The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae

He, Xiangyu; Dong, Shiqi; Gao, Chenshu; Wang, Qirui; Zhou, Manjia; Cheng, Rubin

doi:10.1007/s11756-022-01038-2

Cited by 5 publications

(4 citation statements)

References 67 publications

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“…The species of C. lipskyi is clustered with other species of Inuleae to form a highly supported clade (BS = 100%), which is consistent with previous results (He et al. 2022 ; Shi, Hou, et al. 2022 ; Shi, Xu, et al.…”

Section: Discussionsupporting

confidence: 91%

Characterization and phylogenetic analysis of the complete chloroplast genome of Carpesium lipskyi (Asteraceae, Inuleae)

Li,

Chen,

Chen

et al. 2024

Mitochondrial DNA Part B

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The species of Carpesium lipskyi C.Winkl. 1998 is an important traditional Chinese medicine in China. In this study, the complete chloroplast (cp) genome of C. lipskyi was determined and analyzed. The result showed that the complete cp genome of C. lipskyi was 151,244 bp in length, consisting of a large single-copy (LSC) region of 82,908 bp, a small single-copy (SSC) region of 18,430 bp, and a pair of inverted repeats (IRs) of 24,953 bp. The overall GC content of the C. lipskyi is 37.68%. The species of C. lipskyi possessed 127 genes, including 83 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. The present study found that Inula is sister groups with the closest genetic relationship. The obtained knowledge could provide useful information for future phylogenetic, taxonomic, and evolutionary studies on Inuleae.

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Section: Discussionsupporting

confidence: 91%

Characterization and phylogenetic analysis of the complete chloroplast genome of Carpesium lipskyi (Asteraceae, Inuleae)

Li,

Chen,

Chen

et al. 2024

Mitochondrial DNA Part B

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“…The codons encoding all amino acids, except for Met and Trp, showed a strong bias for A or U in the third codon positions. It was in agreement with Cicer echinospermum 31 and Carpesium abrotanoides 32 , but not with Glechoma longituba 33 and Aconitum coreanum 34 . The difference might be related to the different number of tRNAs in different species, and the use of codons with high abundance of paired tRNAs could guarantee efficient protein expression.…”

Section: Discussionmentioning

confidence: 64%

Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots

Tian,

Liu,

et al. 2023

Sci Rep

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Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people’s republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.

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“…Angiosperm cp genomes are known for their structural and sequence conservation 12 . The cp genome has a distinctive quadripartite structure consisting of a large single-copy (LSC) region and small single-copy (SSC) regions separated by a pair of long inverted repeat (IRa and IRb) regions 10 , 13 . Although the cp genome is conserved, recent studies have identified many genetic mutations in the cp genome, such as loss of gene or intron fragments, insertion and deletion of bases, changes in the length of reverse repeat regions, insertion/deletion of partial fragments, expansion or deletion of entire reverse repeat regions, and gene rearrangement 14 – 17 , which may lead to variations in plant structure and adaptation and contribute to plant species identification and future selective breeding 18 .…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla

Qin,

Ma,

Liu

et al. 2024

Sci Rep

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Clematis nannophylla is a perennial shrub of Clematis with ecological, ornamental, and medicinal value, distributed in the arid and semi-arid areas of northwest China. This study successfully determined the chloroplast (cp) genome of C. nannophylla, reconstructing a phylogenetic tree of Clematis. This cp genome is 159,801 bp in length and has a typical tetrad structure, including a large single-copy, a small single-copy, and a pair of reverse repeats (IRa and IRb). It contains 133 unique genes, including 89 protein-coding, 36 tRNA, and 8 rRNA genes. Additionally, 66 simple repeat sequences, 50 dispersed repeats, and 24 tandem repeats were found; many of the dispersed and tandem repeats were between 20–30 bp and 10–20 bp, respectively, and the abundant repeats were located in the large single copy region. The cp genome was relatively conserved, especially in the IR region, where no inversion or rearrangement was observed, further revealing that the coding regions were more conserved than the noncoding regions. Phylogenetic analysis showed that C. nannophylla is more closely related to C. fruticosa and C. songorica. Our analysis provides reference data for molecular marker development, phylogenetic analysis, population studies, and cp genome processes to better utilise C. nannophylla.

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The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae

Cited by 5 publications

References 67 publications

Characterization and phylogenetic analysis of the complete chloroplast genome of Carpesium lipskyi (Asteraceae, Inuleae)

Characterization and phylogenetic analysis of the complete chloroplast genome of Carpesium lipskyi (Asteraceae, Inuleae)

Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots

Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla

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