Localization of three chloroplast ribosomal protein genes at the left junction of the large single copy region and the inverted repeat of Spirodela oligorhiza chloroplast DNA

1985 ◽  
Vol 9 (3) ◽  
pp. 211-219 ◽  
Author(s):  
Mark Posno ◽  
Dick J. Torenvliet ◽  
Henk Lustig ◽  
Marjolein van Noort ◽  
Gert S. P. Groot
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Protein ◽  
Inverted Repeat ◽  
Single Copy ◽  
Ribosomal Protein Genes ◽  
Large Single Copy ◽  
Spirodela Oligorhiza ◽  
Large Single Copy Region

Genome walking with consensus primers: application to the large single copy region of chloroplast DNA

2001 ◽  
Vol 1 (4) ◽  
pp. 345-349 ◽  
Author(s):  
D. Grivet ◽  
B. Heinze ◽  
G. G. Vendramin ◽  
R. J. Petit
Keyword(s):  
Chloroplast Dna ◽  
Single Copy ◽  
Genome Walking ◽  
Large Single Copy ◽  
Consensus Primers ◽  
Large Single Copy Region

Localization of chloroplast ribosomal protein genes on Spirodela oligorhiza chloroplast DNA

1986 ◽  
Vol 10 (12) ◽  
pp. 923-930 ◽  
Author(s):  
Mark Posno ◽  
Anja van Vliet ◽  
Gert S. P. Groot
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Protein ◽  
Ribosomal Protein Genes ◽  
Spirodela Oligorhiza

Sequence analysis of the junction of the large single copy region and the large inverted repeat in the petunia chloroplast genome

1988 ◽  
Vol 14 (5) ◽  
pp. 487-492 ◽  
Author(s):  
Jane Aldrich ◽  
Barry W. Cherney ◽  
Charlotte Williams
Keyword(s):  
Sequence Analysis ◽  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Single Copy ◽  
Large Single Copy ◽  
Large Single Copy Region

scholarly journals Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 199 ◽  
Author(s):  
Arif Khan ◽  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Tariq Shehzad ◽  
Ahmed Al-Rawahi ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Sequence Variation ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Large Single Copy ◽  
Monophyletic Clade ◽  
Protein Coding ◽  
The Family ◽  
Generation Sequencing ◽  
Large Single Copy Region

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.

scholarly journals The contraction in inverted repeat regions in the complete plastome sequence ofCressa creticaL

2018 ◽  
Author(s):  
Pritesh P. Bhatt ◽  
Vrinda S. Thaker
Keyword(s):  
Molecular Evolution ◽  
Inverted Repeat ◽  
High Salinity ◽  
Physical Map ◽  
Single Copy ◽  
Harsh Environment ◽  
Large Single Copy ◽  
Circular Molecule ◽  
Small Single Copy ◽  
Large Single Copy Region

AbstractPlastome studies have been the focus of research in plant molecular evolution and systematics.C. creticaL. (Convolvulaceae) is a halophyte, habitat in the ecologically challenged area with high salinity and drought. The complete physical map of plastome revealed that it is 141,419bp long, circular molecule. It contains typical quadripartite structure of large single copy region (LSC 94,808bp), small single copy region (SSC 32,527bp) separated by a pair of inverted repeat regions (IRs 7042bp). This plastome is compared with the complete plastomes of other members of Convolvulaceae showed notable distinctions. An exceptional shift in IRs to SC regions is experienced inC. creticaled to many genes shift in both SC regions and contraction in IRs. The size of IRs reduced to 2 to 4 times as compared to those of the Convolvulaceae members studied. The shifted IRs regions showed remarkable variation in nucleotides patterns. Further, the shift was from the IR boundaries and in between the IR regions led to segment IRs. It is concluded that the shift in IRs may be the strategic move for adaptation in the harsh environment.

Transcription study of the genes encoded in the region of the junction between the large single copy and the inverted repeat A of spinach chloroplast DNA

1988 ◽  
Vol 10 (5) ◽  
pp. 447-457 ◽  
Author(s):  
Frank Thomas ◽  
Guo-Qing Zeng ◽  
R�gis Mache ◽  
Jean-Fran�ois Briat
Keyword(s):  
Chloroplast Dna ◽  
Inverted Repeat ◽  
Single Copy ◽  
Spinach Chloroplast ◽  
Large Single Copy

Physical map and gene localization on sunflower (Helianthus annuus) chloroplast DNA: evidence for an inversion of a 23.5-kbp segment in the large single copy region

1987 ◽  
Vol 9 (5) ◽  
pp. 485-496 ◽  
Author(s):  
Fran�oise Heyraud ◽  
Pascale Serror ◽  
Marcel Kuntz ◽  
Andr� Steinmetz ◽  
Philippe Heizmann
Keyword(s):  
Chloroplast Dna ◽  
Helianthus Annuus ◽  
Physical Map ◽  
Single Copy ◽  
Gene Localization ◽  
Large Single Copy ◽  
Dna Evidence ◽  
Large Single Copy Region

scholarly journals Structural rearrangements in plastid genomes of Apiaceae as phylogenetic markers

2021 ◽  
Vol 38 ◽  
pp. 00107
Author(s):  
Tahir Samigullin ◽  
Carmen Vallejo-Roman ◽  
Galina Degtjareva ◽  
Elena Terentieva
Keyword(s):  
Single Copy ◽  
Sampling Scheme ◽  
Taxon Sampling ◽  
Inverted Repeats ◽  
Structural Rearrangements ◽  
Large Single Copy ◽  
Plastid Genomes ◽  
Dense Sampling ◽  
Large Single Copy Region

Apiaceae belong to angiosperm families with frequent plastome structural rearrangements, some of which are generally regarded as synapomorphic for large clades, although typically with limited taxon sampling. Our study aims to improve understanding of the structural rearrangements in plastome within the Tordylieae tribe (ApiaceaeApioideae) with a dense sampling scheme of its species. We showed that presence of psbA pseudogene in inverted repeats near the border with a large single-copy region, which is found in the Tordylieae tribe, may be a clade-specific synapomorphy.

scholarly journals Primary structure of human ribosomal protein S14 and the gene that encodes it.

1986 ◽  
Vol 6 (8) ◽  
pp. 2774-2783 ◽  
Author(s):  
D D Rhoads ◽  
A Dixit ◽  
D J Roufa
Keyword(s):  
Ribosomal Protein ◽  
Hybrid Cell ◽  
Chinese Hamster ◽  
Housekeeping Genes ◽  
Single Copy ◽  
Sequence Motifs ◽  
Ribosomal Protein Genes ◽  
Alu Sequence ◽  
Exon 1 ◽  
Human Genomic

Chinese hamster ribosomal protein S14 cDNA was used to recognize homologous human cDNA and genomic clones. Human and Chinese hamster S14 protein sequences deduced from the cDNAs are identical. Two overlapping human genomic S14 DNA clones were isolated from a Charon 28 placental DNA library. A fragment of single-copy DNA derived from an intron region of one clone was mapped to the functional RPS14 locus on human chromosome 5q by using a panel of human X Chinese hamster hybrid cell DNAs. The human S14 gene consists of five exons and four introns spanning 5.9 kilobase pairs of DNA. Polyadenylated S14 transcripts purified from HeLa cell cytoplasma display heterogeneous 5' ends that map within noncoding RPS14 exon 1. This precludes assignment of a unique 5' boundary of RPS14 transcripts with respect to the cloned human genomic DNA. Apparently HeLa cells either initiate transcription at multiple sites within RPS14 exon 1, or capped 5' oligonucleotides are removed from most S14 mRNAs posttranscription. In contrast to the few murine ribosomal protein and several other mammalian housekeeping genes whose structures are known, human RPS14 contains a TATA sequence (TATACTT) upstream from exon 1. Three related short sequence motifs, also observed in murine and yeast ribosomal protein genes, occur in this region of the RPS14 gene. RPS14 introns 3 and 4 both contain Alu sequences. Interestingly, the Alu sequence in intron 3 is located slightly downstream from a chromosome 5 deletion breakpoint in one human X hamster hybrid clone analyzed.

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