ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp.

K, Muhammad Anaz; Sasidharan, N.; Remakanthan, A.; Dilsha, M V

doi:10.1016/j.compbiolchem.2021.107438

Cited by 5 publications

(7 citation statements)

References 32 publications

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“…when the TaxonDNA tool was used. Anaz, Sasidharan [15] confirm the current finding by analyzing delimited ITS2 sequences utilizing a neighbor-joining tree and ITS2 secondary structure.…”

Section: Discussionsupporting

confidence: 80%

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An exploration of the phylogeny and phylogeographic relationships of the subfamily Salacioideae

Bajpe¹,

Marulasiddaswamy²,

Manu³

et al. 2023

J App Biol Biotech

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Salacioideae is one of the subfamilies of the family Celastraceae. Salacia is a rare, endangered, and threatened genus found in India. Salacia is one of the Western Ghats' endemic species. Salacia species segregation and delimitation are difficult to achieve just based on taxonomic identification. The current research is an attempt to conduct a complete investigation into molecular phylogeny, estimation of age, and geographical implications of Salacia species. Salacia sp. Internal transcribed spacers (ITS), matK, and rcbL sequences from the Western Ghats of Karnataka, Kerala, and sequences from GenBank were utilized for the present study. Bayesian inference analysis (BI) and maximum likelihood (ML) to construct a phylogenetic tree using MrBayes and RAxML software. BI tree was used to calculate the divergence age of the Salacia species. Utilizing RASP v.2.0b geographic inferences were analyzed. A Well resolved phylogenetic tree was observed in the ITS and ITS + matK + rbcl concatenated sequence of the old world (OWC) and new world (NWC) samples forming two major clades. However, a poorly resolved phylogenetic tree was observed in the matK + rbcL sequences. The crown age of OWC and NWC was 9.82 Ma and 17.4 Ma, respectively. Madagascar and East Africa Salacia species had common tip node age of 3.13 Ma. Phylogeographic analysis suggests a total of 50 dispersals and 25 vicariance events. Phylogeographic analysis reveals the Salacia species could have originated from Southeast Asia. The endemism and diversity of Salacia species in the Western Ghats are explained by the fact that Salacia species from various geographic regions were positioned discordantly in the phylogenetic trees, demonstrating a high level of sequence similarity and congruence.

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“…when the TaxonDNA tool was used. Anaz, Sasidharan [15] confirm the current finding by analyzing delimited ITS2 sequences utilizing a neighbor-joining tree and ITS2 secondary structure.…”

Section: Discussionsupporting

confidence: 80%

“…Using ITS2 sequence secondary structure the variation within the Salacia sp. sampled with the Western Ghats was assessed by Anaz, Sasidharan [15]. The current research focuses on the phylogeny and phylogeography of the subfamily Salacioideae.…”

Section: Introductionmentioning

confidence: 99%

An exploration of the phylogeny and phylogeographic relationships of the subfamily Salacioideae

Bajpe¹,

Marulasiddaswamy²,

Manu³

et al. 2023

J App Biol Biotech

View full text Add to dashboard Cite

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“…According to a previous study, the features of the ITS2 region are conserved, which in turn provides molecular and morphological features that could be used to improve the resolution of species identification [ 40 ]. The usefulness of ITS2 sequences and the ITS2 secondary structure as genetic markers has been reported for several medicinal plant species [ 20 , 41 , 42 ]. Regarding the ITS2 secondary structure, the conservative standard structural model contained the feature of a “loop” with four “helices.” Among the four “helices,” helix I and helix IV had the most variations, helix II and helix III were more conserved, helix II was shorter with a pyrimidine–pyrimidine mismatch “bridge,” while helix III was the longest with many branches [ 30 , 43 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana

Saidon

Wagiran

Samad

et al. 2023

Genes

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Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose-bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.

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“…One line leads to the present-day S. chinensis and the other line further diversified and led to the rest of the Salacia spp. i.e., S. agasthiamalana , S. brunoniana , S. fruticosa , S. gambleana , S. oblonga , S. malabarica , and S. wayanadica Muhammad Anaz et al 2021 S. reticulata S. oblonga S. chinensis Genetic identification, confirmation of food adulteration nrDNA ITS sequences, RFLP Useful information to authenticate Salacia species and results confirm that S. chinensis and S. reticulata are the major sources of commercially available Salacia -derived food products Zhu et al 2021 S. chinensis S. fruticosa S. macrosperma S. oblonga Genetic diversity, species authentication ISSR, rbcL , matK , ITS ISSR primers revealed 29.21 ± 7.89% of polymorphism among Salacia spp. and nine other genera of family Celastraceae.…”

Section: Introductionmentioning

confidence: 99%

Salacia spp.: recent insights on biotechnological interventions and future perspectives

Chavan,

Patil,

Patil

et al. 2024

Appl Microbiol Biotechnol

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The plants of the genus Salacia L. are the storehouse of several bioactive compounds, and are involved in treating human diseases and disorders. Hitherto, a number of reports have been published on in vitro biotechnology as well as microbial involvement in the improvement of Salacia spp. The present review provides comprehensive insights into biotechnological interventions such as tissue culture for plant propagation, in vitro cultures, and endophytic microbes for up-scaling the secondary metabolites and biological potential of Salacia spp. Other biotechnological interventions such as molecular markers and bio-nanomaterials for up-grading the prospective of Salacia spp. are also considered. The in vitro biotechnology of Salacia spp. is largely focused on plant regeneration, callus culture, cell suspension culture, somatic embryogenesis, and subsequent ex vitro establishment of the in vitro–raised plantlets. The compiled information on tissue cultural strategies, involvement of endophytes, molecular markers, and nanomaterials will assist the advanced research related to in vitro manipulation, domestication, and commercial cultivation of elite clones of Salacia spp. Moreover, the genetic diversity and other molecular-marker based assessments will aid in designing conservation policies as well as support upgrading and breeding initiatives for Salacia spp. Key points: • Salacia spp. plays a multifaceted role in human health and disease management. • Critical and updated assessment of tissue culture, endophytic microbes, metabolites, molecular markers, and bio-nanomaterials of Salacia spp. • Key shortcomings and future research directions for Salacia biotechnology.

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ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp.

Cited by 5 publications

References 32 publications

An exploration of the phylogeny and phylogeographic relationships of the subfamily Salacioideae

An exploration of the phylogeny and phylogeographic relationships of the subfamily Salacioideae

DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana

Salacia spp.: recent insights on biotechnological interventions and future perspectives

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