DNA barcoding and molecular systematics of selected species of family Acanthaceae

Khan, Ibrahim; Shinwari, Zabta Khan; Zahra, Nida; Jan, Sohail Ahmad; Shinwari, Shehla; Najeebullah, Syed

doi:10.30848/pjb2020-1(27)

Cited by 10 publications

(14 citation statements)

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“…The selection pressure of protein-coding genes (PCGs) was analyzed using the aBSREL (adaptive branch-site random effects likelihood) model implemented in the Hyphy software (Smith et al 2015 ). We used ecoPrimers software to identify potential DNA barcoding markers to distinguish the four Justicia species (Riaz et al 2011 ; Khan et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)

Zhou

Jiang

et al. 2021

Mitochondrial DNA Part B

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Justicia ventricosa is a characteristic ethnic herb commonly used to treat Orthopedic pains. Here, to confirm its phylogenetic position and to develop molecular markers that can distinguish different Justicia species, we obtained and analyzed the plastome of Justicia ventricosa. The plastome was sequenced using the Illumina HiSeq sequencing platform, assembled with NOVOPlasty, and annotated with CPGAVAS2. The genome has a circular structure of 149,700 bp, containing a large single-copy region of 82,324 bp, a small single-copy region of 17,260 bp, and two reverse repeat regions of 25,058 bp each. It encodes 112 unique genes, including 76 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. Twenty cis-splicing genes were found. In total, we predicted 19 microsatellite repeats and 13 tandem repeat sequences. For distributed repeats, four were palindrome repeats and five were direct repeats. To find the highly variable intergenic spacer (IGS) regions, we calculated the K2P distances for IGS regions from four Justicia species. The K2P values ranged from 6.11 to 57.82. The largest K2P distances were found for ccs A -ndh D, pet B -pet D, psb K -psb I, and ycf 4 -cem A. Phylogenetic analysis results showed that J. ventricosa was most closely related to J. leptostachya . To determine how Justicia species adapt to the environment, we performed selection pressure analysis. Nine genes were found to have undergone positive selection. Lastly, we performed a genome-wise DNA barcode prediction, seven pairs of primers were found. The results provide valuable information that can be used for molecular marker development and bioprospecting in Justicia species.

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Section: Methodsmentioning

confidence: 99%

Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)

Zhou

Jiang

et al. 2021

Mitochondrial DNA Part B

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“…Intraspecific genetic variation of West Asian leopards was analyzed using the mitochondrial gene, NADH dehydrogenase subunit 5 (NADH-5), which exhibits a relatively high rate of mutation in leopards (19). Mitochondrial markers have been employed to identify leopard coalescence and lineage sorting processes (1,12,18,20). The MtDNA has been used to address questions of genetic diversity, phylogeography, and population evolution within Asian leopards, especially the Sri Lankan leopard (21)(22)(23)(24).…”

Section: Introductionmentioning

confidence: 99%

A unique single nucleotide polymorphism in Agouti Signalling Protein (ASIP) gene changes coat colour of Sri Lankan Leopard (Panthera pardus kotiya) to dark black

Bandaranayake

Sooriyabandara²,

Bandaranayake

et al. 2022

Preprint

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The Sri Lankan Leopard ( Panthera pardus kotiya ) is an endangered subspecies restricted to isolated and fragmented populations in Sri Lanka. Among them, the melanistic leopards have been recorded on rare occasions. The existing literature suggests that melanism evolved several times in the Felidae family, with three separate species revealing distinct mutations. Nevertheless, the mutations in the remaining species, including Sri Lankan black leopard, are unknown. We used reference-based assembled the nuclear genomes of Sri Lankan normal and black leopard and de novo assembled mitogenomes of the same to investigate the genetic basis, adaptive significance, and evolutionary history of the Sri Lankan black leopard. Our data suggested coalescence time of Sri Lankan regular and black leopards at ~0.5 Million years, sisters to Panthera pardus lineage. Interestingly, in the black leopard, a single nucleotide polymorphism in exon-4 possibly completely ablates Agouti Signaling Protein (ASIP) function. Existing genomic data suggest new a species-specific mutation of the ASIP gene in the Felidae family, contributing to naturally occurring colouration polymorphism. As such, the Sri Lankan black leopard and normal leopard probably evolved from the same ancestor, while the mutation in the ASIP gene resulted in black coat colour. This rare mutation could be adaptable to the environment that back leopards reported, camouflage, with a likelihood of recurrence and transmission to future generations. However, protecting this sensitive environment is critical for the conservation of the existing populations and providing breeding grounds.

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“…Various intra familial categorizations have been proposed for the Acanthaceae, but no taxonomic accord has yet been obtained (Scotland et al 1995). To limit these complexities and shortcomings of morphological identifications, molecular characterizations which is cost effective and sustainable can be used by molecular biologists to identify and classify such complex families (Channa et al 2018, Ayaz et al 2020, Khan et al 2020. Recent research on the morphological variation and evolution of Acanthaceae provides a phylogenetic framework for understanding and identifying the taxonomic characters (including micro-morphological structures) contained by the family (McDade et al 2008, Morais et al 2019, Khan et al 2020.…”

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confidence: 99%

“…Molecular studies provide a new insight to plant taxonomy and systematics botany (Asghar et al 2022. Researchers recommended the requirements of molecular studies to trace the phylogenetic assembling and lineages among the members of Acanthaceae (Scotland et al 1995, McDade and Moody 1999, Khan et al 2020. Assembling and analyzing of molecular markers facilitated the botanists to move toward inclusion of Avicenniaceae in family Acanthaceae (Schwarzbach and McDade 2002).…”

mentioning

confidence: 99%

“…Assembling and analyzing of molecular markers facilitated the botanists to move toward inclusion of Avicenniaceae in family Acanthaceae (Schwarzbach and McDade 2002). Some previous studies reported higher level systematics of Acanthaceae by using different genetic markers such as rbcL, ndhF, trnL-trnF and trnL-trnF separately and combined with ITS, respectively (Hedrén et al 1995, Scotland et al 1995, McDade and Moody 1999, McDade et al 2000, Khan et al 2020). In addition, several genetic regions and combination of genetic regions have been tested by experts of Acanthaceae for classification, however no taxonomic agreement has yet been achieved.…”

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confidence: 99%

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Diversity, Phylogeny and 3-D Protein Modeling of Family Acanthaceae Based on Rps14 Gene Sequence in Pakistan

2023

THE JAPS

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The Acanthaceae is an important family of plants and it is also known as acanthus family, comprised of 250 genera and 4000 species spread globally in subtropical and tropical areas. From various geographical areas of Pakistan twelve species of Acanthaceae were collected to study its phylogeny utilizing ribosomal protein subunit 14 (rps14) gene. CTAB method was followed for the extraction of DNA from the leaves of collected plant samples. Primer was designed by using an online software primer3 (version 4.0). The sequence analysis was done using molecular evolutionary genetic analysis (MEGA 7), Iterative Threading Assembly Refinement (I-TASSER) and The Structure Analysis and Verification Server (SAVES). Our results showed two main clades of all twelve species revealing low genetic diversity (0.01) based on well supported bootstrap (BS) values. Furthermore, the pairwise distances ranged from 0.027 to 0.130 with mean value 0.078 was observed. To determine the 3-D protein structure and function of rps14 amino acid sequences, stereochemical analysis was performed using Ramachandran plots and I-TASSER. 3-D protein modeling depicted that rps14 protein from ten species out of twelve have the best quality structure with ≤ 2.0 % residues in disallowed region. Both phylogenetic analysis (amino acid and nucleotide sequences) revealed monophyletic origin of all species. Based on these results future studies should focus on physiological, taxonomical and molecular characters of family Acanthaceae species to determine lineages of all taxa within this diverse family.

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DNA barcoding and molecular systematics of selected species of family Acanthaceae

Cited by 10 publications

References 0 publications

Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)

Characterization and comparative analysis of the plastome sequence from Justicia ventricosa (Lamiales: Acanthaceae)

A unique single nucleotide polymorphism in Agouti Signalling Protein (ASIP) gene changes coat colour of Sri Lankan Leopard (Panthera pardus kotiya) to dark black

Diversity, Phylogeny and 3-D Protein Modeling of Family Acanthaceae Based on Rps14 Gene Sequence in Pakistan

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