Palindromic repeated sequences (PRSs) in the mitochondrial genome of rice: evidence for their insertion after divergence of the genus Oryza from the other Gramineae

1994 ◽  
Vol 24 (2) ◽  
pp. 273-281 ◽  
Author(s):  
Mikio Nakazono ◽  
Akira Kanno ◽  
Nobuhiro Tsutsumi ◽  
Atsushi Hirai
Keyword(s):  
Mitochondrial Genome ◽  
Repeated Sequences ◽  
The Other ◽  
Genus Oryza ◽  
Palindromic Repeated Sequences

Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 944-953 ◽  
Author(s):  
Xinping Zhao ◽  
Gary Kochert
Keyword(s):  
Dna Sequences ◽  
Blot Hybridization ◽  
Rice Genome ◽  
Repeated Sequence ◽  
Repeated Sequences ◽  
Repeated Dna ◽  
Rice Varieties ◽  
Slot Blot Hybridization ◽  
Repeated Dna Sequence ◽  
Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

The Playful Lexicon in the Romance Languages: Prosodic Templates, Onomatopoeia, Reduplication, Clipping, Blending

2020 ◽  
Author(s):  
David Pharies
Keyword(s):  
Lexical Item ◽  
Repeated Sequences ◽  
The Other ◽  
Romance Languages ◽  
Social Convention ◽  
Separate Category ◽  
Semantic Effect ◽  
Full Form ◽  
Per Se ◽  
Lexical Items

A lexical item is described as “playful” or “ludic” when it shows evidence of manipulation of the relation that inheres between its form (signifier) and its meaning (signified). The playful lexicon of any given language, therefore, is the sum total of its lexical items that show signs of such manipulation. Linguists have long recognized that the only necessary link between a word’s form and its meaning is the arbitrary social convention that binds them. However, nothing prevents speakers from creating additional, unnecessary and therefore essentially “playful” links, associating forms with meanings in a symbolic, hence non-arbitrary way. This semantic effect is most evident in the case of onomatopoeia, through which the phonetic form of words that designate sounds is designed to be conventionally imitative of the sound. A second group of playful words combines repeated sequences of sounds with meanings that are themselves suggestive of repetition or related concepts such as collectivity, continuity, or actions in sequence, as well as repeated, back-and-forth, or uncontrolled movements, or even, more abstractly, intensity and hesitation. The playfulness of truncated forms such as clips and blends is based on a still more abstract connection between forms and meanings. In the case of clipping, the truncation of the full form of a word triggers a corresponding connotative truncation or diminution of the meaning, that is, a suggestion that the referent is small—either endearingly, humorously, or contemptuously so. In blending, truncation is often accompanied by overlapping, which symbolically highlights the interrelatedness or juxtaposition of the constituents’ individual meanings. Prosodic templates do not constitute a separate category per se; instead, they may play a part in the formation or alteration of words in any of the other categories discussed here.

scholarly journals MITOCHONDRIAL GENETICS. VI THE PETITE MUTATION IN SACCHAROMYCES CEREVISIAE: INTERRELATIONS BETWEEN THE LOSS OF THE ρ+ FACTOR AND THE LOSS OF THE DRUG RESISTANCE MITOCHONDRIAL GENETIC MARKERS

Genetics ◽  
1974 ◽  
Vol 76 (2) ◽  
pp. 195-219
Author(s):  
J Deutsch ◽  
B Dujon ◽  
P Netter ◽  
E Petrochilo ◽  
P P Slonimski ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Mitochondrial Genome ◽  
Genetic Marker ◽  
Genetic Markers ◽  
The Other ◽  
Mitochondrial Genetics ◽  
Petite Mutation ◽  
Target Theory

ABSTRACT The survival of the ρ+ factor and of DrugR mitochondrial genetic markers after exposure to ethidium bromide has been studied. A technique allowing the determination of DrugR genetic markers among a great number of both grande and petite colonies has been developed. The results have been analyzed by the target theory. The survival of the ρ+ factor is always less than the survival of any DrugR genetic marker. The survivals of CR and ER are similar to each other, while that of OR is greater than that of the other two DrugR markers. All possible combinations of DrugR markers have been found among the ρ- petite cells induced, while the only type found among the grande colonies is the preexisting one. The loss of the CR and ER genetic markers was found to be the most frequently concomitant, while the correlation between the loss of the OR marker and the other two DrugR markers is less strong. Similar results have been obtained after U.V. irradiation. Interpretations concerning the structure of the yeast mitochondrial genome are given and hypotheses on the mechanism of petite mutation discussed.

scholarly journals Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

2018 ◽  
Author(s):  
Xin-Yan Gao ◽  
Yin-Yin Cai ◽  
Dan-Na Yu ◽  
Kenneth B. Storey ◽  
Jia-Yong Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Nucleotide Composition ◽  
The Other ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Duplicated Genes ◽  
Sister Clade ◽  
Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

scholarly journals Mitochondrial sequence diversity reveals the hybrid origin of invasive gibel carp (Carassius gibelio) populations in Hungary

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12441
Author(s):  
Szilvia Keszte ◽  
Arpad Ferincz ◽  
Katalin Tóth-Ihász ◽  
Réka Enikő Balogh ◽  
Ádám Staszny ◽  
...  
Keyword(s):  
Invasive Species ◽  
Mitochondrial Genome ◽  
Carassius Auratus ◽  
The Other ◽  
Hybrid Origin ◽  
Gibel Carp ◽  
Mitochondrial Markers ◽  
D Loop ◽  
Reference Sequences ◽  
Ncbi Blast

Background Invasive gibel carp, Carassius gibelio (Bloch, 1782) has become well-established in the Hungarian waters and now are spreading in the European waters. On major concern now is the potential hybridization between gibel carp and the other invasive species in the Carassius auratus complex (CAC), which may further accelerate the spread of the whole invasive species complex. The identification of gibel carp and their hybrids is difficult because of its morphological similarity to the other species in CAC. Here we carry out a genomic assessment to understand the history of gibel carp invasion and its phylogenetic relationship with the other species in CAC. Three loci of the mitochondrial genome (D-loop, CoI, Cytb) were used to determine the phylogenetic origin of individuals and relarionship among six gibel carp populations and the other species in the CAC. Methodolgy A total of 132 gibel carp samples from six locations in Southern Transdanubia (Hungary) were collected after phenotypic identification to measure the genetic diversity within and among gibel carp populations of Southern Transdanubia (Hungary). The genetic background was examined by the sequences of the mitochondrial genome: D-loop, Cytochrome c oxidase I (CoI) and Cytochrome b (Cytb). Mitochondrial genetic markers are excellent tools for phylogenetic studies because they are maternally inherited. Successfully identified haplotypes were aligned and with reference sequences in nucleotide databases (i.e., NCBI-BLAST: National Centre for Biotechnology Information and BOLD: Barcode of Life Data System). The phylogenetic relationships among gibel carp populations were then analyzed together with the reference sequences to understand the relationship and the level of hybridization with the species in CAC. Results Among the 132 aligned D-loop sequences 22 haplotypes were identified. Further examination of representative individuals of the 22 haplotypes, six Cytb and four CoI sequences were detected. The largest number of haplotypes of all three loci were found in Lake Balaton, the largest shallow lake in Central Europe. Based on the NCBI-BLAST alignment of the D-loop, haplotypes of Carassius auratus auratus and Carassius a. buergeri in CAC were identified in the C. gibelio samples. Further analysis of haplotypes with the other two mitochondrial markers confirmed the occurrence of intragenus hybridization of C. gibelio in the Hungarian waters. Conclusion By using three mitochondrial markers (D-loop, Cytb, CoI), we genomically characterized a gibel carp-complex in Hungarian waters and assessed the C. gibelio phylogenetic status between them. Hybrid origin of locally invasive Carassius taxon was detected in Hungary. It points out that invasive species are not only present in Hungary but reproduce with each other in the waters, further accelerating their spread.

scholarly journals Strategies and difficulties in assembling highly recombinogenic plant organelle genomes: a case study

2015 ◽  
Author(s):  
Concita Cantarella ◽  
Rachele Tamburino ◽  
Nunzia Scotti ◽  
Teodoro Cardi ◽  
Nunzio D'Agostino
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
De Novo ◽  
Sequence Data ◽  
Repeated Sequences ◽  
Read Length ◽  
Plant Mitochondrial Genome ◽  
Sequencing Platform ◽  
Organelle Genomes ◽  
Long Read

Mitochondrial genomes in plants are larger and more complex than in other eukaryotes due to their recombinogenic nature as widely demonstrated. The mitochondrial DNA (mtDNA) is usually represented as a single circular map, the so-called master molecule. This molecule includes repeated sequences, some of which are able to recombine, generating sub-genomic molecules in various amounts, depending on the balance between their recombination and replication rates. Recent advances in DNA sequencing technology gave a huge boost to plant mitochondrial genome projects. Conventional approaches to mitochondrial genome sequencing involve extraction and enrichment of mitochondrial DNA, cloning, and sequencing. Large repeats and the dynamic mitochondrial genome organization complicate de novo sequence assembly from short reads. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality (fewer gaps and longer contigs). However, recently published articles revealed that PacBio sequencing is still not sufficient to address mtDNA assembly-related issues. Here we present a preliminary hybrid assembly of a potato mtDNA based on both PacBio and Illumina reads and debate the strategies and obstacles in assembling genomes containing repeated sequences that are recombinationally active and serve as a constant source of rearrangements.

scholarly journals Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dawei Liu ◽  
Yongwu Zhou ◽  
Yiling Fei ◽  
Chunping Xie ◽  
Senlin Hou
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
The Other ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Recent Estimate ◽  
Maximum Likelihood Methods ◽  
Taxonomic Studies

AbstractHistorically, the diving duck, Baer’s Pochard (Aythya baeri) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of A. baeri has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between A. baeri and the other three Aythya mitochondrial genomes. Among 13 protein-coding genes of the four Aythya species, the fastest-evolving gene was ATP8 while the slowest-evolving gene was COII. Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows: Dendrocygna was an early diverging lineage that was fairly distant from the other ingroup taxa; Cygnus, Branta, and Anser were clustered into one branch that corresponded to the Anserinae subfamily; and Aythya, Asarcornis, Netta, Anas, Mareca, Mergus, Lophodytes, Bucephala, Tadorna, Cairina, and Aix were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other Aythya species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.

scholarly journals A Comparison of Three Circular Mitochondrial Genomes of Fagus sylvatica from Germany and Poland Reveals Low Variation and Complete Identity of the Gene Space

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 571
Author(s):  
Bagdevi Mishra ◽  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Sebastian Ploch ◽  
Jaroslaw Burczyk ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Central Europe ◽  
Glacial Refugia ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Organelle Dna ◽  
Phylogenetic Studies ◽  
Low Degree ◽  
Multiple Copies ◽  
Mitochondrial Sequences

Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.

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