A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants

Guo, Shuai; Liao, Xuejiao; Chen, Shiyu; Liao, Baosheng; Guo, Yiming; Cheng, Ruiyang; Xiao, Shaobo; Hu, Haoyu; Pei, Jin; Chen, Yangjin; Xu, Jiang; Chen, Shilin

doi:10.3389/fgene.2022.764534

Cited by 21 publications

(28 citation statements)

References 77 publications

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“…The IR areas contained four rRNA genes with high GC content, which supported the hypothesis of previous research [ 46 , 47 , 48 , 49 ]. A previous study found that the GC content was substantially higher, most likely due to the abundance of rRNA in the IR regions [ 50 ]. However, the exact specifics are still unknown.…”

Section: Discussionmentioning

confidence: 99%

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Chen

Zhang

Liang

et al. 2022

IJMS

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Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.

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Section: Discussionmentioning

confidence: 99%

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Chen

Zhang

Liang

et al. 2022

IJMS

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“… 2020 ), Castanopsis echinocarpa NC_023801.1 (Guo et al. 2022 ), Castanopsis tibetana ON710842 (Sanchez-Puerta and Abbona 2014 ), Castanopsis eyrei ON550006, Castanopsis chinensis ON500675, Castanopsis fordii ON710841 (Li et al. 2022 ), Lithocarpus balansae KP299291.1 (Shi et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

Wang

Huang

et al. 2023

Mitochondrial DNA Part B

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Castanopsis fordii Hance 1884 is a typical evergreen broad-leaved forest plant in the south subtropical and middle subtropical regions of China. It has high utilization value in wood production and soil erosion protection. Here, we first reported and characterized the complete chloroplast (cp) genome sequence of C. fordii based on Illumina paired-end sequencing data. The complete cp genome sequence of C. fordii was 160,853 base pairs (bp) in length which contained two inverted repeats (IRs) of 25,699 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 90,474 bp and 18,981 bp, respectively. The cpDNA contained 129 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes. The overall GC content of the plastome was 36.8%. Phylogenetic analysis base on 14 chloroplast genomes indicated that C. fordii was closely related to the species C. tibetana and C. concinna in Fagaceae.

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“…Introns regulate the expression of some genes and play an important role in alternative splicing [19,31].…”

Section: Discussionmentioning

confidence: 99%

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

Feng

Zhao

An³

et al. 2023

Preprint

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Background Prunus Cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. Cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast (cp) genome of P. Cistena and compared it with related species of Prunus genus based on chloroplast genome.Results The complete chloroplast genome of P. Cistena was 157,935 bp in length, which had a typical tetrad structure. The overall GC content was 36.72%, while IR regions displayed a higher GC content than LSC and SSC regions. It encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes had two introns; the longest intron was trnK-UUU gene in the LSC region. There were 253 SSRs, and the mononucleotide SSRs were the most abundant. The chloroplast sequences and gene arrangements of P. Cistena were conserved, which overall structure and gene order were similar to other Prunus species. The atpE, ccsA, petA, rps8 and matK gene had significant positive selection in Prunus species. P. Cistena had a close evolutionary relationship with the P. jamasakura. The coding region and IR region were more conserved than noncoding region, and the cpDNA sequences highly conserved throughout the genus Prunus.Conclusions The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of genus Prunus.

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A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants

Cited by 21 publications

References 77 publications

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

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