Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

Shen, Xiaofeng; Guo, Shuai; Yao, Yin; Zhang, Jingjing; Yin, Xiao; Liang, Conglian; Wang, Zhangwei; Huang, Bolin; Liu, Yanhong; Xiao, Shaobo; Zhu, Guangwei

doi:10.3390/molecules23102426

Cited by 47 publications

(44 citation statements)

References 63 publications

(65 reference statements)

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“…We also detected variation in the number and distribution of two types of repeats, SSRs and LDRs, in both non-coding (IGS and intron) and coding regions. The occurrence of repeats was more prevalent in the non-coding regions than in the coding regions, similar to reports in other species (Kim et al 2015b;Meng et al 2019;Shen et al 2018). Differential distribution of these repeats is associated with cp genome rearrangement and nucleotide substitution (Weng et al 2014).…”

Section: Discussionsupporting

confidence: 84%

Peer Review #2 of "A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains (v0.1)"

2020

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Background. Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental, and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods. The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results. The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531), and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes, and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order, and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

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Section: Discussionsupporting

confidence: 84%

Peer Review #2 of "A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains (v0.1)"

2020

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“…The overall cp genome structures and sequences in the three C. boreale strains examined here were conserved and displayed the classical quadripartite structure of land plant cp genomes ( Shen et al, 2018 ). The gene content, gene order and gene orientation in the cp genomes were conserved.…”

Section: Discussionmentioning

confidence: 91%

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

Jung

Kim

Won

2020

PeerJ

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Background Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

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“…Intron-containing genes were also analysis in this article. In total, there are 17 genes which contains one or two introns found in the CP genomes of L. chinense (Table 3), including 12 CDS and 5 tRNA genes, as listed in the table, while two of them, ycf3 and clpP, contain two intron and a single intron was detected in the other 15 genes, which has also been reported in other plants (Guo et al 2017, Shen et al 2018 .…”

Section: Cp Genome Organization and Gene Contentsupporting

confidence: 59%

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Supplemental Information 1: Codon Usage of L. Chinense Chloroplast Genome

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Lycium chinense Mill, an important Chinese herbal medicine, is emphasized as a healthy food and is widely used as a dietary supplement. Here we sequenced and analyzed the complete chloroplast (CP) genome of the L. chinense, which is 155,756 bp in length and with 37.8% GC content. This CP genome consists of a pair of inverted repeat regions (IRa and IRb) of 25,476 bp, separated by a large single-copy region (LSC) and a small singlecopy region (SSC), with length of 86,595 and 18,209 bp, respectively. Annotation results revealed that the L. chinense CP genome contains 114 genes, 16 of which are duplicated genes. Most of the 85 protein-coding genes have a usual ATG start codon, except for 3 genes including rps12, psbL and ndhD. Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to the high AT content of the chloroplast genome. Revealing of the complete sequences and annotation of the L. chinense chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

Cited by 47 publications

References 63 publications

Peer Review #2 of "A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains (v0.1)"

Peer Review #2 of "A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains (v0.1)"

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

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