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

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

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.

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.

scholarly journals Comparative chloroplast genomic analyses revealed extensive genomic arrangement in some core and non-core caryophyllales

2019 ◽  
Vol 26 (1) ◽  
pp. 106-117 ◽  
Author(s):  
M. Ajmal Ali
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationship ◽  
Reference Genome ◽  
Gene Organization ◽  
Genomic Rearrangement ◽  
Coding Region ◽  
Genomic Arrangement ◽  
Genomic Analyses

The order Caryophyllales exhibit diverse diversity in morphology to molecules, which leads to taxonomic complexities in circumscribing especially to its families. The comparative analysis of the available chloroplast genome to detect pattern of genomic arrangement and variation is lacking; hence, the alignment pattern and genomic rearrangement across the Caryophyllales were detected, and the phylogenetic relationship among the families of the Caryophyllales based on maximum cp genes were inferred. The comparison of the Caryophyllales cp genomes based on representatives of 10 families with Taxillus chinensis as reference genome revealed that coding region were more conserved than the non-coding region; however, clpP, rpl16 and ycf15 were the most divergent coding region among all taxa. Further, the genomic rearrangement occurred in gene organization of the taxa among different families of Caryophyllales, the extensive rearrangement were observed in Amaranthaceae, Caryophyllaceae, Chenopodiaceae,Droseraceae and Cactaceae.

scholarly journals Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

2018 ◽  
Vol 87 (1) ◽  
Author(s):  
Hanna Kijak ◽  
Weronika Łodyga ◽  
Ireneusz J. Odrzykoski
Keyword(s):  
Chloroplast Genome ◽  
Sequence Variation ◽  
Sequence Divergence ◽  
Intergenic Spacer ◽  
Marchantia Polymorpha ◽  
Homologous Sequences ◽  
Clonal Lines ◽  
Suspension Line ◽  
Marchantia Paleacea ◽  
Almost All

<p>The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of <em>Marchantia polymorpha</em> sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the <em>rps4</em> gene along with the <em>rps4-trnT</em> intergenic spacer and an intron of the tRNA<sup>Gly</sup> (UCC) gene. Samples of <em>Marchantia paleacea</em> ssp. <em>diptera</em> from Japan were used for comparative purposes.</p><p>Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between <em>M. polymorpha</em> and <em>M. paleacea</em> was tenfold greater (0.0331–0.0340). We did not detect any differences between <em>M. paleacea</em> and homologous sequences from the reference chloroplast genome of <em>M. polymorpha</em> obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.</p>

Structure and organization of Marchantia polymorpha chloroplast genome

1988 ◽  
Vol 203 (2) ◽  
pp. 299-331 ◽  
Author(s):  
Kazuhiko Umesono ◽  
Hachiro Inokuchi ◽  
Yasuhiko Shiki ◽  
Masayuki Takeuchi ◽  
Zhen Chang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Marchantia Polymorpha
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