The complete plastid genome of Scopolia parviflora (Dunn.) Nakai (Solanaceae)

Park, Jin Hee; Lee, Jung-Ho

doi:10.11110/kjpt.2016.46.1.60

Cited by 9 publications

(6 citation statements)

References 19 publications

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“… 2016 ), NC030543 (Park et al. 2016 ), KR078312 (Shim et al. 2016 ), NC026570, KP296185, NC029833, KP998157, NC026694, NC026906, KP280057, NC026567.…”

Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome sequence of Solanum iopetalum , one of the tuber-bearing wild potato relatives

Park

2023

Mitochondrial DNA Part B

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Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes ( S. tuberosum ) and is closely related to Mexican Solanum species ( S. stoloniferum , S. verrucosum , S. hougasii , S. hjertingii , and S. demissum ). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.

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“… 2016 ), NC030543 (Park et al. 2016 ), KR078312 (Shim et al. 2016 ), NC026570, KP296185, NC029833, KP998157, NC026694, NC026906, KP280057, NC026567.…”

Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome sequence of Solanum iopetalum , one of the tuber-bearing wild potato relatives

Park

2023

Mitochondrial DNA Part B

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“…The long and small single-copy regions (LSC and SSC) are 86,479 bp and 18,031 bp long, separated by two inverted repeats (IRa and IRb) of 25,903 bp each. The overall GC content is 37.6% (IR, 42.9%; LSC, 35.7%; SSC, 31.9%), resembling other Hyoscyameae species (Gandini et al, 2019;Park & Lee, 2016;Sanchez-Puerta & Abbona, 2014;Zhang & Chi, 2019). The cpDNA presents 115 unique genes, including 80 protein-coding genes or conserved hypothetical chloroplast ORFs, four ribosomal RNAs, and 30 transfer RNAs (Table S1).…”

Section: General Organization Of Scopolia Carniolica Chloroplast Genomementioning

confidence: 99%

“…A study based on the gene "waxy" revealed the hybrid history of the polyploid Atropa belladonna and showed that it is sister to the rest of the tribe (Yuan et al, 2006). Recently, short reports described the complete chloroplast genomes (cpDNAs) of several members of the tribe Hyoscyameae (Jiang et al, 2019;Park & Lee, 2016;Tian et al, 2020;Tong et al, 2019;Zhang et al, 2017;Zhang & Chi, 2019) opening the possibility of a phylogenomic approach to understanding the relationships within the Hyoscyameae. A few of these studies included preliminary trees based on a subset of the taxa available, suggesting that chloroplast genome comparisons promise to resolve relationships among genera of the tribe (Jiang et al, 2019;Tian et al, 2020;Tong et al, 2019;Zhang & Chi, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)

et al. 2021

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Within the family Solanaceae, the tribe Hyoscyameae comprises eight genera distributed across Eurasia. Despite a few attempts to understand the relationships within this tribe, the affiliations among most genera remain unresolved. Recently, complete chloroplast genomes from several species of Hyoscyameae were published, enabling phylogenomic inferences. We sequenced the plastome of Scopolia carniolica, the second species of the genus to be reported. Genomic comparisons across the tribe revealed identical gene content and small differences in genome length. Phylogenetic analyses confirmed that Atropa is an early-diverging lineage sister to the rest of the tribe, resolved as two clades. One includes well-supported relationships between Przewalskia, Physochlaina, and Scopolia, and these three genera are sister to Atropanthe. This clade is sister to a second clade composed of Hyoscyamus and Anisodus. The strongly supported phylogenetic affiliations of Atropanthe, Anisodus, and Hyoscyamus represent the major advancements as previous studies were not able to resolve these relationships. Interestingly, the genus Scopolia is paraphyletic in respect to Physochlaina, based on ITS2 sequences. Finally, the evolution of the mitochondrial cox1 intron is reinterpreted. Two independent horizontal acquisitions are inferred, one in the ancestor of Przewalskia, Physochlaina, and S. japonica and another in Hyoscyamus, with no intron losses.

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“…et al, 2018 ). Unlike the other genomes, the whole chloroplast genome has a self-replication mechanism, relatively independent evolution, slow evolving nature, and unique maternal inheritance ( Park and Lee, 2016 ; Li et al, 2019 ). It is feasible for the reconstruction of plant phylogeny and the construction of taxonomy between families and genera from the perspective of population genetics to investigate deep comparisons of angiosperm, gymnosperm, and fern families ( Huang et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genomes and Comparative Analyses of Three Ornamental Impatiens Species

et al. 2022

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Impatiens L., the largest genus in the family Balsaminaceae with approximately 1,000 species, is a controversial genus. Due to the conflict of morphological features and insufficient genomic resources, the studies of systematic evolution and understanding of taxonomic identification are considered to be very limited. Hence, we have sequenced the complete chloroplast genomes of three ornamental species (Impatiens balsamina, I. hawkeri, and I. walleriana), and compared them with previously published wild species data. We performed a detailed comparison of a highly similar basic structure, size, GC content, gene number, order, and functional array among them. Similarly, most divergent genes were detected from previous work in the literature. The mutational regions containing highly variable nucleotide hotspots were identified and may be used as potential markers for species identification and taxonomy. Furthermore, using whole chloroplast genome data to analysis the phylogenetic relationship of the Balsaminaceae species, we found that they were all part of a single clade. The three phenotypically different ornamental species were clustered together, suggesting that they were very likely to be closely related. We achieved and characterized the plastid genome structure, identified the divergence hotspots, and determined the phylogenetic and taxonomic positions of the three cultivated species in the Impatiens genus. The results may show that the chloroplast genome can be used to solve phylogenetic problems in or between the Impatiens genus and also provide genomic resources for the study of the Balsaminaceae family’s systematics and evolution.

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The complete plastid genome of Scopolia parviflora (Dunn.) Nakai (Solanaceae)

Cited by 9 publications

References 19 publications

Complete chloroplast genome sequence of Solanum iopetalum , one of the tuber-bearing wild potato relatives

Complete chloroplast genome sequence of Solanum iopetalum , one of the tuber-bearing wild potato relatives

Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)

Complete Chloroplast Genomes and Comparative Analyses of Three Ornamental Impatiens Species

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