Characterization of the Complete Chloroplast Genomes of Sequences of Two Diploid Species: Paeonia lactiflora ‘Da Fugui’ and Paeonia ostii ‘Fengdan’ in the Paeoniaceae Family

Sun, Jing; Chen, Ming; Yujiang,; Zhao, Daqiu; Tao, Jun

doi:10.4172/2376-0354.1000247

Cited by 2 publications

(2 citation statements)

References 18 publications

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“…The ratio of Ts and Tv in the plastid genomes ranged from 1.09 to 1.2 in the LSC and between 0 and 1 in the SSC, while varying from 1 to 5 in the IR region (Table S3). In general, the Ts were more frequent in Withania, in line with observations in other plant species [59,60]. InDels were also examined, using DnaSP in all regions of the plastid genome.…”

Section: Divergence Hotspots In Withaniasupporting

confidence: 75%

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Mehmood¹,

Abdullah²,

Ubaid³

et al. 2020

Preprint

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Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled, complete, plastomed genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,198 base pairs (bp) to 154,361 bp and contained a pair of inverted repeats (IRa and IRb) of 25,027--25,071 bp that were separated by a large single-copy (LSC) region of 85,675--85,760 bp and a small single-copy (SSC) region of 18,457--18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastid genomes, which revealed close resemblance among the species. Both the substitution and insertion and deletion analyses confirmed that the IR region was significantly conserved compared with the LSC and SSC regions. Further comparative analysis among the Withania species highlighted 30 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification.

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Section: Divergence Hotspots In Withaniasupporting

confidence: 75%

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Mehmood¹,

Abdullah²,

Ubaid³

et al. 2020

Preprint

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“…The IRs contained only a few indels (Table 4). This may have been due to the observation that IR sequences evolve under concerted evolution compared to LSC and SSC regions that contain more substitutions [63]. When all positions with single-or multinucleotide variations as SNPs were considered, 207 SNPs were identified, which corresponds to a mean SNP frequency of 0.2070 SNPs/kb in Withania species.…”

Section: Divergence Hotspots In Withaniamentioning

confidence: 99%

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Mehmood

Abdullah

Ubaid

et al. 2020

Plants

View full text Add to dashboard Cite

Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635–85,765 bp and a small single-copy (SSC) region of 18,457–18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.

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Characterization of the Complete Chloroplast Genomes of Sequences of Two Diploid Species: Paeonia lactiflora ‘Da Fugui’ and Paeonia ostii ‘Fengdan’ in the Paeoniaceae Family

Cited by 2 publications

References 18 publications

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

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