Aquilaria</i> (Thymelaeaceae) Species through DNA Barcoding

“…17) The ITS sequence was introduced for the identification of Aquilaria in past decade. 9,18) Lee et al showed that the ITS sequence could be used to distinguish Aquilaria malaccensis from three geographical regions. 6) However, our results suggest that the ITS sequence may not be suitable to identify A. sinensis, as its sequences is highly similar to A. crassna.…”

“…1), even if ITS sequence alone may have served as a barcode to distinguish in most Aquilaria species. 5,9) A combination of both nuclear and cpDNA barcodes have shown to result in better species discrimination than cpDNA or nuclear barcodes alone. 19) Higher species discrimination using this pattern of DNA barcoding has been recorded in many studies that have focused on closely related genera or species, such as Dalbergia (ITS+matK+rbcL), 10) Gossypium (ITS2+matK+rbcL) 20) and Tripterygium (ITS2+psbA-trnH).…”

“…DNA Extraction and PCR Amplification Genomic DNA was extracted using the modified cetyl trimethyl ammonium bromide (CTAB) protocol. 10) PCR amplifications were carried out on a S1000 Thermal Cycler (Bio-Rad, U.S.A.). For ITS region, the universal primer pairs were: ITS5 (5′-GGA AGT AAA AGT CGT AAC AAG G-3′) and ITS4 (5′-TCC TCC GCT TAT TGA TAT GC-3′), 11,12) and PCR conditions were 3 min at 95°C, 30 cycles of 1 min at 94°C, 50 s at 56°C, 55 s at 72°C, followed by 10 min at 72°C.…”

Unraveling genetic variations of Dalbergia latifolia (Fabaceae) from Yogyakarta and Lombok Island, Indonesia

“…The genus Dalbergia (Fabaceae: Papilionaceae) contains ca. 250 species (Li et al 2017) that has a wide distribution in tropical and subtropical regions in South America, Africa, Asia and Madagascar (Cardoso et al 2013;Saha et al 2013;Vatanparast et al 2013). Some species of Dalbergia have high-quality timber, including D. latifolia Roxb.…”

Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective

“…To be truly universal, metabarcoding would require the inclusion of multiple loci, each optimized to capture species-level resolution in different taxa (e.g., CO1 for fauna, matK/rbcL for plants, ITS for fungi). However, whereas multiple loci sequence data can be combined for analysis of individual specimens in barcoding to improve taxonomic resolution (e.g., Li et al, 2017), the single bulk sample used in metabarcoding prohibits such treatment. Instead where multiple loci are utilized in metabarcoding, their results must be analyzed independently then combined to produce a list of likely taxa in the sample (Arulandhu et al, 2017).…”