scholarly journals Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Yang He ◽  
Hongtao Xiao ◽  
Cao Deng ◽  
Gang Fan ◽  
Shishang Qin ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Rrna Gene ◽  
Coptis Chinensis ◽  
Medicinal Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Next Generation Sequencing Technology ◽  
Complete Sequencing ◽  
Chloroplast Genome Sequence

The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.

scholarly journals Comparative genome analysis revealed gene inversions, boundary expansion and contraction, and gene loss in Stemona sessilifolia (Miq.) Miq. chloroplast genome

2021 ◽  
Author(s):  
Jingting Liu ◽  
Mei Jiang ◽  
Haimei Chen ◽  
Yu Liu ◽  
Chang Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gene Loss ◽  
Herbal Medicines ◽  
Single Copy ◽  
Asparagus Officinalis ◽  
Accurate Identification ◽  
Protein Coding ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Next Generation Sequencing Technology

AbstractStemona sessilifolia (Miq.) Miq., commonly known as Baibu, is one of the most popular herbal medicines in Asia. In Chinese Pharmacopoeia, Baibu has multiple authentic sources, and there are many homonym herbs sold as Baibu in the herbal medicine market. The existence of the counterfeits of Baibu brings challenges to its identification. To assist the accurate identification of Baibu, we sequenced and analyzed the complete chloroplast genome of Stemona sessilifolia using next-generation sequencing technology. The genome was 154,039 bp in length, possessing a typical quadripartite structure consisting of a pair of inverted repeats (IRs: 27,094 bp) separating by a large single copy (LSC: 81,950 bp) and a small single copy (SSC: 17,901 bp). A total of 112 unique genes were identified, including 80 protein-coding, 28 transfer RNA, and four ribosomal RNA genes. Besides, 45 tandem, 27 forward, 23 palindromic, and 72 simple sequence repeats were detected in the genome by repeat analysis. Compared with its counterfeits (Asparagus officinalis and Carludovica palmate), we found that IR expansion and SSC contraction events of Stemona sessilifolia resulted in two copies of the rpl22 gene in the IR regions and partial duplication of the ndhF gene in the SSC region. Secondly, an approximately 3-kb-long inversion was identified in the LSC region, leading to the petA and cemA gene presented in the complementary strand of the chloroplast DNA molecule. Comparative analysis revealed some highly variable regions, including trnF-GAA_ndhJ, atpB_rbcL, rps15_ycf1, trnG-UCC_trnR-UCU, ndhF_rpl32. Finally, gene loss events were investigated in the context of phylogenetic relationships. In summary, the complete plastome of Stemona sessilifolia will provide valuable information for the molecular identification of Baibu and assist in elucidating the evolution of Stemona sessilifolia.

scholarly journals Complete chloroplast genome sequence of a vegetative Bermudagrass cultivar Tifeagle (Cynodon dactylon × Cynodon transvaalensis)

2019 ◽  
Vol 48 (4) ◽  
pp. 1083-1089
Author(s):  
Yancai Shi ◽  
Shaofeng Jiang ◽  
Shilian Huang
Keyword(s):  
Chloroplast Genome ◽  
Cynodon Dactylon ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Common Bermudagrass ◽  
Trampling Tolerance ◽  
Small Single Copy

Hybrid (Cynodonn dactylon × C. transvaalensis) is a widely distributed turfgrass and shows a great value of environment, horticulture and economic. Though, the chloroplast genome of C. dactylon has been reported, it might be helpful finding reasons that triploid bermudagrass shows a better drought and trampling tolerance than common bermudagrass through comparing chloroplast genome analysis. The present results showed the complete chloroplast genome of the C. dactylon × C. transvaalensis is 134655 bp in length. The tetramerous genome contained a large single copy (LSC) region (79,998 bp), a small single copy (SSC) region (12,517 bp), and a pair of inverted repeat (IR) regions (42,140 bp). In the chloroplast genome, 116 genes were predicted, including 83 protein-coding, 29 tRNA and 4 rRNA genes. Furthermore, a total of 80 repeat sequences were identified. Only 0.23% intergenicnon-collinear sequences were found between the chloroplast genome of Cynodon dactylon × C. transvaalensis and Cynodon dactylon.

scholarly journals Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Samaila S. Yaradua ◽  
Dhafer A. Alzahrani ◽  
Enas J. Albokhary ◽  
Abidina Abba ◽  
Abubakar Bello
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

scholarly journals The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1405
Author(s):  
Gurusamy Raman ◽  
SeonJoo Park
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Gene Evolution ◽  
Single Copy ◽  
Specific Marker ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

scholarly journals Characterization of the complete chloroplast genome sequence of Vitis vinifera ‘Guifeimeigui’

2021 ◽  
pp. 001-003
Author(s):  
Liu Li ◽  
Yang Yang ◽  
Li Xiujie ◽  
Li Bo
Keyword(s):  
Vitis Vinifera ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Cp Genome ◽  
Eurasian Species ◽  
Rna Genes

Vitis vinifera ‘Guifeimeigui’ is a diploid table grape, a Eurasian species. This research first reported the complete chloroplast (cp) genome of Vitis vinifera ‘Guifeimeigui’. The size of the complete cp genome is 160,928 bp and its GC content is 37.38%, including a pair of inverted repeats (26,353 bp each) separated by large (89,150 bp) and small (19,072 bp) single-copy regions. It encodes 85 genes, including 40 protein coding genes, 37 transfer RNA genes (tRNA), and 8 ribosomal RNA genes (rRNA). The Maximum Likelihood (ML) phylogenetic tree demonstrated that Vitis vinifera ‘Guifeimeigui’ is close to Vitis vinifera.

scholarly journals Complete chloroplast genome sequence and structural analysis of the medicinal plant Lycium chinense Mill

2018 ◽  
Author(s):  
Zerui Yang ◽  
Yuying Huang ◽  
Xiasheng Zheng ◽  
Song Huang ◽  
Lingling Liang
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Start Codon ◽  
Lycium Chinense ◽  
Protein Coding ◽  
Engineering Research ◽  
Complete Sequences ◽  
Chloroplast Genome Sequence ◽  
Cp Genome

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 single-copy 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.

scholarly journals Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2426 ◽  
Author(s):  
Xiaofeng Shen ◽  
Shuai Guo ◽  
Yu Yin ◽  
Jingjing Zhang ◽  
Xianmei Yin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Chinese Herb ◽  
Single Copy ◽  
Future Research ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Rna Genes ◽  
Small Single Copy

We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

scholarly journals Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 996
Author(s):  
Ting Wang ◽  
Ren-Ping Kuang ◽  
Xiao-Hui Wang ◽  
Xiao-Li Liang ◽  
Vincent Okelo Wanga ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gc Content ◽  
Taxonomic Status ◽  
Single Copy ◽  
Ring Structure ◽  
Protein Coding ◽  
Coding Regions ◽  
Second Generation Sequencing ◽  
Chloroplast Genome Sequence ◽  
Independent Species

Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.

scholarly journals Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7713 ◽  
Author(s):  
Yong Yang ◽  
Ying Zhang ◽  
Yukai Chen ◽  
Juma Gul ◽  
Jingwen Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Genome Sequence ◽  
Related Species ◽  
Kandelia Obovata ◽  
Mangrove Species ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genome Sequence

As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.

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