Department Of Botany

Permanent URI for this communityhttps://kr.cup.edu.in/handle/32116/28

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Author: search.filters.author.Bast, FelixSubject: search.filters.subject.Phylogeny

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    First report of Planomicrobium okeanokoites associated with Himantothallus grandifolius (Desmarestiales, Phaeophyta) from Southern Hemisphere
    (Public Library of Science, 2023-04-14T00:00:00) Chand Saini, Khem; Gupta, Kriti; Sharma, Sheetal; Gautam, Ajay K.; Shamim, Samrin; Mittal, Divya; Kundu, Pushpendu; Bast, Felix
    Gram-positive, aerobic, motile, rod-shaped, mesophilic epiphytic bacterium Planomicrobium okeanokoites was isolated from the surface of endemic species Himantothallus grandifolius in Larsemann Hills, Eastern Antarctica. The diversity of epiphytic bacterial communities living on marine algae remains primarily unexplored; virtually no reports from Antarctic seaweeds. The present study used morpho-molecular approaches for the macroalgae and epiphytic bacterium characterization. Phylogenetic analysis was performed using mitochondrial genome encoded COX1 gene; chloroplast genome encodes rbcL; nuclear genome encoded large subunit ribosomal RNA gene (LSU rRNA) for Himantothallus grandifolius and ribosomal encoded 16S rRNA for Planomicrobium okeanokoites. Morphological and molecular data revealed that the isolate is identified as Himantothallus grandifolius, which belongs to Family Desmarestiaceae of Order Desmarestiales in Class Phaeophyceae showing 99.8% similarity to the sequences of Himantothallus grandifolius, from King George Island, Antarctica (HE866853). The isolated bacterial strain was identified on the basis of chemotaxonomic, morpho-phylogenetic, and biochemical assays. A phylogenetic study based on 16S rRNA gene sequences revealed that the epiphytic bacterial strain SLA-357 was closest related to the Planomicrobium okeanokoites showing 98.7% sequence similarity. The study revealed the first report of this species from the Southern Hemisphere to date. Also, there has been no report regarding the association between the Planomicrobium okeanokoites and Himantothallus grandifolius; however, there are some reports on this bacterium isolated from sediments, soils, and lakes from Northern Hemisphere. This study may open a gateway for further research to know about the mode of interactions and how they affect the physiology and metabolism of each other. � 2023 Saini et al.
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    Molecular data reveals two new species of Hypnea (Cystocloniaceae, Rhodophyta) from India: Hypnea indica sp. Nov. And Hypnea bullata sp. Nov.
    (De Gruyter Open Ltd, 2021-03-22T00:00:00) Kundu, Pushpendu; Bast, Felix
    We used three molecular markers (COI-5P, rbcL and UPA) to investigate the diversity of Hypnea spp., an economically important red algal genus, collected from India. Our concatenated tree (COI-5P and rbcL) supported the monophyly of two new species, Hypnea indica sp. nov. and Hypnea bullata sp. nov. H. indica diverged from its closest two sister species, Hypnea cervicornis and Hypnea tenuis (by 15.9 and 11.2%, respectively, in COI-5P; and 3.4 and 3.2% in rbcL). We describe H. indica as a new species characterised by an erect, percurrent main axis with spinelike branchlets in acute angles, straight and forked apices, axial cells surrounded by large periaxial cells or two cells similar in size to the axial cell, and the presence of lenticular thickening in the cross-section of the thallus. H. bullata diverged from its closest sister species, Hypnea brasiliensis (by 10.9% in COI-5P and 3.3% in rbcL). H. bullata is characterized by a prostrate thallus up to 1.5 cm in height, highly anastomosed, with an axial cell surrounded by similar sized, or smaller, periaxial cells, tetrasporangia present near the base of branchlets, and the presence of lenticular thickening. � 2021 De Gruyter. All rights reserved.
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    Morpho-molecular characterization of rock-inhabiting lichen Dermatocarpon miniatum (Verrucariaceae, Ascomycota) and its symbiont in Indian Himalayas
    (Springer, 2021-03-24T00:00:00) Saini, Khem Chand; Bast, Felix; Nayaka, Sanjeeva; Gautam, Ajay Kumar
    The genus Dermatocarpon (Verrucariaceae) is a rock-inhabiting lichen, mostly grows along the edges of lakes, rivers, streams, and watercourses. Dermatocarpon species are widely distributed from the tropics to the polar regions. In present study, D. miniatum samples were collected from the Indian Himalayas; the mycobiont and their photobionts are identified using morphological and molecular methods. The ITS rDNA markers was amplified for the DNA extracted from cultured photobiont isolates and mycobiont. The light and confocal laser scanning microscope were used for morphological evaluation of the photobionts. The nuclear ITS rDNA gene of the mycobionts and photobionts were sequenced to confirm identity. The phylogenetic trees of mycobionts and photobionts were constructed using the Maximum likelihood method that revealed an evolutionary affinity of lichen D. miniatum and photobiont Diplosphaera chodatii with similar taxa. The D. chodatii (Trebouxiophyceae) was associated with all samples of D. miniatum. This study concludes that Diplosphaera chodatii is the primary photobiont associated with D. miniatum. To the best of our knowledge this is the first study of diversity for the photobiont associated with D. miniatum from India. � 2021, Archana Sharma Foundation of Calcutta.
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    First report of Planomicrobium okeanokoites associated with Himantothallus grandifolius (Desmarestiales, Phaeophyta) from Southern Hemisphere
    (Public Library of Science, 2023-04-14T00:00:00) Chand Saini, Khem; Gupta, Kriti; Sharma, Sheetal; Gautam, Ajay K.; Shamim, Samrin; Mittal, Divya; Kundu, Pushpendu; Bast, Felix
    Gram-positive, aerobic, motile, rod-shaped, mesophilic epiphytic bacterium Planomicrobium okeanokoites was isolated from the surface of endemic species Himantothallus grandifolius in Larsemann Hills, Eastern Antarctica. The diversity of epiphytic bacterial communities living on marine algae remains primarily unexplored; virtually no reports from Antarctic seaweeds. The present study used morpho-molecular approaches for the macroalgae and epiphytic bacterium characterization. Phylogenetic analysis was performed using mitochondrial genome encoded COX1 gene; chloroplast genome encodes rbcL; nuclear genome encoded large subunit ribosomal RNA gene (LSU rRNA) for Himantothallus grandifolius and ribosomal encoded 16S rRNA for Planomicrobium okeanokoites. Morphological and molecular data revealed that the isolate is identified as Himantothallus grandifolius, which belongs to Family Desmarestiaceae of Order Desmarestiales in Class Phaeophyceae showing 99.8% similarity to the sequences of Himantothallus grandifolius, from King George Island, Antarctica (HE866853). The isolated bacterial strain was identified on the basis of chemotaxonomic, morpho-phylogenetic, and biochemical assays. A phylogenetic study based on 16S rRNA gene sequences revealed that the epiphytic bacterial strain SLA-357 was closest related to the Planomicrobium okeanokoites showing 98.7% sequence similarity. The study revealed the first report of this species from the Southern Hemisphere to date. Also, there has been no report regarding the association between the Planomicrobium okeanokoites and Himantothallus grandifolius; however, there are some reports on this bacterium isolated from sediments, soils, and lakes from Northern Hemisphere. This study may open a gateway for further research to know about the mode of interactions and how they affect the physiology and metabolism of each other. � 2023 Saini et al.
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    Molecular data reveals two new species of Hypnea (Cystocloniaceae, Rhodophyta) from India: Hypnea indica sp. Nov. And Hypnea bullata sp. Nov.
    (De Gruyter Open Ltd, 2021-03-22T00:00:00) Kundu, Pushpendu; Bast, Felix
    We used three molecular markers (COI-5P, rbcL and UPA) to investigate the diversity of Hypnea spp., an economically important red algal genus, collected from India. Our concatenated tree (COI-5P and rbcL) supported the monophyly of two new species, Hypnea indica sp. nov. and Hypnea bullata sp. nov. H. indica diverged from its closest two sister species, Hypnea cervicornis and Hypnea tenuis (by 15.9 and 11.2%, respectively, in COI-5P; and 3.4 and 3.2% in rbcL). We describe H. indica as a new species characterised by an erect, percurrent main axis with spinelike branchlets in acute angles, straight and forked apices, axial cells surrounded by large periaxial cells or two cells similar in size to the axial cell, and the presence of lenticular thickening in the cross-section of the thallus. H. bullata diverged from its closest sister species, Hypnea brasiliensis (by 10.9% in COI-5P and 3.3% in rbcL). H. bullata is characterized by a prostrate thallus up to 1.5 cm in height, highly anastomosed, with an axial cell surrounded by similar sized, or smaller, periaxial cells, tetrasporangia present near the base of branchlets, and the presence of lenticular thickening. � 2021 De Gruyter. All rights reserved.
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    Morpho-molecular characterization of rock-inhabiting lichen Dermatocarpon miniatum (Verrucariaceae, Ascomycota) and its symbiont in Indian Himalayas
    (Springer, 2021-03-24T00:00:00) Saini, Khem Chand; Bast, Felix; Nayaka, Sanjeeva; Gautam, Ajay Kumar
    The genus Dermatocarpon (Verrucariaceae) is a rock-inhabiting lichen, mostly grows along the edges of lakes, rivers, streams, and watercourses. Dermatocarpon species are widely distributed from the tropics to the polar regions. In present study, D. miniatum samples were collected from the Indian Himalayas; the mycobiont and their photobionts are identified using morphological and molecular methods. The ITS rDNA markers was amplified for the DNA extracted from cultured photobiont isolates and mycobiont. The light and confocal laser scanning microscope were used for morphological evaluation of the photobionts. The nuclear ITS rDNA gene of the mycobionts and photobionts were sequenced to confirm identity. The phylogenetic trees of mycobionts and photobionts were constructed using the Maximum likelihood method that revealed an evolutionary affinity of lichen D. miniatum and photobiont Diplosphaera chodatii with similar taxa. The D. chodatii (Trebouxiophyceae) was associated with all samples of D. miniatum. This study concludes that Diplosphaera chodatii is the primary photobiont associated with D. miniatum. To the best of our knowledge this is the first study of diversity for the photobiont associated with D. miniatum from India. � 2021, Archana Sharma Foundation of Calcutta.
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    Tutorial on Phylogenetic Inference – 1
    (Indian Academy of Science, 2015) Bast, Felix
    Phylogenetic Inference is a statistical technique to trace the evolutionary legacy of a wide range of subjects including biological taxa (species), biomolecules, languages, ancient texts and so on. In Part 1 of the tutorial, we begin with an introduction to this field and discuss phenetics and cladistics — two major techniques used for phylogenetic inference. A number of fundamental concepts for understanding phylogenetic inference are introduced. In Part 2, we will learn models of molecular evolution and methods of phylogenetic inference, concluding with a worked-out example.
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    Tutorial on Phylogenetic Inference Part-2
    (Indian Academy of Science, 2015) Bast, Felix
    Phylogenetic Inference (PI) is a statistical technique to trace the evolutionary legacy of a wide range of subjects; including biological taxa (species), biomolecules, languages, ancient texts and so on. The first part 1 of this tutorial introduced a number of fundamental concepts including phenetics, cladistics, homology, homoplasy, synapomorphy, symplesiomorphy, orthology and paralogy. In this part, we will learn about models of molecular evolution, choosing the best model, overview of various genetic loci used in PI, methods of PI (including distance matrix method, NJ, and discrete data methods ML, MP and BI), issue of lineage sorting and conclude with a worked-out example.
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    Chloroplast DNA phylogeography of holy basil (Ocimum tenuiflorum) in Indian subcontinent
    (2014) Bast, Felix; Rani, Pooja; Meena, Devendra
    Ocimum tenuiflorum L., holy basil "Tulsi", is an important medicinal plant that is being grown and traditionally revered throughout Indian Subcontinent for thousands of years; however, DNA sequence-based genetic diversity of this aromatic herb is not yet known. In this report, we present our studies on the phylogeography of this species using trnL-trnF intergenic spacer of plastid genome as the DNA barcode for isolates from Indian subcontinent. Our pairwise distance analyses indicated that genetic heterogeneity of isolates remained quite low, with overall mean nucleotide p-distance of 5?10-4. However, our sensitive phylogenetic analysis using maximum likelihood framework was able to reveal subtle intraspecific molecular evolution of this species within the subcontinent. All isolates except that from North-Central India formed a distinct phylogenetic clade, notwithstanding low bootstrap support and collapse of the clade in Bayesian Inference. North-Central isolates occupied more basal position compared to other isolates, which is suggestive of its evolutionarily primitive status. Indian isolates formed a monophyletic and well-supported clade within O. tenuiflorum clade, which indicates a distinct haplotype. Given the vast geographical area of more than 3 million km 2 encompassing many exclusive biogeographical and ecological zones, relatively low rate of evolution of this herb at this locus in India is particularly interesting. ? 2014 Felix Bast et al.
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    Phylogenetics: Tracing the Evolutionary Legacy of Organisms, Metastatic Clones, Bioactive Compounds and Languages
    (OMICS, 2015) Bast, Felix
    Since its inception seventy-five years ago, the field of phylogenetics has steadily been expanding to contribute in a number of scientific fields including biogeography, medicinal chemistry, forensics, transcriptomics, cancer biology and even linguistics, in addition to systematic biology -for which it was originally erupted by Willi Hennig. In this invited editorial contributed to the Journal of Phylogenetics and Evolutionary Biology a big picture of this ever evolving field is expounded. Application of phylogenetic inference in biosystematics, phylogeography, phylogenetic selection of target taxa in medicinal chemistry, cancer phylogenetics, and linguistic phylogeny are reviewed with a personal perspective summarizing contribution to this interdisciplinary field from my group. Parametric methods such as Maximum Likelihood and Bayesian Inference have dramatically improved for last one decade, yet empirical solutions to some of the most fundamental issues, including homoplasmy and lineage sorting, remains to be materialized.