Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes

1994 ◽  
Vol 12 (2) ◽  
pp. S29-S30 ◽  
Author(s):  
Richard B. Hallick ◽  
Amos Bairoch
Keyword(s):  
Open Reading Frames ◽  
Chloroplast Genes ◽  
Chloroplast Genomes ◽  
Reading Frames

Identification of functional open reading frames in chloroplast genomes

Gene ◽  
1988 ◽  
Vol 66 (2) ◽  
pp. 215-222 ◽  
Author(s):  
Kenneth H. Wolfe ◽  
Paul M. Sharp
Keyword(s):  
Open Reading Frames ◽  
Chloroplast Genomes ◽  
Reading Frames

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 Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3325 ◽  
Author(s):  
Hilary A. McManus ◽  
Daniel J. Sanchez ◽  
Kenneth G. Karol
Keyword(s):  
Gene Order ◽  
Size Variation ◽  
Open Reading Frames ◽  
Gene Content ◽  
Intron Insertion ◽  
Sister Relationship ◽  
Hydrodictyon Reticulatum ◽  
Green Algal ◽  
Chloroplast Genomes ◽  
Reading Frames

Background Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex. Methods Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed. Results The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae. Discussion The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex, representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

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