Twintrons are not unique to the Euglena chloroplast genome: structure and evolution of a plastome cpn60 gene from a cryptomonad

Abstract The 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.

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Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Agronomy ◽

10.3390/agronomy8090159 ◽

2018 ◽

Vol 8 (9) ◽

pp. 159 ◽

Cited By ~ 4

Author(s):

Xiaojun Nie ◽

Xian Zhao ◽

Sue Wang ◽

Ting Zhang ◽

Chong Li ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Panicum Virgatum ◽

Genome Structure ◽

Structural Features ◽

Panicum Miliaceum ◽

Genomic Knowledge ◽

Broomcorn Millet ◽

Evolutionary Studies ◽

Cp Genome

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

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Chloroplast genome structure and phylogeny of Spiranthes sinensis, an endangered medicinal orchid plant

Mitochondrial DNA Part B ◽

10.1080/23802359.2019.1664345 ◽

2019 ◽

Vol 4 (2) ◽

pp. 2994-2996 ◽

Cited By ~ 1

Author(s):

Jing Fan ◽

Ming-Yuan Huang

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Spiranthes Sinensis ◽

Medicinal Orchid

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Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis

Tree Genetics & Genomes ◽

10.1007/s11295-012-0469-8 ◽

2012 ◽

Vol 8 (4) ◽

pp. 841-854 ◽

Cited By ~ 47

Author(s):

Shingo Terakami ◽

Yuichiro Matsumura ◽

Kanako Kurita ◽

Hiroyuki Kanamori ◽

Yuichi Katayose ◽

...

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Genome Structure ◽

Complete Sequence ◽

Pyrus Pyrifolia

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The complete chloroplast genome of Lilium cernuum: genome structure and evolution

Conservation Genetics Resources ◽

10.1007/s12686-016-0562-7 ◽

2016 ◽

Vol 8 (4) ◽

pp. 375-378 ◽

Cited By ~ 8

Author(s):

Yunpeng Du ◽

Yu Bi ◽

Xuqing Chen ◽

Fengping Yang ◽

Jing Xue ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Complete Chloroplast Genome

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Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

10.1101/655241 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ting Yang ◽

Xuezhu Liao ◽

Lingxiao Yang ◽

Yang Liu ◽

Weixue Mu ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Strong Support ◽

Gc Content ◽

Taxon Sampling ◽

Data Sets ◽

Green Plants ◽

Comparative Analyses ◽

Chloroplast Genomes ◽

The Matrix

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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