The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae)

Kurian, Anoja; Dev, Suma Arun; Sreekumar, V. B.; Muralidharan, E. M.

doi:10.1007/s12298-020-00864-5

Cited by 7 publications

(8 citation statements)

References 74 publications

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“…For this reference library, the use of nuclear loci such as the ITS was not considered because of poor amplification success across land plants (Hollingsworth, 2011) and paralogous copies (Poczai & Hyvönen, 2010). However, future studies, especially those focused on specific taxonomic groups, could have success using the shorter ITS2 region (China Plant B. O. L. Group et al, 2011), or potentially other low‐copy nuclear loci (Kurian et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

A DNA barcode reference library for the native woody seed plants of Japan

Setsuko

Yoshimura

Ueno

et al. 2023

Molecular Ecology Resources

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DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.

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Section: Discussionmentioning

confidence: 99%

A DNA barcode reference library for the native woody seed plants of Japan

Setsuko

Yoshimura

Ueno

et al. 2023

Molecular Ecology Resources

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“…A high copy number is often seen as an asset in processed material, but there is often poor knowledge about the extent of concerted evolution among the various copies [28]. However, Kurian et al [27] reported that the low copy nuclear gene RBP2 was variable enough to identify Calamus species and a potential DNA barcode for other Palm species.…”

Section: Discussionmentioning

confidence: 99%

“…A few single-copy loci from the nuclear genome were recently tested for their species discrimination ability in plants 27 . The major advantage of single-copy genes from the nuclear genome is their high rate of variation that helped in easy species identification 27 . The granule bound starch synthase ( GBSS1 ) region from any nuclear genome is a single copy gene that has been useful for the phylogenetic assignment of several plant taxa 28 , 29 , 30 .…”

Section: Introductionmentioning

confidence: 99%

“…Hence, more loci apart from ITS from the nuclear genome are required to identify and authentic Salvia sp. A few single-copy loci from the nuclear genome were recently tested for their species discrimination ability in plants [27]. The major advantage of single-copy genes from the nuclear genome is their high rate of variation that helped in easy species identification [27].…”

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The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

et al. 2021

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Morphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 – 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.

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“…For this database the use of nuclear loci such as the internal transcribed spacer (ITS) was not considered because of poor amplification success across land plants (Hollingsworth, 2011) and paralogous copies (Poczai & Hyvönen, 2010). However, future studies, especially those focussed on specific taxonomic groups, could have success using the shorter ITS2 region (China Plant B. O. L. Group et al, 2011), or potentially other low copy nuclear loci (Kurian et al, 2020). Figure 4 The species level identification rate for 18 selected plant families for which there are over 10 species in Japan and over 70% of species were sampled and over 50% sequence success for each three regions.…”

Section: Discussionmentioning

confidence: 99%

A DNA barcode database for the woody plants of Japan

Setsuko

Yoshimura

Ueno

et al. 2021

Preprint

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DNA barcode databases are increasingly available for a range of organisms facilitating the wide application of DNA barcode-based pursuits. Here we announce the development of a comprehensive DNA barcode database of the Japanese woody flora representing 43 orders, 99 families, 303 genera and 834 species and comprising 77.3% of genera and 72.2% of species of woody plants in Japan. A total of 6,216 plant specimens were collected from 223 sites (municipalities, i.e. city, town, village) across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This database utilised three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,404 barcode sequences. Individual regions varied in their identification rates with species-level and genus-level rates for rbcL, trnH-psbA and matK being 57.4%/ 96.2%, 78.5%/ 99.1 % and 67.8%/ 98%, respectively. Identification rates were higher using region combinations with total species level rates for two region combinations (rbcL & trnH, rbcL & matK, and trnH-psbA & matK) ranging between 90.6–95.8%, and for all three regions equal to 98.6%. Genus level identification rates were even higher ranging between 99.7–100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode database is an effective resource for investigations of woody plants in Japan using DNA barcodes and provides a useful template for development of libraries for other components of the Japanese flora.

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The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae)

Cited by 7 publications

References 74 publications

A DNA barcode reference library for the native woody seed plants of Japan

A DNA barcode reference library for the native woody seed plants of Japan

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

A DNA barcode database for the woody plants of Japan

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