The complete chloroplast genome of <i>Torreya nucifera</i> (Taxaceae) and phylogenetic analysis

Shin, Soo-Kyung; Kim, Sang-Chul; Hong, Kyung-Nak; Kang, Hyesoon; Lee, Jei-Wan

doi:10.1080/23802359.2019.1640091

Cited by 10 publications

(5 citation statements)

References 8 publications

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“…However, this typical structure is altered in some plant lineages. For instance, in Cupressaceae [4] and Taxaceae [5], one IR has been lost. In Pinaceae, the IR length is reduced to below 1 kb [6,7].…”

Section: Introductionmentioning

confidence: 99%

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Kim

Lee

Choi

2021

Forests

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In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.

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Section: Introductionmentioning

confidence: 99%

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Kim

Lee

Choi

2021

Forests

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“…In addition, we found that some ndh genes (such as ndhD and ndhH ) may have been lost randomly regardless of genome rearrangement ( Fig 9 ). The loss and pseudogenization of ndh genes are known to occur frequently in heterotrophic plants, but have also been consistently identified in gymnosperms, such as conifers [ 10 , 13 ] and Gnetales [ 71 ], and angiosperms such as Circaeasteraceae [ 72 ] and Orchidaceae [ 70 ]. Further studies are needed to assess whether the ndh genes in Corydalis spp.…”

Section: Discussionmentioning

confidence: 99%

“…Major genomic structural changes-such as gene loss, large inversions, and contraction or expansion of the IR region-are frequently reported in the plastid genomes of certain plant lineages. For example, certain conifers [9,10] and some Fabaceae plants [11] have lost one IR region. Some Pinaceae species have been shown to possess smaller IRs with a size of less than 1 kb [12,13], and some Ericaceae species exhibit a greatly reduced SSC region [14][15][16][17] due to IR extension.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome

Kim,

Ha,

Park

et al. 2023

PLoS ONE

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Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

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“…The genomic content of chloroplasts is rich with valuable information, making them ideal models for research, particularly in the fields of molecular markers, barcoding identification, plant phylogenetics, evolution, and comparative genomic studies [17][18][19][20]. The chloroplast genome is recognized for its greater conservation compared to nuclear or mitochondrial genomes in terms of genetic structure, gene content, and nucleotide sequence.…”

Section: Introductionmentioning

confidence: 99%

Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)

Zhan,

Huang,

Xue

et al. 2024

BMC Genom Data

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Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.

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The complete chloroplast genome of Torreya nucifera (Taxaceae) and phylogenetic analysis

Cited by 10 publications

References 8 publications

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome

Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)

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