Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

Recent advances in molecular phylogenetics provide us with information of Allium L. taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A. cyathophorum var. farreri was sister to A. spicatum with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽

10.3390/plants9010061 ◽

2020 ◽

Vol 9 (1) ◽

pp. 61 ◽

Cited By ~ 5

Author(s):

Huyen-Trang Vu ◽

Ngan Tran ◽

Thanh-Diem Nguyen ◽

Quoc-Luan Vu ◽

My-Huyen Bui ◽

...

Keyword(s):

Chloroplast Genome ◽

Inverted Repeat ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Complete Chloroplast Genome ◽

Critically Endangered Species ◽

Plastid Genomes ◽

Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

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Complete chloroplast genome sequences of Schisandra chinensis: genome structure, comparative analysis, and phylogenetic relationship of basal angiosperms

Science China Life Sciences ◽

10.1007/s11427-017-9098-5 ◽

2017 ◽

Vol 60 (11) ◽

pp. 1286-1290 ◽

Cited By ~ 9

Author(s):

Haojie Guo ◽

Jiushi Liu ◽

Li Luo ◽

Xueping Wei ◽

Jin Zhang ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationship ◽

Genome Structure ◽

Schisandra Chinensis ◽

Genome Sequences ◽

Basal Angiosperms ◽

Complete Chloroplast Genome ◽

Relationship Of

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The complete chloroplast genome of Tetradoxa omeiensis (Adoxaceae) provides insights into the phylogenetic relationship of Adoxaceae

Mitochondrial DNA Part B ◽

10.1080/23802359.2018.1493363 ◽

2018 ◽

Vol 3 (2) ◽

pp. 1149-1151

Author(s):

Yaling Wang ◽

Xiaoyue Yang ◽

Zefu Wang ◽

Hong Chen ◽

Guohua Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationship ◽

Complete Chloroplast Genome ◽

Relationship Of

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The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

BMC Genomics ◽

10.1186/s12864-021-07484-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Feng Wen ◽

Xiaozhu Wu ◽

Tongjian Li ◽

Mingliang Jia ◽

Xinsheng Liu ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Dna Sequences ◽

Dna Barcode ◽

Species Discrimination ◽

Evolutionary Analysis ◽

Variable Regions ◽

Triterpenoid Saponins ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes

Abstract Background Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. Results A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. Conclusions This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

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Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

PeerJ ◽

10.7717/peerj.7480 ◽

2019 ◽

Vol 7 ◽

pp. e7480 ◽

Cited By ~ 5

Author(s):

Qi Chen ◽

Xiaobo Wu ◽

Dequan Zhang

Keyword(s):

Chloroplast Genome ◽

Related Species ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Gc Content ◽

Closely Related Species ◽

Complete Chloroplast Genome ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Fritillaria Cirrhosa

Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.

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Characterization and phylogenetic relationship of the complete chloroplast genome of Stemona japonica as an herb to treat bone tuberculosis at China

Mitochondrial DNA Part B ◽

10.1080/23802359.2020.1735971 ◽

2020 ◽

Vol 5 (2) ◽

pp. 1395-1396

Author(s):

Ruikai Wu ◽

Yanjun Wang

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationship ◽

Complete Chloroplast Genome ◽

Bone Tuberculosis ◽

Relationship Of

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The Complete Chloroplast Genome Sequence of Clerodendranthus Spicatus, A Medicinal Plant For Preventing And Treating Kidney Diseases From Lamiaceae Family

10.21203/rs.3.rs-497985/v1 ◽

2021 ◽

Author(s):

Qing Du ◽

Mei Jiang ◽

Sihui Sun ◽

Liqiang Wang ◽

Shengyu Liu ◽

...

Keyword(s):

Chloroplast Genome ◽

Tandem Repeats ◽

Kidney Diseases ◽

Gc Content ◽

Intergenic Spacer ◽

Tectona Grandis ◽

Single Copy ◽

Complete Chloroplast Genome ◽

Distance Analysis ◽

Cistanche Deserticola

Abstract Clerodendranthus spicatus (Thunb.) C.Y.Wu is one of the most important medicine for the treatment of nephrology which distributes in south-east of China. In this study, we obtained the complete chloroplast genome of C. spicatus with a length of 152155bp, including a large single copy (LSC) region of 83098bp, small single copy (SSC) region of 17665bp and a pair of inverted repeat (IR) regions of 25696bp with the GC content of 37.86%. The genome contains 36 tRNA, 8 rRNA and 87 protein-coding genes. Most of them have one intron except the ycf3, rps12 and clpP genes. The length of rRNAs varies from 131bp to 2811bp and the GC contents are between 45.28% and 56.54%. The frequency of Isoleucine is fruitful accounting for 4.17%. The codons of AUG, UUA and AGA codon had presence of higher codon usage bias. For the repetitive sequence analysis, Thirty-six tandem repeats were identified with certain conditions. Forty interspersed repeats were identified, including 22 palindromic repeats and 18 direct repeats. The diverse positions of the specific rps19, ycf1, rpl2, trnH, psbA genes within the IR boundary analysis. The genetic distance analysis of the intergenic spacer regions for 5 relative species showed the areas of ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD had high K2p value to distinguish the species through developing the molecular markers. From phylogenetic tree, C. spicatu was closely related to the genus of two Salvia speices, Tectona grandis, Cistanche deserticola and Glechoma longituba belonged to the Lamiales.

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Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

BioMed Research International ◽

10.1155/2020/4374801 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Junjun Yao ◽

Fangyu Zhao ◽

Yuanjiang Xu ◽

Kaihui Zhao ◽

Hong Quan ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

De Novo ◽

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Complete Chloroplast Genome ◽

Ssr Analysis ◽

Chloroplast Genomes

Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene’s lengths of 82,221 bp and 81,450 bp, large single-copy region’s (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region’s (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region’s (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.

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Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species

Plants ◽

10.3390/plants9050568 ◽

2020 ◽

Vol 9 (5) ◽

pp. 568

Author(s):

Swati Tyagi ◽

Jae-A Jung ◽

Jung Sun Kim ◽

So Youn Won

Keyword(s):

Chloroplast Genome ◽

Gc Content ◽

Single Copy ◽

The Other ◽

Complete Chloroplast Genome ◽

Coding Regions ◽

Chloroplast Genomes ◽

Redundant Genes ◽

Intron Structure ◽

Contraction And Expansion

Aster spathulifolius, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland A. spathulifolius and compared it with those of the island type and other Aster species. The chloroplast genome of mainland A. spathulifolius is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two A. spathulifolius lines and the other Aster species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All Aster species clustered into a monophyletic group, but the chloroplast genome of mainland A. spathulifolius was more similar to the other Aster species than to that of the island A. spathulifolius. The accD and ndhF genes were detected to be under positive selection within the Aster lineage compared to other related taxa. The complete chloroplast genome of mainland A. spathulifolius presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the Aster genus and the Asteraceae.

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