scholarly journals Small, Repetitive DNAs Contribute Significantly to the Expanded Mitochondrial Genome of Cucumber

Genetics ◽  
2001 ◽  
Vol 159 (1) ◽  
pp. 317-328
Author(s):  
Jason W Lilly ◽  
Michael J Havey
Keyword(s):  
Mitochondrial Genome ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Dot Blot ◽  
Replication Slippage ◽  
Repetitive Dnas ◽  
Dna Motifs ◽  
Coding Regions ◽  
Strong Hybridization ◽  
Mitochondrial Sequences

Abstract Closely related cucurbit species possess eightfold differences in the sizes of their mitochondrial genomes. We cloned mitochondrial DNA (mtDNA) fragments showing strong hybridization signals to cucumber mtDNA and little or no signal to watermelon mtDNA. The cucumber mtDNA clones carried short (30–53 bp), repetitive DNA motifs that were often degenerate, overlapping, and showed no homology to any sequences currently in the databases. On the basis of dot-blot hybridizations, seven repetitive DNA motifs accounted for >13% (194 kb) of the cucumber mitochondrial genome, equaling >50% of the size of the Arabidopsis mitochondrial genome. Sequence analysis of 136 kb of cucumber mtDNA revealed only 11.2% with significant homology to previously characterized mitochondrial sequences, 2.4% to chloroplast DNA, and 15% to the seven repetitive DNA motifs. The remaining 71.4% of the sequence was unique to the cucumber mitochondrial genome. There was <4% sequence colinearity surrounding the watermelon and cucumber atp9 coding regions, and the much smaller watermelon mitochondrial genome possessed no significant amounts of cucumber repetitive DNAs. Our results demonstrate that the expanded cucumber mitochondrial genome is in part due to extensive duplication of short repetitive sequences, possibly by recombination and/or replication slippage.

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

2017 ◽  
Vol 152 (3) ◽  
pp. 148-157 ◽  
Author(s):  
Larisa S. Biltueva ◽  
Dimitry Y. Prokopov ◽  
Alexey I. Makunin ◽  
Alexey S. Komissarov ◽  
Anna V. Kudryavtseva ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Repetitive Sequences ◽  
Satellite Dnas ◽  
Repetitive Dnas ◽  
Acipenser Ruthenus ◽  
Isolation And Characterization ◽  
And Cluster Analysis ◽  
Cryptic Sex ◽  
Sterlet Acipenser Ruthenus

Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.

The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 252-257 ◽  
Author(s):  
Xiaobing Wu ◽  
Tao Zheng ◽  
Zhigang Jiang ◽  
Lei Wei
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Protein Coding ◽  
Acinonyx Jubatus ◽  
Clouded Leopard ◽  
Coding Regions ◽  
Neofelis Nebulosa ◽  
Complete Mitochondrial Genomes

The complete 16 844 bp mitochondrial genome of Neofelis nebulosa has been sequenced and compared with the complete mitochondrial genomes of Felis catus and the Acinonyx jubatus . The base composition of the mitochondrial genome of N. nebulosa is as follows: A, 5343 bp (31.7%); C, 4441 bp (26.4%); G, 2491 bp (14.8%); T, 4569 bp (27.1%). The genome complement and the gene order of this mitochondrial genome was found to be typical of those reported for other mammals. Several unusual features of this genome, however, were found. First, in protein-coding regions, AT bias in the genome was not prevalent in the third position of codons, as it is in most other mammals, but was found in the second position of codons. Second, in tRNA regions, tRNASer (AGY), which lacked the “DHU” arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, no repetitive sequences (RS)-2 were found. However, RS-2 repetitive motifs usually occurr in the control regions of most great cats. In addition, 4 variable sites were found in CSB-3 of the control region. Fourth, AT content in the control region of the mtDNA from the clouded leopard was lower than it is in other regions.

A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 299-307 ◽  
Author(s):  
Grzegorz Bartoszewski ◽  
Piotr Gawronski ◽  
Marek Szklarczyk ◽  
Henk Verbakel ◽  
Michael J. Havey
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Physical Map ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Bac Contig ◽  
Repetitive Dnas ◽  
Dna Motifs

Cucumber ( Cucumis sativus ) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 bp repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression.

Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 565-576 ◽  
Author(s):  
Jeffrey L. Bennetzen ◽  
Kathrin Schrick ◽  
Patricia S. Springer ◽  
Willis E. Brown ◽  
Phillip SanMiguel
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Copy Number ◽  
Repetitive Sequences ◽  
Restriction Enzymes ◽  
Single Copy ◽  
Chromosomal Dna ◽  
Coding Regions ◽  
Highly Repetitive Dna ◽  
Copy Dna

We have characterized the copy number, organization, and genomic modification of DNA sequences within and flanking several maize genes. We found that highly repetitive DNA sequences were tightly linked to most of these genes. The highly repetitive sequences were not found within the coding regions but could be found within 6 kb either 3′ or 5′ to the structural genes. These highly repetitive regions were each composed of unique combinations of different short repetitive sequences. Highly repetitive DNA blocks were not interrupted by any detected single copy DNA. The 13 classes of highly repetitive DNA identified were found to vary little between diverse Zea isolates. The level of DNA methylation in and near these genes was determined by scoring the digestibility of 63 recognition/cleavage sites with restriction enzymes that were sensitive to 5-methylation of cytosines in the sequences 5′-CG-3′ and 5′-CNG-3′. All but four of these sites were digestible in chromosomal DNA. The four undigested sites were localized to extragenic DNA within or near highly repetitive DNA, while the other 59 sites were in low copy number DNAs. Pulsed field gel analysis indicated that the majority of cytosine modified tracts range from 20 to 200 kb in size. Single copy sequences hybridized to the unmodified domains, while highly repetitive sequences hybridized to the modified regions. Middle repetitive sequences were found in both domains.Key words: genome organization, interspersed repetitive DNA, DNA modification.

scholarly journals Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal

2019 ◽  
Vol 17 (04) ◽  
pp. 386-389
Author(s):  
Miguel Bento ◽  
Sónia Gomes Pereira ◽  
Wanda Viegas ◽  
Manuela Silva
Keyword(s):  
Durum Wheat ◽  
Repetitive Sequences ◽  
Inter Simple Sequence Repeat ◽  
Wheat Breeding ◽  
Genomic Diversity ◽  
Varietal Diversity ◽  
Wheat Varieties ◽  
Coding Sequences ◽  
Coding Regions ◽  
High Level

AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in one variety. Contrastingly, molecular markers targeting repetitive elements like microsatellites and retrotransposons – Inter Simple Sequence Repeat (ISSR) and Inter Retrotransposons Amplified Polymorphism (IRAP) – disclosed significant inter and intra-varietal diversity. This high level of polymorphism was revealed by the 20 distinct ISSR/IRAP concatenated profiles observed among the 23 individuals analysed. Interestingly, median joining networks and PCoA analysis grouped individuals of the same variety and clustered varieties accordingly with geographical origin. Globally, this work demonstrates that durum wheat breeding strategies induced selection pressure for some relevant coding sequences while maintaining high levels of genomic variability in non-coding regions enriched in repetitive sequences.

scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
Author(s):  
Vaclav Brazda ◽  
Miroslav Fojta ◽  
Richard P. Bowater
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Repetitive Sequences ◽  
Biological Significance ◽  
Human Diseases ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Diverse Range ◽  
Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

scholarly journals MysTR: an Endogenous Retrovirus Family in Mammals That Is Undergoing Recent Amplifications to Unprecedented Copy Numbers

2005 ◽  
Vol 79 (23) ◽  
pp. 14698-14707 ◽  
Author(s):  
Michael A. Cantrell ◽  
Martina M. Ederer ◽  
Issac K. Erickson ◽  
Vicki J. Swier ◽  
Robert J. Baker ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
South American ◽  
Coding Regions ◽  
Copy Numbers ◽  
Species Analysis ◽  
Outgroup Species ◽  
Mammalian Genomes ◽  
Oryzomys Palustris

ABSTRACT A large percentage of the repetitive elements in mammalian genomes are retroelements, which have been moved primarily by LINE-1 retrotransposons and endogenous retroviruses. Although LINE-1 elements have remained active throughout the mammalian radiation, specific groups of endogenous retroviruses generally remain active for comparatively shorter periods of time. Identification of an unusual extinction of LINE-1 activity in a group of South American rodents has opened a window for examination of the interplay in mammalian genomes between these ubiquitous retroelements. In the course of a search for any type of repetitive sequences whose copy numbers have substantially changed in Oryzomys palustris, a species that has lost LINE-1 activity, versus Sigmodon hispidus, a closely related species retaining LINE-1 activity, we have identified an endogenous retrovirus family differentially amplified in these two species. Analysis of three full-length, recently transposed copies, called mysTR elements, revealed gag, pro, and pol coding regions containing stop codons which may have accumulated either before or after retrotransposition. Isolation of related sequences in S. hispidus and the LINE-1 active outgroup species, Peromyscus maniculatus, by PCR of a pro-pol region has allowed determination of copy numbers in each species. Unusually high copy numbers of approximately 10,000 in O. palustris versus 1,000 in S. hispidus and 4,500 in the more distantly related P.maniculatus leave open the question of whether there is a connection between endogenous retrovirus activity and LINE-1 inactivity. Nevertheless, these independent expansions of mysTR represent recent amplifications of this endogenous retrovirus family to unprecedented levels.

A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 138-142 ◽  
Author(s):  
Michael S. Zwick ◽  
Robert E. Hanson ◽  
M. Nurul Islam-Faridi ◽  
David M. Stelly ◽  
Rod A. Wing ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Copy Number ◽  
Genomic Dna ◽  
Mammalian Species ◽  
Repetitive Dnas ◽  
Rapid Procedure ◽  
Dna Elements ◽  
Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

A porcine brain-wide RNA editing landscape

2020 ◽  
Author(s):  
Jinrong Huang ◽  
Lin Lin ◽  
Zhanying Dong ◽  
Ling Yang ◽  
Tianyu Zheng ◽  
...  
Keyword(s):  
Rna Editing ◽  
Repetitive Sequences ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Protein Coding ◽  
Porcine Brain ◽  
Coding Regions ◽  
Pig Brain ◽  
Genome Wide ◽  
A Genome

Abstract Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. The porcine brain-wide RNA landscape provides a rich resource to better understand the evolutionally importance of post-transcriptional RNA editing.

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