The chloroplast genome of plants: a unique origin

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 169-174 ◽  
Author(s):  
Haruo Ozeki ◽  
Kazuhiko Umesono ◽  
Hachiro Inokuchi ◽  
Takayuki Kohchi ◽  
Kanji Ohyama
Keyword(s):  
Nicotiana Tabacum ◽  
Chloroplast Genome ◽  
Complete Sequence ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Marchantia Polymorpha ◽  
Chloroplast Genes ◽  
Functional Protein ◽  
Chloroplast Genomes ◽  
Rna Genes

Complete nucleotide sequences of chloroplast genomes are now available for two green plants: Marchantia polymorpha (a liverwort) and Nicotiana tabacum (tobacco). Although these two plant species are taxonomically very distant from one another, their deduced gene organization is remarkably similar. This implies that the chloroplast genomes in all land plants may have arisen from a unique ancestor. Including the unidentified open reading frames, we establish the number of distinct chloroplast genes at about 125, consisting of 4 species of ribosomal RNA genes, 30 or 31 species of transfer RNA genes, and about 90 protein genes. About half of these genes are concerned with the basic mechanisms of gene expression in the chloroplast, such as transcription and translation, and share many features with prokaryotic organisms. Complete sequence analysis revealed that each functional protein complex containing components encoded by the chloroplast genes also contains nuclear-encoded ones, as if some of the genes from each complex have "migrated" to the nucleus from a symbiotic prokaryote during the course of evolution. By this process, the basis of the present nuclear–chloroplast relationships had been established in very early times (300–400 million years ago) before the branching of Bryophytina and Tracheophytina. From this unified single origin the present-day chloroplast genomes in plants have evolved mainly by mutations in nucleotides and rearrangement of DNA, but rarely by changes in gene content.Key words: chloroplast genome, complete DNA sequence, gene organization, Marchantia polymorpha, Nicotiana tabacum, unified origin.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA

1992 ◽  
Vol 223 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Kenji Oda ◽  
Katsuyuki Yamato ◽  
Eiji Ohta ◽  
Yasukazu Nakamura ◽  
Miho Takemura ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Complete Sequence ◽  
Gene Organization ◽  
Marchantia Polymorpha

scholarly journals The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wei Tan ◽  
Han Gao ◽  
Weiling Jiang ◽  
Huanyu Zhang ◽  
Xiaolei Yu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Reconstruction ◽  
Gene Organization ◽  
Rrna Genes ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Gleditsia Sinensis ◽  
Candidate Regions ◽  
Molecular Marker Development

Abstract Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.

Gene organization and newly identified groups of genes of the chloroplast genome from a liverwort, Marchantia polymorpha

1988 ◽  
pp. 27-42
Author(s):  
Kanji Ohyama ◽  
Takayuki Kohchi ◽  
Hideya Fukuzawa ◽  
Tohru Sano ◽  
Kazuhiko Umesono ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gene Organization ◽  
Marchantia Polymorpha

scholarly journals Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiao Fang ◽  
Benwen Liu ◽  
Guoxiang Liu ◽  
Heroen Verbruggen ◽  
Huan Zhu
Keyword(s):  
Genetic Code ◽  
Chloroplast Genome ◽  
Genetic Information ◽  
Vascular Plants ◽  
Gc Content ◽  
Valid Species ◽  
Chloroplast Genes ◽  
Rates Of Evolution ◽  
Chloroplast Genomes ◽  
Shed Light

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26–36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD-GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.

scholarly journals Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

2021 ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background: Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.Results: The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions: Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Gene organization and newly identified groups of genes of the chloroplast genome from a liverwort, Marchantia polymorpha

1988 ◽  
Vol 16 (1-2) ◽  
pp. 7-22 ◽  
Author(s):  
Kanji Ohyama ◽  
Takayuki Kohchi ◽  
Hideya Fukuzawa ◽  
Tohru Sano ◽  
Kazuhiko Umesono ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Gene Organization ◽  
Marchantia Polymorpha

scholarly journals Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenpan Dong ◽  
Yanlei Liu ◽  
Chao Xu ◽  
Yongwei Gao ◽  
Qingjun Yuan ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Ribosomal Rna ◽  
Leaf Size ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Chloroplast Genomes ◽  
Conserved Gene ◽  
Rna Genes ◽  
Simple Sequence

Abstract Background Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. Results The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. Conclusions The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.

scholarly journals Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

2020 ◽  
Author(s):  
yiheng wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In this study, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42-47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

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