Study of molecular genetic diversity and evolutionary history of medicinally important endangered genus Chlorophytum using DNA barcodes

Patil, Swapnil M.; Rane, Niraj R.; Adsul, Avinash A.; Gholave, Avinash R.; Yadav, Shrirang R.; Jadhav, Jyoti P.; Govindwar, Sanjay P.

doi:10.1016/j.bse.2016.02.035

Cited by 5 publications

(3 citation statements)

References 33 publications

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“…Earlier studies revealed that sequencing data generated from chloroplast genes could provide sufficient information to delineate plant species and phylogenetic reconstruction of taxa (Bell et al 2016;Patil et al 2016;Bezeng et al 2017;Braukmann et al 2017). Each chloroplast is uniparentally inherited and non-recombinant; simplifying phylogenetic reconstructions (Zhang et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

et al. 2018

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Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.

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Section: Introductionmentioning

confidence: 99%

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

et al. 2018

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“…Despite the fact that the combined dataset of mat K+ rbc L could properly delimit the samples apart, some of the branch nodes were not well-supported (Patil et al. 2016 ). Based on the phylogenetic tree reconstructed using the combined dataset, C. laxum is closely related to C. tuberosum , and is clustered with the other two species, C. bharuchae and C. kolhapurense .…”

Section: Discussionmentioning

confidence: 99%

The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae)

Li,

Cai,

Lee

et al. 2024

Mitochondrial DNA Part B

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Chlorophytum laxum of Asparagaceae is a valuable ornamental plant native to the tropical regions of Asia, Africa, and Australia. The plant also has medicinal properties and is used as source for folk medicine. Despite being commercially important, genetic studies of C. laxum are still limited. To expand the genomic information of this plant species, we sequenced, assembled, and characterized its complete chloroplast genome. The chloroplast genome was 153,678 bp in length, with a large single-copy region (83,225 bp) and a small single-copy region (18,031 bp) separated by a pair of inverted repeat regions (26,211 bp each). A total of 127 genes were predicted, including 81 protein-coding, 38 tRNA, and eight rRNA genes. The overall GC content was 37.3%. Based on current sampling size, phylogenetic analysis using the maximum likelihood based on the complete chloroplast genome sequence revealed that the relationship in Chlorophytum is well resolved; C. laxum was closely related to C. rhizopendulum .

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“…This method is also used to check herbal medicines. As well as using DNA barcodes for phylogenetic analysis and genetic diversity, Patil et al (2016) used eight plastid (matK, rbcL, trnH-psbA, rpoC1, ycf5, rpoB, atp and psbK-psbI) and six nuclear ITS markers to examine the phylogenetic relationships among 19 species of the genus Chlorophytum. Silva et al (2015) studied the phylogenetic relationships among 18 species of Spondias of the family Anacardiaceae using cpDNA barcodes for the trnH-psbA spacer gene.…”

Section: Introductionmentioning

confidence: 99%

Research Article Evaluation of the capacity of the DNA barcode ITS2 for identifying and discriminating dryland plants

Al-Juhani¹

2019

Genet. Mol. Res.

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Many of the plants that grow in arid and semi-arid regions under harsh conditions (drought, salinity and misuse) are of medical importance. Desert plants also provide other benefits; so conservation efforts should be strengthened in these areas. In this study, three DNA barcodes-chloroplast maturase-K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and secondary internal transcribed spacer (ITS2)-were tested in order to determine the ability of these markers to distinguish between various species. A total of 93 fresh and dry samples belonging to 30 plant families were examined. These are native to the arid lands around Makkah in the Kingdom of Saudi Arabia. Various tools and tests were used to evaluate the efficiency of the barcode markers; these included the basic local alignment search tool (BLAST), as well as the use of inter-and intraspecific distances, barcode gap, prediction of the secondary structure of the ITS2 and phylogenetic methods. The results confirmed the efficiency and superiority of the ITS2 loci over two chloroplast genes: matK and rbcL. ITS2 had a 97% success rate with amplification and a 95% success rate with sequencing, showing 100% identification at the family level, 77% identification at the genus level and 70% species resolution. A clear barcode gap was observed between inter-and intraspecific distances. Identification was achieved even in cases of degraded samples or old herbarium ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (1): gmr18133 W.S. Al-Juhani 2 specimens. This study contributes to DNA barcode data by adding 224 DNA sequences of desert plants to the National Center for Biotechnology Information NCBI database. The results of this study are important and useful for application in each of the following fields: validation of medicinal plant identity, conservation, and taxonomic and evolutionary studies.

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Study of molecular genetic diversity and evolutionary history of medicinally important endangered genus Chlorophytum using DNA barcodes

Cited by 5 publications

References 33 publications

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae)

Research Article Evaluation of the capacity of the DNA barcode ITS2 for identifying and discriminating dryland plants

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