The Plastid Genome of Deschampsia cespitosa (Poaceae)

Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.

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

Scientific Journal of Genetics and Gene Therapy ◽

10.17352/sjggt.000019 ◽

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.

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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

International Journal of Molecular Sciences ◽

10.3390/ijms19082443 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2443 ◽

Cited By ~ 16

Author(s):

Xuan Li ◽

Yongfu Li ◽

Mingyue Zang ◽

Mingzhi Li ◽

Yanming Fang

Keyword(s):

Chloroplast Genome ◽

Simple Sequence Repeat ◽

Gc Content ◽

Single Copy ◽

Biological Research ◽

Sequence Repeat ◽

Quercus Acutissima ◽

Cp Genome ◽

Rna Genes ◽

Simple Sequence

Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the Q. acutissima chloroplast genome is 161,124 bp, including one large single copy (LSC) region of 90,423 bp and one small single copy (SSC) region of 19,068 bp, separated by two inverted repeat (IR) regions of 51,632 bp. The GC content of the whole genome is 36.08%, while those of LSC, SSC, and IR are 34.62%, 30.84%, and 42.78%, respectively. The Q. acutissima chloroplast genome encodes 136 genes, including 88 protein-coding genes, four ribosomal RNA genes, and 40 transfer RNA genes. In the repeat structure analysis, 31 forward and 22 inverted long repeats and 65 simple-sequence repeat loci were detected in the Q. acutissima cp genome. The existence of abundant simple-sequence repeat loci in the genome suggests the potential for future population genetic work. The genome comparison revealed that the LSC region is more divergent than the SSC and IR regions, and there is higher divergence in noncoding regions than in coding regions. The phylogenetic relationships of 25 species inferred that members of the Quercus genus do not form a clade and that Q. acutissima is closely related to Q. variabilis. This study identified the unique characteristics of the Q. acutissima cp genome, which will provide a theoretical basis for species identification and biological research.

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Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽

10.3390/molecules23092137 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2137 ◽

Cited By ~ 6

Author(s):

Xiang-Xiao Meng ◽

Yan-Fang Xian ◽

Li Xiang ◽

Dong Zhang ◽

Yu-Hua Shi ◽

...

Keyword(s):

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Chloroplast Genomes ◽

Close Relationship ◽

Cp Genome ◽

Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

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The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Forests ◽

10.3390/f11111179 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1179

Author(s):

Ueric José Borges de Souza ◽

Luciana Cristina Vitorino ◽

Layara Alexandre Bessa ◽

Fabiano Guimarães Silva

Keyword(s):

Plastid Genome ◽

Structural Characteristics ◽

Gc Content ◽

Single Copy ◽

Chloroplast Genes ◽

Artocarpus Heterophyllus ◽

Plastid Genomes ◽

The Family ◽

High Degree ◽

Degree Of Similarity

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.

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The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽

10.3390/molecules24020261 ◽

2019 ◽

Vol 24 (2) ◽

pp. 261 ◽

Cited By ~ 8

Author(s):

Yongfu Li ◽

Steven Paul Sylvester ◽

Meng Li ◽

Cheng Zhang ◽

Xuan Li ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Genome Structure ◽

Phylogenetic Reconstruction ◽

Strong Support ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Critically Endangered Species ◽

Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

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Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

10.21203/rs.3.rs-822059/v1 ◽

2021 ◽

Author(s):

Jiaxin Yang ◽

Guoxiong Hu ◽

Guangwan Hu

Keyword(s):

Endangered Species ◽

Chloroplast Genome ◽

Genome Size ◽

Gc Content ◽

Genomic Analysis ◽

Single Copy ◽

Comparative Genomic ◽

Eurycorymbus Cavaleriei ◽

Cp Genome ◽

Relationship Of

Abstract Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisted of Aesculus chinensis and A. wangii, strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller across Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

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Characterization of the complete chloroplast genome sequence and phylogenetic analysis of B. oleracea var. italica

10.21203/rs.2.20976/v1 ◽

2020 ◽

Author(s):

Zhenchao Zhang ◽

Zhongliang Dai ◽

Yuemei Yao ◽

Yongfei Pan ◽

Guosheng Sun ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Genomic Structure ◽

Gc Content ◽

Single Copy ◽

Biological Research ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome ◽

Functional Components

Abstract Backgrounds: Broccoli (Brassica. oleracea var. italica L.) is known as one of the most nutritionally rich vegetables, as well as rich in functional components that benefit to health. The main purposes of this research were sequencing, assembling and annotation of chloroplast genome of broccoli based on Illumina HiSeq2500 sequencing platform. Results: The size of the broccoli cp genome is 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The GC content of the complete genome is 36.36%, while those of SSC, LSC, and IR are 29.1%, 34.15% and 42.35%, respectively. It harbors 134 functional genes, including 87 protein-coding genes, 39 tRNAs and 8 rRNAs, with 31 duplicates in the IRs. The most abundant amino acid in the protein-coding genes is leucine, while the least is cysteine. Codon usage frequency showed bias for A/T-ending codons in the cp genome. In the repeat structure analysis, a total of 34 repeat sequences and 291 simple sequence repeat (SSRs) were detected in the work. Although cp genomic structure and size are highly conserved, the SC-IR boundary regions are variable between the 7 cp genomes. The phylogenetic relationships based on complete cp genome from 9 species suggest that B. oleracea var. italica is closely related to Brassica juncea. Conclusions: The complete cp genome sequence was obtained and annotated for broccoli for the first time. The information acquired from this research will be useful for further species identification, population genetics and biological research of broccoli.

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Analyzing and characterization of the chloroplast genome of Salix suchowensis

10.7287/peerj.preprints.2388 ◽

2016 ◽

Author(s):

Congrui Sun ◽

Jie Li ◽

Xiaogang Dai ◽

Yingnan Chen

Keyword(s):

Tandem Repeats ◽

Gene Annotation ◽

Repetitive Sequences ◽

Single Copy ◽

Phylogenetic Position ◽

Shrub Willow ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome ◽

Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

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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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A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties

PeerJ ◽

10.7717/peerj.5349 ◽

2018 ◽

Vol 6 ◽

pp. e5349 ◽

Cited By ~ 9

Author(s):

Juan Wang ◽

Chunjuan Li ◽

Caixia Yan ◽

Xiaobo Zhao ◽

Shihua Shan

Keyword(s):

Comparative Analysis ◽

High Throughput Sequencing ◽

Evolutionary Relationship ◽

Gc Content ◽

Oilseed Crop ◽

Nucleotide Polymorphisms ◽

Genome Sequences ◽

Genome Data ◽

Cp Genome ◽

Botanical Varieties

BackgroundArachis hypogaeaL. is an economically important oilseed crop worldwide comprising six botanical varieties. In this work, we characterized the chloroplast (cp) genome sequences of the four widely distributed peanut varieties.MethodsThe cp genome data of these four botanical varieties (var.hypogaea, var.hirsuta, var.fastigiata, and var.vulgaris) were obtained by next-generation sequencing. These high-throughput sequencing reads were then assembled, annotated, and comparatively analyzed.ResultsThe total cp genome lengths of the studiedA. hypogaeavarieties were 156,354 bp (var.hypogaea), 156,878 bp (var.hirsuta), 156,718 bp (var.fastigiata), and 156,399 bp (var.vulgaris). Comparative analysis of theses cp genome sequences revealed that their gene content, gene order, and GC content were highly conserved, with only a total of 46 single nucleotide polymorphisms and 26 insertions/deletions identified. Most of the variations were restricted to non-coding sequences, especially, thetrnI-GAU intron region was detected to be highly variable and will be useful for future evolutionary studies.DiscussionThe four cp genome sequences acquired here will provide valuable genetic resources for distinguishingA. hypogaeabotanical varieties and determining their evolutionary relationship.

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