scholarly journals Nucleotide sequence of soybean chloroplast DNA regions which contain thepsbA andtrnH genes and cover the ends of the large single copy region and one end of the inverted repeats

1983 ◽  
Vol 11 (20) ◽  
pp. 7157-7167 ◽  
Author(s):  
Albert Spielmann ◽  
Erhard Stutz
Keyword(s):  
Nucleotide Sequence ◽  
Chloroplast Dna ◽  
Single Copy ◽  
Inverted Repeats ◽  
Large Single Copy ◽  
Chloroplast Dna Regions ◽  
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 Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Robert Lanfear
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Land Plant ◽  
Inverted Repeats ◽  
Equal Frequency ◽  
Large Single Copy ◽  
Chloroplast Genomes ◽  
Long Read ◽  
Small Single Copy ◽  
Large Single Copy Region

AbstractThe chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.Significance StatementChloroplast genome consists of a large single copy region, a small single copy region, and two inverted repeats. Some decades ago, a discovery showed that there are two types chloroplast genome in some plants, which differ the way that the four regions are put together. However, this phenomenon has been shown in just a small number of species, and many open questions remain. Here, we develop a fast method to measure the chloroplast genome structures, based on long-reads. We show that almost all plants we analysed contain two possible genome structures, while a few plants contain only one structure. Our findings hint at the causes of the phenomenon, and provide a convenient new method with which to make rapid progress.

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.

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