Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis

Mahadani, Asim Kumar; Awasthi, Shashank; Sanyal, Goutam; Bhattacharjee, Partha; Pippal, Sanjeev Kumar

doi:10.1080/23335777.2021.1879274

Cited by 27 publications

(7 citation statements)

References 31 publications

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“…Reconstruction of phylogenetic trees and analysis of genetic distances were performed using the MEGA X software. The phylogenetic trees were reconstructed using the Neighbor-Joining approach (Hong et al 2021) and using the Kimura-2-Parameter analytical model with a bootstrap test 1,000 times (Mahadani et al 2022).…”

Section: Discussionmentioning

confidence: 99%

Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit

et al. 2023

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Abstract. Aristya GR, Dyatama GR, Zuyyina C, Maulina NTA, Arif MF, Musthofa A, Kasiamdari RS. 2023. Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit. Biodiversitas 24: 87-97. The difference in the phenotypes characters and gene expressionof strawberries (Fragaria spp.) is influenced by changes in hormone signaling mechanisms to receptors due to the adaptation to various types of environments. Abscisic acid (ABA) is one of the phytohormones that plays a role in the growth and development of strawberries, response to environmental stress, and fruit ripening. One of the ABA receptors is the PYR1 protein which is encoded by FaPYR1 gene. ABA also plays a role in inducing the FaCHS gene associated with pigmentation in strawberry fruit. This study aimed to analyze the relationship between FaPYR1 and FaCHS gene sequences in three strawberry species encoding fruit ripening. The FaPYR1 (585-633 bp) and FaCHS (90-93 bp) genes from three strawberries species namely Fragaria moschata, Fragaria vesca L. 'Californica', and Fragariax ananassa 'Festival' were successfully amplified. The results of the gene family relationship analysis of FaPYR1 gene sequences showed a close relationship with the comparative three species to GenBank, with a genetic distance value of 0.01-0.02. Meanwhile, FaCHS gene sequences from three species of strawberries showed a close relationship with the comparable FaCHS gene sequence from GenBank, with a genetic distance of 0.1-0.2.

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Section: Discussionmentioning

confidence: 99%

Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit

et al. 2023

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“…The BLASTN programme was used to match the sequences of these genes to those that are accessible from GenBank. Distances were determined using Kimura’s two-parameter correction 27 , which was applied to the calculations. The neighbor-joining approach was utilized when it came to the construction of phylogenetic trees 28 .…”

Section: Methodsmentioning

confidence: 99%

Extracellular L-Asparaginase Synthesis Bacillus niacin Isolation, Optimization, and Characterization from Marine Saltern Sediment Sources

Abdul Wahab,

Palaniyandi,

Wyson

et al. 2023

AJMB

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Background: Asparagine is an amino acid that can be converted into aspartic acid and ammonia by the enzyme L-asparaginase. Some forms of cancer, such Acute Lymphoblastic Leukaemia (ALL) and Non-Hodgkin Lymphoma (NHL), respond well to this enzyme when employed as a chemotherapeutic drug. The purpose of this research was to find bacteria that can manufacture the enzymes L-asparaginasein marine slattern sediment which can be employed in commercial and industrial scale production. Methods: All of the strains were identified as Bacillus niacini spp. by biochemical and molecular testing. The strain belongs to the Bacillus genus, according to nutritional, biochemical, PCR and 16srRNA sequencing data. Results: According to the findings of this research, Bacillus niacin spp. have the potential to create a substance that is helpful in a variety of medical applications. The results of this study hint to the possibility that bacteria have the ability to produce antimicrobial compounds, which have the potential to be successful in a wide variety of environments. Conclusion: Numerous opportunities may arise for researchers interested in utilizing the medical potential of enzyme-producing bacteria if they are successfully isolated and screened from aquatic and terrestrial habitats.

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“…The chloroplast genome sequences of 23 species from Salvia genera were compared with the annotated S. bowleyana chloroplast as the reference using the mVISTA program in a Shuffle-LAGAN mode with default parameters (Rank VISTA probability threshold = 0.5) [ 75 , 76 ]. The genetic distances of IGS regions from the chloroplast genomes of 23 Salvia species were calculated using the distmat program from EMBOSS (v6.3.1) [ 77 ] with the Kimura 2-parameters (K2p) evolutionary model [ 78 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration

Yang

Zeng

et al. 2022

IJMS

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To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments.

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Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis

Cited by 27 publications

References 31 publications

Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit

Relationship analysis of FaPYR1 and FaCHS genes encoding fruit ripening of three species of strawberries (Fragaria spp.) fruit

Extracellular L-Asparaginase Synthesis Bacillus niacin Isolation, Optimization, and Characterization from Marine Saltern Sediment Sources

Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration

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