The chloroplast genome of the lichen‐symbiont microalga Trebouxia sp. Tr9 (Trebouxiophyceae, Chlorophyta) shows short inverted repeats with a single gene and loss of the rps4 gene, which is encoded by the nucleus

2019 ◽  
Vol 56 (1) ◽  
pp. 170-184 ◽  
Author(s):  
Fernando Martínez‐Alberola ◽  
Eva Barreno ◽  
Leonardo M. Casano ◽  
Francisco Gasulla ◽  
Arantzazu Molins ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Gene ◽  
Inverted Repeats ◽  
Rps4 Gene

scholarly journals Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Robert Lanfear
Keyword(s):  
Chloroplast Genome ◽  
Genome Structure ◽  
Single Copy ◽  
Land Plant ◽  
Inverted Repeats ◽  
Individual Plant ◽  
Single Individual ◽  
Equal Frequency ◽  
Flip Flop ◽  
Chloroplast Genomes

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.

scholarly journals Evolution of the chloroplast genome

2003 ◽  
Vol 358 (1429) ◽  
pp. 99-107 ◽  
Author(s):  
Christopher J. Howe ◽  
Adrian C. Barbrook ◽  
V. Lila Koumandou ◽  
R. Ellen R. Nisbet ◽  
Hamish A. Symington ◽  
...  
Keyword(s):  
Borrelia Burgdorferi ◽  
Chloroplast Genome ◽  
Genome Organization ◽  
Plastid Genome ◽  
Single Gene ◽  
Selective Advantage ◽  
Nucleotide Composition ◽  
Large Circle ◽  
Nuclear Genomes ◽  
Adenine Thymine

We discuss the suggestion that differences in the nucleotide composition between plastid and nuclear genomes may provide a selective advantage in the transposition of genes from plastid to nucleus. We show that in the adenine, thymine (AT)–rich genome of Borrelia burgdorferi several genes have an AT–content lower than the average for the genome as a whole. However, genes whose plant homologues have moved from plastid to nucleus are no less AT–rich than genes whose plant homologues have remained in the plastid, indicating that both classes of gene are able to support a high AT–content. We describe the anomalous organization of dinoflagellate plastid genes. These are located on small circles of 2–3 kbp, in contrast to the usual plastid genome organization of a single large circle of 100–200 kbp. Most circles contain a single gene. Some circles contain two genes and some contain none. Dinoflagellate plastids have retained far fewer genes than other plastids. We discuss a similarity between the dinoflagellate minicircles and the bacterial integron system.

scholarly journals Gene Loss and Evolution of the Plastome

2020 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Adil Khan ◽  
Abdul Latif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Inverted Repeats ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
Chloroplast Genomes ◽  
Duplication Events

Abstract Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of CDS in the chloroplasts of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) that span across the lineages that comprise algae, bryophytes, pteridophytes, gymnosperm, angiosperms, magnoliids, and protists. Genome-wide analyses revealed that the loss of the Rbcl gene in parasitic and heterotrophic plant species occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; while none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast encoding genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analysed species; suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages. Additionally, our findings support the hypothesis that these recombination events are the most probable cause behind the dynamic loss of chloroplast genes and inverted repeats in different species.

scholarly journals Gene Loss and Evolution of the Plastome

2019 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Adil Khan ◽  
Abdul Latif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Inverted Repeats ◽  
Rbcl Gene ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
Chloroplast Genomes ◽  
Duplication Events

Abstract Chloroplasts are unique organelles within plant cells and are ultimately responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of CDS in the chloroplasts of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) that span across the lineages that comprise algae, bryophytes, pteridophytes, gymnosperm, angiosperms, magnoliids, and protists. Genome-wide analyses revealed that the loss of the RBCL gene in parasitic and heterotrophic plant species occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and RPL21 were found to be characteristic signature genes of chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; while none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast encoding genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analysed species; suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages. Additionally, our findings support the hypothesis that these recombination events are the most probable cause behind the dynamic loss of chloroplast genes and inverted repeats in different species.

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 Assembly of the durian chloroplast genome using long PacBio reads

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jeremy R. Shearman ◽  
Chutima Sonthirod ◽  
Chaiwat Naktang ◽  
Duangjai Sangsrakru ◽  
Thippawan Yoocha ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Complete Sequence ◽  
Inverted Repeats ◽  
Direct Repeats ◽  
Durio Zibethinus ◽  
Chloroplast Genomes ◽  
Long Reads

Abstract We have assembled the complete sequence of the Durio zibethinus chloroplast genome using long PacBio reads. Durian is a valuable commercial tree that produces durian fruit, which is popular in Southeast Asia. The chloroplast genome assembled into a single 143 kb cyclic contig that contained 111 genes. There were 46 short direct repeats (45 to 586 bp) and five short inverted repeats (63 to 169 bp). The long reads that were used for the assembly span the entire chloroplast with > 10 kb overlaps and multiple long reads join the start of the contig to the end of the contig. The durian chloroplast was found to lack the large inverted repeat that is common in chloroplast genomes. An additional 24 durian varieties were sequenced and compared to the assembly and found to also lack the large inverted repeat. There were nine SNPs among the varieties.

scholarly journals Peculiarities of the inverted repeats in the complete chloroplast genome of Strobilanthes bantonensis Lindau

2021 ◽  
Vol 6 (4) ◽  
pp. 1440-1447
Author(s):  
Wuwei Wu ◽  
Jingling Li ◽  
Yu Liu ◽  
Mei Jiang ◽  
Mingsheng Lan ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeats ◽  
Complete Chloroplast Genome
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