The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families

1997 ◽  
Vol 31 (5) ◽  
pp. 419-429 ◽  
Author(s):  
M. E. Cosner ◽  
Robert K. Jansen ◽  
Jeffrey D. Palmer ◽  
Stephen R. Downie
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Repeat Expansion

Recombination within the inverted repeat sequences of the Chlamydomonas reinhardii chloroplast genome produces two orientation isomers

1985 ◽  
Vol 9 (3) ◽  
pp. 233-238 ◽  
Author(s):  
Jane Aldrich ◽  
Barry Cherney ◽  
Ellis Merlin ◽  
Charlotte Williams ◽  
Laurens Mets
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Chlamydomonas Reinhardii ◽  
Repeat Sequences

scholarly journals Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 61 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ngan Tran ◽  
Thanh-Diem Nguyen ◽  
Quoc-Luan Vu ◽  
My-Huyen Bui ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Critically Endangered Species ◽  
Plastid Genomes ◽  
Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

scholarly journals The complete chloroplast genome of an inverted-repeat-lacking species, Vicia sepium, and its phylogeny

2018 ◽  
Vol 3 (1) ◽  
pp. 137-138 ◽  
Author(s):  
Chaoyang Li ◽  
Yunlin Zhao ◽  
Huimin Huang ◽  
Yi Ding ◽  
Yinhui Hu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Complete Chloroplast Genome ◽  
Its Phylogeny

scholarly journals Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Samaila S. Yaradua ◽  
Dhafer A. Alzahrani ◽  
Enas J. Albokhary ◽  
Abidina Abba ◽  
Abubakar Bello
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

scholarly journals The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

2012 ◽  
Vol 4 (3) ◽  
pp. 374-381 ◽  
Author(s):  
Ching-Ping Lin ◽  
Chung-Shien Wu ◽  
Ya-Yi Huang ◽  
Shu-Miaw Chaw
Keyword(s):  
Chloroplast Genome ◽  
Ginkgo Biloba ◽  
Inverted Repeat ◽  
Complete Chloroplast Genome
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