Detection of CRISPR cassettes and cas genes in the Arabidopsis thaliana genome

The state of the art in the evolution of plant viruses allows the genetic foundations of antiviral immunity in higher (including the most important crops) plants to be categorized as one of the most pressing issues of genetics and selection. According to the endosymbiotic theory, mitochondria descended from alphaproteobacteria that had been absorbed but not degraded by the host cell. The discovery of CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins), which implement the adaptive immunity function in prokaryotes, raises the question whether such a mechanism of antiviral protection could be caught up by evolution and used by representatives of eukaryotes (in particular, plants). The purpose of this work was to analyze the complete sequences of nuclear, mitochondrial, and chloroplast genomes of Arabidopsis thaliana in order to search for genetic elements similar to those in CRISPR-Cas systems of bacteria and archaea. As a result, in silico methods helped us to detect a locus of regularly intermittent short direct repeats in the mitochondrial genome of A. thaliana ecotypes. The structure of this locus corresponds to the CRISPR locus of the prokaryotic adaptive antiviral immune system. The probable connection between the locus found in the mitochondrial genome of the higher plant and the function of adaptive immunity is indicated by a similarity between the spacer sequences in the CRISPR cassette found and the genome of Cauliflower mosaic virus affecting Arabidopsis plants. Sequences of repeats and spacers of CRISPR cassettes in Arabidopsis C24 and Ler lines are perfectly identical. However, the locations of the CRISPR locus in the mitochondrial genomes of these lines differ significantly. The CRISPR cassette in the Col-0 line was found to be completely broken as a result of four deletions and one insertion. Although cas genes were not detected in the mitochondrial genome of the studied Arabidopsis ecotypes, their presence was detected in the nuclear genome. Both cas genes and numerous CRISPR cassettes were found on all the five chromosomes in the nuclear genome of the Col-0 ecotype. The results suggest the existence of a system of adaptive immunity in plants, which is similar to the CRISPR immunity of bacteria and archaea.

Download Full-text

copia-, gypsy- and LINE-Like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/142.2.579 ◽

1996 ◽

Vol 142 (2) ◽

pp. 579-585 ◽

Cited By ~ 3

Author(s):

Volker Knoop ◽

Michael Unseld ◽

Joachim Marienfeld ◽

Petra Brandt ◽

Sabine Sünkel ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Mitochondrial Genome ◽

Evolutionary History ◽

Nuclear Genome ◽

Plant Mitochondrial Genome ◽

Gypsy Group ◽

History Of

Abstract Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Tyl/copia, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover ≥5% of the mitochondrial genome in Arabidopsis.

Download Full-text

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

Genome ◽

10.1139/gen-2012-0153 ◽

2013 ◽

Vol 56 (4) ◽

pp. 187-193 ◽

Cited By ~ 6

Author(s):

Mai Tsujimura ◽

Naoki Mori ◽

Hiroshi Yamagishi ◽

Toru Terachi

Keyword(s):

Mitochondrial Genome ◽

Nuclear Genome ◽

Mitochondrial Genomes ◽

Chloroplast Microsatellite ◽

Wheat Evolution ◽

Closely Related Species ◽

Genome Type ◽

Sequence Characterized Amplified Region ◽

Chloroplast Genomes ◽

Different Types

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence–absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

Download Full-text

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

BMC Genomics ◽

10.1186/s12864-021-07967-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhou Hong ◽

Xuezhu Liao ◽

Yuanjun Ye ◽

Ningnan Zhang ◽

Zengjiang Yang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Networks ◽

Complete Mitochondrial Genome ◽

Genome Structure ◽

Nuclear Genome ◽

Trna Genes ◽

Important Species ◽

Comparative Analyses ◽

Chloroplast Genomes ◽

Dalbergia Odorifera

Abstract Background Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. Results We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. Conclusion For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

Download Full-text

Identification and Validation of Reference Genes for Normalization of Transcripts from Virus-Infected Arabidopsis thaliana

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-10-0236 ◽

2011 ◽

Vol 24 (3) ◽

pp. 294-304 ◽

Cited By ~ 65

Author(s):

S. T. Lilly ◽

R. S. M. Drummond ◽

M. N. Pearson ◽

R. M. MacDiarmid

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Mosaic Virus ◽

Reference Genes ◽

Quantitative Polymerase Chain Reaction ◽

Plant Viruses ◽

Cauliflower Mosaic Virus ◽

Yellow Mosaic Virus ◽

Complementary Dna ◽

Family Protein

Real-time quantitative polymerase chain reaction (qPCR) of complementary DNA is now a standard method for studies of gene expression. However, qPCR can identify genuine variation only when transcript quantities are accurately normalized to an appropriate reference. To identify the most reliable reference genes for transcript quantification by qPCR, we describe a systematic evaluation of candidate reference genes of Arabidopsis thaliana ecotype Columbia-0 (Col-0). Twelve genes were selected for transcript stability studies by qPCR of complementary DNA prepared from Arabidopsis leaf tissue infected with one of five plant viruses (Cauliflower mosaic virus, Tobacco mosaic virus, Tomato spotted wilt virus, Turnip mosaic virus, and Turnip yellow mosaic virus). The F-box family protein, elongation factor 1-α, sand family protein, and protodermal factor 2 gene transcripts showed the most stable accumulation, whereas a traditionally used reference gene, Actin8, showed the least stable accumulation as measured by the geNorm algorithm. The data furnish plant virologists with reference genes for normalization of qPCR-derived gene expression in virus-infected Arabidopsis and will be beneficial to the selection and design of primers targeting orthologous genes in other plant species.

Download Full-text

Antisense Inhibition of the PsbX Protein Affects PSII Integrity in the Higher Plant Arabidopsis thaliana

Plant and Cell Physiology ◽

10.1093/pcp/pcn188 ◽

2008 ◽

Vol 50 (2) ◽

pp. 191-202 ◽

Cited By ~ 16

Author(s):

José G. García-Cerdán ◽

Dmitry Sveshnikov ◽

David Dewez ◽

Stefan Jansson ◽

Christiane Funk ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Antisense Inhibition ◽

Higher Plant ◽

Plant Arabidopsis Thaliana

Download Full-text

Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

BMC Genomics ◽

10.1186/s12864-021-07544-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shizhuo Xiao ◽

Pan Xu ◽

Yitong Deng ◽

Xibin Dai ◽

Lukuan Zhao ◽

...

Keyword(s):

Comparative Analysis ◽

Genetic Structure ◽

Chloroplast Genome ◽

Wild Species ◽

Ipomoea Batatas ◽

Nuclear Genome ◽

Ipomoea Trifida ◽

Chloroplast Markers ◽

Chloroplast Genomes ◽

Chloroplast Dna Markers

Abstract Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

Download Full-text

Mitochondrial DNA Methylation and Human Diseases

International Journal of Molecular Sciences ◽

10.3390/ijms22094594 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4594

Author(s):

Andrea Stoccoro ◽

Fabio Coppedè

Keyword(s):

Dna Methylation ◽

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Nuclear Genome ◽

Epigenetic Modifications ◽

Human Diseases ◽

Loop Region ◽

D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

Download Full-text

Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum

Genome ◽

10.1139/g98-123 ◽

1999 ◽

Vol 42 (2) ◽

pp. 237-247 ◽

Cited By ~ 24

Author(s):

Ted HM Mes ◽

Reinhard M Fritsch ◽

Sven Pollner ◽

Konrad Bachmann

Keyword(s):

Concerted Evolution ◽

Morphological Evolution ◽

Restriction Analysis ◽

Nuclear Genome ◽

Restriction Enzymes ◽

Border Region ◽

Chloroplast Genomes ◽

Central Asian ◽

Its Regions ◽

Chloroplast Haplotypes

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.Key words: polymorphic, phylogeny, restriction analysis.

Download Full-text