DNA barcodes for delineating Clerodendrum species of North East India

Gogoi, Barnali; Wann, Sawlang Borsingh; Saikia, Siddhartha Proteem

doi:10.1038/s41598-020-70405-3

Cited by 15 publications

(10 citation statements)

References 45 publications

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“…Gogoi et al [ 33 ] evaluated four barcode candidates ( ITS2 , matK , rbcL , ycf1 ) and their combinations in different Clerodendrum species of Northeast India. The reliability of these barcodes to distinguish the species was evaluated by genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods.…”

Section: Discussionmentioning

confidence: 99%

Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode

Chen

Wang

et al. 2023

PLoS ONE

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Background The plants of the genus Clerodendrum L. have great potential for development as an ornamental and important herbal resource. There is no significant morphological difference among many species of the genus Clerodendrum, which will lead to confusion among the herbs of this genus and ultimately affect the quality of the herbs. The chloroplast genome will contribute to the development of new markers used for the identification and classification of species. Methods and results Here, we obtained the complete chloroplast genome sequences of Clerodendrum chinense (Osbeck) Mabberley and Clerodendrum thomsoniae Balf.f. using the next generation DNA sequencing technology. The chloroplast genomes of the two species all encode a total of 112 unique genes, including 80 protein-coding, 28 tRNA, and four rRNA genes. A total of 44–42 simple sequence repeats, 19–16 tandem repeats and 44–44 scattered repetitive sequences were identified. Phylogenetic analyses showed that the nine Clerodendrum species were classified into two clades and together formed a monophyletic group. Selective pressure analyses of 77 protein-coding genes showed that there was no gene under positive selection in the Clerodendrum branch. Analyses of sequence divergence found two intergenic regions: trnH-GUG-psbA, nhdD-psaC, exhibiting a high degree of variations. Meanwhile, there was no hypervariable region identified in protein coding genes. However, the sequence identities of these two intergenic spacers (IGSs) are greater than 99% among some species, which will result in the two IGSs not being used to distinguish Clerodendrum species. Analysis of the structure at the LSC (Large single copy) /IR (Inverted repeat) and SSC (Small single copy)/IR boundary regions showed dynamic changes. The above results showed that the complete chloroplast genomes can be used as a super-barcode to identify these Clerodendrum species. The study lay the foundation for the understanding of the evolutionary process of the genus Clerodendrum.

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Section: Discussionmentioning

confidence: 99%

Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode

Chen

Wang

et al. 2023

PLoS ONE

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“…Fifth, the application of QR codes is always a research focus. To date, this technique has been applied to not only life but also various fields of science, such as optical retrieval 41 and taxonomy of species 42 .…”

Section: Comparisons Between This Work and Related Onesmentioning

confidence: 99%

A novel approach for audible acoustic quick response codes

Zhu

Gao

Wang

2022

Sci Rep

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Compared to image-based quick response (QR) codes, acoustic QR codes have some advantages. However, an acoustic QR scanner cannot recognize an acoustic QR code at a distance of more than two meters from an acoustic QR announcer. To this end, we propose a new sort of acoustic QR code, called an audible acoustic QR code (AAQRC), which employs humanly audible sound to carry users’ information directly. First, a user’s string of characters is translated into a string of pitches. Then, the related algorithms convert the string of pitches into a playable audio file. As a result, an AAQRC is generated, consisting of the audio itself. AAQRC recognition is the opposite process of AAQRC generation. Compared with the existing approach for acoustic QR codes, the new method can recognize acoustic QR codes at a longer distance, even if there are obstacles between the AAQRC announcer and AAQRC scanner.

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“…The present study reports the DNA barcoding of critically endangered jewel orchid A. rotundifolia. The barcode regions matK and rbcL are routinely used as a marker for its well-known cost effectiveness and its own rate of molecular evolution resulting in sharp identity for each species (Wattoo et al 2016;Barbi et al 2020). These barcode regions are well known for established pattern of resolution and universality (Li et al 2011).…”

Section: Genetic Fidelity Assessment Of In Vitro Raised Plantsmentioning

confidence: 99%

DNA barcoding and genetic fidelity assessment of micropropagated Aenhenrya rotundifolia (Blatt.) C.S. Kumar and F.N. Rasm.: a critically endangered jewel orchid

Sherif

Kumar

Rao

2020

Physiol Mol Biol Plants

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Aenhenrya rotundifolia is a critically endangered terrestrial jewel orchid. It is monotypic and endemic to evergreen forests of southern western ghats of India. In the present study, identification of this plant species is validated with DNA barcoding using matK and rbcL chloroplast markers. Further, germ-free juvenile axillary bud explants were cultured on Mitra medium supplemented with different kinds of cytokinins like 6-benzyladenine, 6-furfurylaminopurine, N 6 -(D 2 -isopentyl) adenine, thidiazuron, zeatin and meta-topolin as well as auxins such as a-naphthaleneacetic acid, indole-3-acetic acid and indole-3-butyric acid at different concentrations and combinations for successful proliferation and establishment in vitro. After 12 weeks of culture, axillary bud explants produced an average of 30.12 ± 0.71 shoots per explant, 3.87 ± 0.06 cm shoot length, 1671 ± 2.82 mg fresh mass of proliferated shoots with a proliferation frequency of 100% on Mitra medium supplemented with 6.20 lM metatopolin and 2.25 lM thidiazuron. No root formation was observed in in vitro proliferated microshoots. However, tiny hair like projections were observed in some elongated shoots on Mitra medium pertaining to 5.37 lM NAA. The tiny hair like structure bearing plantlets were hardened and acclimatized with 100% survival rate in the polytunnel chamber. After 8-10 months of establishment ex vitro, flowering was observed. Additionally, the genetic fidelity of in vitro derived plants was tested with ISSR and SCoT marker profiling. The test results revealed that the plants derived from the protocol has 99% genetic similarity to that of the donor mother plant. This study can be applied in forensic interventions of this species, describes the maintenance of germplasm in vitro and establishment of new viable population in its original habitats by restoring existing sites of this critically endangered jewel orchid.

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DNA barcodes for delineating Clerodendrum species of North East India

Cited by 15 publications

References 45 publications

Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode

Conserved chloroplast genome sequences of the genus Clerodendrum Linn. (Lamiaceae) as a super-barcode

A novel approach for audible acoustic quick response codes

DNA barcoding and genetic fidelity assessment of micropropagated Aenhenrya rotundifolia (Blatt.) C.S. Kumar and F.N. Rasm.: a critically endangered jewel orchid

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