A 16 kb small single-copy region separates the plastid DNA inverted repeat of the unicellular red alga Cyanidium caldarium: physical mapping of the IR-flanking regions and nucleotide sequences of the psbD-psbC, rps16, 5S rRNA and rpl21 genes

1992 ◽  
Vol 19 (6) ◽  
pp. 1001-1010 ◽  
Author(s):  
Udo Maid ◽  
Klaus Zetsche
Keyword(s):  
Physical Mapping ◽  
Inverted Repeat ◽  
Plastid Dna ◽  
Single Copy ◽  
Red Alga ◽  
Nucleotide Sequences ◽  
5S Rrna ◽  
Cyanidium Caldarium ◽  
Flanking Regions ◽  
Small Single Copy

scholarly journals The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Ming-Zhu Bai ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Substitution Rates ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

The ndhH genes of gramminean plastomes are linked with the junctions between small single copy and inverted repeat regions

1990 ◽  
Vol 18 (3) ◽  
pp. 245-250 ◽  
Author(s):  
R. M. Maier ◽  
I. D�ry ◽  
G. Igloi ◽  
H. K�ssel
Keyword(s):  
Inverted Repeat ◽  
Single Copy ◽  
Small Single Copy

scholarly journals airpg: automatically accessing the inverted repeats of archived plastid genomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tilman Mehl ◽  
Michael Gruenstaeudl
Keyword(s):  
Inverted Repeat ◽  
Genome Structure ◽  
Single Copy ◽  
Flowering Plants ◽  
Automatic Identification ◽  
Inverted Repeats ◽  
Plastid Genomes ◽  
Python Package ◽  
Small Single Copy

Abstract Background In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. Results We introduce , a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using , followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. Conclusion The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg.

Structure and evolution of junctions between inverted repeat and small single copy regions of chloroplast genome in non-core Caryophyllales

2009 ◽  
Vol 43 (5) ◽  
pp. 757-765 ◽  
Author(s):  
M. D. Logacheva ◽  
A. A. Penin ◽  
C. M. Valiejo-Roman ◽  
A. S. Antonov
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Single Copy ◽  
Small Single Copy

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.

scholarly journals Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 405
Author(s):  
Wei Ren ◽  
Dongquan Guo ◽  
Guojie Xing ◽  
Chunming Yang ◽  
Yuanyu Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Inverted Repeat ◽  
Single Copy ◽  
Cyperus Esculentus ◽  
Crop Species ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genome Sequence ◽  
Rna Genes ◽  
Small Single Copy

Cyperus esculentus produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated C. esculentus (var. sativus Boeckeler). The results showed that the complete chloroplast genome of C. esculentus was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of C. esculentus. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four Cyperus species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five Cyperus species within the Cyperaceae formed a clade, and C. esculentus was evolutionarily more related to C. rotundus than to the other three Cyperus species. In summary, the chloroplast genome sequence of the cultivated C. esculentus provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other Cyperus species in the Cyperaceae family.

scholarly journals Complete Plastome Sequence of Ludwigia octovalvis (Onagraceae), a Globally Distributed Wetland Plant

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Shih-Hui Liu ◽  
Christine Edwards ◽  
Peter C. Hoch ◽  
Peter H. Raven ◽  
Janet C. Barber
Keyword(s):  
Inverted Repeat ◽  
Single Copy ◽  
Wetland Plant ◽  
Globally Distributed ◽  
Small Single Copy

Here, we present the first plastome of Ludwigia octovalvis (Onagraceae, Myrtales) as well as the first plastome in the subfamily Ludwigioideae. This genome is notable for its contracted inverted repeat regions and an expanded small single-copy region compared to other species in the orders Myrtales and Geraniales.

scholarly journals Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0142215 ◽  
Author(s):  
Hyoung Tae Kim ◽  
Jung Sung Kim ◽  
Michael J. Moore ◽  
Kurt M. Neubig ◽  
Norris H. Williams ◽  
...  
Keyword(s):  
Gene Family ◽  
Inverted Repeat ◽  
Single Copy ◽  
Small Single Copy

Small single-copy region of plastid DNA in the non-photosynthetic angiosperm Epifagus virginiana contains only two genes

1992 ◽  
Vol 223 (1) ◽  
pp. 95-104 ◽  
Author(s):  
Kenneth H. Wolfe ◽  
Clifford W. Morden ◽  
Jeffrey D. Palmer
Keyword(s):  
Plastid Dna ◽  
Single Copy ◽  
Small Single Copy

scholarly journals The Chloroplast Genome Evolution of Venus Slipper (Paphiopedilum): IR Expansion, SSC Contraction, and Highly Rearranged SSC Regions

2021 ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Genome Structure ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background: Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species. The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum.Results: The plastomes of Paphiopedilum have conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of inverted repeat/small single copy (IR/SSC) boundaries varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates.Conclusions: We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

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