The Complete Chloroplast Genome of Ardisia Japonica（Thunb.）Blume

Abstract Ardisia japonica（Thunb）Blume is a small shrub or sub-shrub of the genus Taurus in the Taurus family. The whole plant and root of A. japonica are used for medicinal purposes. It is a common Chinese herbal medicine and a common flower. To study its complete chloroplast genome, we collected leaves and obtained chloroplast genome information through next-generation sequencing. The results showed that the length of the genome is 155,996 bp, and the GC content ratio is 37.0%. The large single-copy region (LSC) is 86803 bp, the small single-copy region (SSC) is 18080 bp, and the inverted repeat region (IR) is 25507 bp. The chloroplast genome encodes 130 genes, including 85 protein genes, 8 rRNA genes, and 37tRNA genes. By analyzing the phylogeny of A. japonica, it is found that A. japonica and other Ardisia species are closely related.

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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 sequence of a vegetative Bermudagrass cultivar Tifeagle (Cynodon dactylon × Cynodon transvaalensis)

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i4.49056 ◽

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.

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Construction of complete chloroplast genome of the endemic species Paphiopedilum delenatii Guillaumin (1924) of Vietnam

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/18/1/15268 ◽

2020 ◽

Vol 18 (1) ◽

pp. 87-102

Author(s):

Nguyen Thanh Diem ◽

Le Thi Ly ◽

Nguyen Huu Thuan Anh ◽

Nguyen Thanh Cong ◽

Vu Thi Huyen Trang

Keyword(s):

Chloroplast Genome ◽

Evolutionary Relationship ◽

Gc Content ◽

Single Copy ◽

Complete Chloroplast Genome ◽

Genome Data ◽

A Cell ◽

Chloroplast Genome Sequencing ◽

Small Single Copy ◽

Generation Sequencing

Chloroplasts and mitochondria are organelles that have their own genome in a cell. The chloroplast genome provides information on the evolutionary relationship and species identification, valuable markers for transgenic plants, and cloning plants, etc. The application of Next Generation Sequencing has improved the chloroplast genome sequencing. However, the assembly process of chloroplast genome is quite complicated due to the need of different complex bioinformatics tools, high configuration computer and laborous. Here we configured the process of assembling the chloroplast genome of Paphiopedilum delenatii. The assembled chloroplast genome was 160,955 bp in length, including a large and a small single copy region (LSC, SSC) separated by a pair of inverted repeats (IR). Total genes were 130 genes, GC content is 35.6%. Genome data was mapped and registered in GenBank under accession number MK463585. The optimal parameters for genome assembling were recommended. This study not only provided information for conservation of the Vietnam endemic Paphiopedilum delenatii species but also supported the genome assemble researches which could be applied on other subjects.

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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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Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽

10.3390/plants9101354 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1354

Author(s):

Slimane Khayi ◽

Fatima Gaboun ◽

Stacy Pirro ◽

Tatiana Tatusova ◽

Abdelhamid El Mousadik ◽

...

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Important Species ◽

Complete Chloroplast Genome ◽

Argania Spinosa ◽

Protein Coding Genes ◽

Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

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Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics

Genome ◽

10.1139/g11-026 ◽

2011 ◽

Vol 54 (8) ◽

pp. 663-673 ◽

Cited By ~ 113

Author(s):

Dai-Yong Kuang ◽

Hong Wu ◽

Ya-Ling Wang ◽

Lian-Ming Gao ◽

Shou-Zhou Zhang ◽

...

Keyword(s):

Population Genetics ◽

Gc Content ◽

Single Copy ◽

Phylogenetic Study ◽

Complete Chloroplast Genome ◽

Noncoding Regions ◽

Its Gene ◽

Study Population ◽

Chloroplast Genome Sequence ◽

Small Single Copy

Here, we report a completely sequenced plastome using Illumina/Solexa sequencing-by-synthesis (SBS) technology. The plastome of Magnolia kwangsiensis Figlar & Noot. is 159 667 bp in length with a typical quadripartite structure: 88 030 bp large single-copy (LSC) and 18 669 bp small single-copy (SSC) regions, separated by two 26 484 bp inverted repeat (IR) regions. The overall predicted gene number is 129, among which 17 genes are duplicated in IR regions. The plastome of M. kwangsiensis is identical in its gene order to previously published plastomes of magnoliids. Furthermore, the C-to-U type RNA editing frequency of 114 seed plants is positively correlated with plastome GC content and plastome length, whereas plastome length is not correlated with GC content. A total of 16 potential putative barcoding or low taxonomic level phylogenetic study markers in Magnoliaceae were detected by comparing the coding and noncoding regions of the plastome of M. kwangsiensis with that of Liriodendron tulipifera L. At least eight markers might be applied not only to Magnoliaceae but also to other taxa. The 86 mononucleotide cpSSRs that distributed in single-copy noncoding regions are highly valuable to study population genetics and conservation genetics of this endangered rare species.

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The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

10.20944/preprints201703.0139.v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Inkyu Park ◽

Wook-Jin Kim ◽

Sang-Min Yeo ◽

Goya Choi ◽

Young-Min Kang ◽

...

Keyword(s):

Chloroplast Genome ◽

General Structure ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Phylogenic Analysis ◽

Fritillaria Species ◽

Fritillaria Cirrhosa

The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽

10.7717/peerj.6032 ◽

2018 ◽

Vol 6 ◽

pp. e6032 ◽

Cited By ~ 12

Author(s):

Zhenyu Zhao ◽

Xin Wang ◽

Yi Yu ◽

Subo Yuan ◽

Dan Jiang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Single Copy ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Genomic Resources ◽

Chloroplast Genomes ◽

The Family ◽

Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

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

BioMed Research International ◽

10.1155/2019/4370258 ◽

2019 ◽

Vol 2019 ◽

pp. 1-17 ◽

Cited By ~ 4

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.

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Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis

Molecules ◽

10.3390/molecules24030474 ◽

2019 ◽

Vol 24 (3) ◽

pp. 474 ◽

Cited By ~ 13

Author(s):

Dong-Mei Li ◽

Chao-Yi Zhao ◽

Xiao-Fei Liu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Species Identification ◽

Single Copy ◽

Rrna Genes ◽

Genome Sequences ◽

Variable Regions ◽

Complete Chloroplast Genome ◽

Kaempferia Galanga ◽

Chloroplast Genomes

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

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