scholarly journals Authentication and identification markers for medicinal plants: I Aristolochia bracteolata

2021 ◽  
Vol 8 (1) ◽  
pp. 7
Author(s):  
Dharam B. Khandhar ◽  
Pritesh P. Bhatt ◽  
Vrinda S. Thaker
Keyword(s):  
Medicinal Plants ◽  
Phylogenetic Relationships ◽  
Maximum Likelihood Method ◽  
Likelihood Method ◽  
Plant Family ◽  
Protein Coding ◽  
Aristolochic Acids ◽  
Chloroplast Genomes ◽  
Unique Markers ◽  
Aristolochia Bracteolata

<p class="abstract"><strong>Background:</strong> Aristolochiaceae is a unique plant family that contains aristolochic acids (AAs), with around 600 species.</p><p class="abstract"><strong>Methods:</strong> The entire chloroplast genome of <em>Aristolochia bracteolata</em> was sequenced in this work, and fourteen chloroplast (cp) genomes were retrieved from the NCBI database.  </p><p class="abstract"><strong>Results:</strong> We also analyzed six types of microsatellite markers among these species and found some different markers for each species. A molecular phylogeny based on 7 barcode regions i.e. <em>matK,</em> <em>atpF</em> to <em>atpH</em>, <em>psbK</em> to <em>psbI</em>, <em>rbcL, rpoB, rpoC2</em> and <em>rpoC1</em> is proposed for <em>Aristolochia </em>and 16 species from Piperales, <em>Arabidopsis thaliana</em> is taken as an outgroup. Phylogenetic relationships using concatenated protein-coding genes from Chloroplast genomes of Piperales using the maximum likelihood method is also discussed.</p><p class="abstract"><strong>Conclusions:</strong> In the present study we are providing some unique markers<strong> </strong>and phylogenetic relationships among Piperales members which will help in identification, authentication, to prevent adulteration and further investigation of these medicinal plants.</p>

scholarly journals Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bobby Lim-Ho Kong ◽  
Hyun-Seung Park ◽  
Tai-Wai David Lau ◽  
Zhixiu Lin ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Comparative Analysis ◽  
Phylogenetic Relationships ◽  
Species Level ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Plant Group ◽  
Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

scholarly journals The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 456 ◽  
Author(s):  
Cornelius M. Kyalo ◽  
Zhi-Zhong Li ◽  
Elijah M. Mkala ◽  
Itambo Malombe ◽  
Guang-Wan Hu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Structural Features ◽  
Base Pairs ◽  
Protein Coding ◽  
Variable Regions ◽  
Morphological Heterogeneity ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Phylogenomic Analyses

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Occurrence of gilled fungi in Puducherry, India

2021 ◽  
Vol 13 (7) ◽  
pp. 18878-18887
Author(s):  
Vadivelu Kumaresan ◽  
Chakravarthy Sariha ◽  
Thokur Sreepathy Murali ◽  
Gunasekaran Senthilarasu
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Maximum Likelihood Method ◽  
Schizophyllum Commune ◽  
Abundant Species ◽  
Southern India ◽  
Likelihood Method

Thirty-three species of gilled fungi belonging to 23 genera and 14 families were recorded from Puducherry, southern India. Agaricaceae were represented by eight species, followed by Psathyrellaceae (5), Lyophyllaceae & Marasmiaceae (3 each), Hymenogastraceae, Pleurotaceae, Pluteaceae, & Polyporaceae (2 each), and Biannulariaceae, Bolbitiaceae, Omphalotaceae, Schizophyllaceae, Strophariaceae, & Tricholomataceae (1 each). Fourteen species of agarics are new reports from Puducherry. Chlorophyllum rhacodes, Lactocollybia epia, Leucoagaricus meleagris, and Schizophyllum commune were widely distributed. Phylogenetic relationships of the abundant species C. rhacodes, L. epia, and L. meleagris were inferred by maximum likelihood method.

scholarly journals Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species

2019 ◽  
Vol 20 (5) ◽  
pp. 1045 ◽  
Author(s):  
Xiaoqin Li ◽  
Yunjuan Zuo ◽  
Xinxin Zhu ◽  
Shuai Liao ◽  
Jinshuang Ma
Keyword(s):  
Genomic Structure ◽  
Gc Content ◽  
Medicinal Species ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Aristolochic Acids ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome ◽  
Genome Arrangement

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.

scholarly journals Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus

2021 ◽  
Vol 11 ◽  
Author(s):  
Kaihui Zhao ◽  
Lianqiang Li ◽  
Hong Quan ◽  
Junbo Yang ◽  
Zhirong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Evolutionary Analysis ◽  
Classification Problems ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Mutational Hotspots

Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.

A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa

Paleobiology ◽  
1998 ◽  
Vol 24 (4) ◽  
pp. 430-449 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Maximum Likelihood Method ◽  
Character Evolution ◽  
Likelihood Method ◽  
Data Sets ◽  
Data Set ◽  
Parsimony Tree ◽  
Tree Length

Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, L[hypothesized length | parsimony length] can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.

scholarly journals Characteristic and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Medicinal Plants of Schisandraceae

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Dachuan Zhang ◽  
Jiahao Wang ◽  
Liang Xu ◽  
Yanping Xing ◽  
Tingting Zhang ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
Phylogenetic Trees ◽  
Genome Comparison ◽  
Protein Coding ◽  
Useful Knowledge ◽  
Ssr Analysis ◽  
Traditional Medicinal Plants ◽  
Chloroplast Genomes ◽  
Genome Wide ◽  
Chloroplast Dnas

Schisandra chinensis, which has a high development value, has long been used as medicine. Its mature fruits (called Wuweizi in Chinese) have long been used in the famous traditional Chinese medicine (TCM) recorded in the “Chinese Pharmacopoeia.” Chloroplasts (CP) are the highly conserved primitive organelles in plants, which can serve as the foundation for plant classification and identification. This study introduced the structures of the CP genomes of three Schisandraceae species and analyzed their phylogenetic relationships. Comparative analyses on the three complete chloroplast genomes can provide us with useful knowledge to identify the three plants. In this study, approximately 5 g fresh leaves were harvested for chloroplast DNA isolation according to the improved extraction method. A total of three chloroplast DNAs were extracted. Afterwards, the chloroplast genomes were reconstructed using denovo combined with reference-guided assemblies. General characteristics of the chloroplast genome and genome comparison with three Schisandraceae species was analyzed by corresponding software. The total sizes of complete chloroplast genomes of S. chinensis, S. sphenanthera, and Kadsura coccinea were 146875 bp, 146842 bp, and 145399 bp, respectively. Altogether, 124 genes were annotated, including 82 protein-coding genes, 34 tRNAs, and 8 rRNAs of all 3 species. In SSR analysis, only S. chinensis was annotated to hexanucleotides. Moreover, comparative analysis of chloroplast Schisandraceae genome sequences revealed that the gene order and gene content were slightly different among Schisandraceae species. Finally, phylogenetic trees were reconstructed, based on the genome-wide SNPs of 38 species. The method can be used to identify and differentially analyze Schisandraceae plants and offer useful information for phylogenetics as well as further studies on traditional medicinal plants.

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