scholarly journals Repeats Of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

2018 ◽  
Author(s):  
Emily L. Wynn ◽  
Alan C. Christensen
Keyword(s):  
Tandem Repeats ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Interesting Difference ◽  
Adaptive Explanation ◽  
Functional Classes ◽  
Size Groups ◽  
Strand Breakage ◽  
Mitochondrial Sequences ◽  
Dna Maintenance

AbstractPlant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have non-tandem repeats in two size groups: a few large repeats which cause isomerization of the genome by recombination, and numerous repeats longer than 50bp, often found in exactly two copies per genome. It appears that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats are not well-conserved between species, and are infrequently annotated in mitochondrial sequence assemblies. Because they are much larger than expected by chance we call them Repeats Of Unusual Size (ROUS). The repeats consist of two functional classes, those that are involved in genome isomerization through frequent crossing over, and those for which crossovers are rare unless there are mutations in DNA repair genes, or the rate of double-strand breakage is increased. We systematically described and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find non-tandem repeats and analyzed the complete mitochondrial sequences from 135 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss, and the repeats are included in these events. We suggest an adaptive explanation for the existence of the repeats and their evolution.

Numt identification and removal with RtN!

2020 ◽  
Vol 36 (20) ◽  
pp. 5115-5116 ◽  
Author(s):  
August E Woerner ◽  
Jennifer Churchill Cihlar ◽  
Utpal Smart ◽  
Bruce Budowle
Keyword(s):  
Mitochondrial Genome ◽  
Massively Parallel Sequencing ◽  
Sequence Similarity ◽  
Variant Calling ◽  
Supplementary Information ◽  
Mitochondrial Genomes ◽  
Sequencing Data ◽  
Read Mapping ◽  
Genome Data ◽  
Mitochondrial Sequences

Abstract Motivation Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling. Results Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures. Availability and implementation https://github.com/Ahhgust/RtN Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals New Frontiers inSchistosomaGenomics and Transcriptomics

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Laila A. Nahum ◽  
Marina M. Mourão ◽  
Guilherme Oliveira
Keyword(s):  
Large Scale ◽  
Biological Research ◽  
Mitochondrial Genomes ◽  
Future Directions ◽  
Important Species ◽  
Blood Flukes ◽  
Causative Agents ◽  
Mitochondrial Sequences ◽  
Modern Technologies

Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium,S. japonicum, andS. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of sixSchistosomaspecies have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization ofSchistosomagenomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.

Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce

2001 ◽  
Vol 10 (1) ◽  
pp. 257-263 ◽  
Author(s):  
C. Sperisen ◽  
U. Buchler ◽  
F. Gugerli ◽  
G. Matyas ◽  
T. Geburek ◽  
...  
Keyword(s):  
Norway Spruce ◽  
Population Differentiation ◽  
Tandem Repeats ◽  
Mitochondrial Genomes

scholarly journals Organization and closing of mitochondrial deoxyribonucleic acid from Paramecium tetraaurelia and Paramecium primaurelia.

1981 ◽  
Vol 1 (11) ◽  
pp. 972-982 ◽  
Author(s):  
D J Cummings ◽  
J L Laping
Keyword(s):  
Ribosomal Rna ◽  
Deoxyribonucleic Acid ◽  
Recombinant Dna ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Ribosomal Rna Gene ◽  
Ribosomal Ribonucleic Acid ◽  
Linear Mitochondrial Genome ◽  
Rna Genes ◽  
Restriction Enzyme Maps

Previously we showed that the mitochondrial deoxyribonucleic acid (DNA) from Paramecium aurelia consists of a linear genome and that replication of this genome is initiated at one terminus and proceeds unidirectionally to the other terminus. Analyses of mitochondria from four closely related species (1, 4, 5, and 7) indicated that the species 1, 5, and 7 DNAs are essentially completely homologous but that the species 4 mitochondrial DNA is only 40 to 50% homologous with that from species 1. The major regions of homology are those containing the genes for ribosomal ribonucleic acid (RNA). To understand the replication and organization of the linear mitochondrial genome better, we compared species 1 (Paramecium primaurelia) and 4 (Paramecium tetraaurelia) DNAs with regard to restriction fragment mapping and homology between initiation regions; we also identified the sites of the genes for ribosomal RNA. In general, the structures of the species 1 and 4 mitochondrial genomes were quite similar. Each ribosomal RNA gene was present in one copy per genome, with the large ribosomal RNA gene located near the terminal region of replication and the small ribosomal RNA gene located more centrally. These two genes were separated by about 10 kilobases in the species 1 genome and by about 12 kilobases in the species 4 genome. In contrast to our previous findings, by using nonstringent hybridization conditions we detected homology between the species 1 and 4 DNA fragments containing the initiation regions. We constructed recombinant DNA clones for many fragments, especially those containing the initiation region and the ribosomal RNA genes. We also constructed restriction enzyme maps for six enzymes for both P. primaurelia and P. tetraaurelia.

scholarly journals Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

2018 ◽  
Author(s):  
Ji Haishuo ◽  
Xu Xiaofeng ◽  
Jin Xiufeng ◽  
Cheng Zhi ◽  
jin Hong ◽  
...  
Keyword(s):  
Steady State ◽  
High Resolution ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Transcription Initiation ◽  
Tandem Repeats ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Small Rna Sequencing ◽  
Antisense Gene

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. Most of the new annotations were consistent with the previous annotations which were obtained using PacBio full-length transcripts. Two important findings are that animals transcribe both entire strands of mitochondrial genomes and the tandem repeat in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the H-strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, enriching the fundamental knowledge of mitochondrial biology. This sRNA-seq based method uses 5′ and 3′ end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution and can also be used to identify new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). Animal mitochondrial genomes containing one control region only encode two steady-state lncRNAs, which are the Mitochondrial D-loop 1 (MDL1) and its antisense gene (MDL1AS), while all other reported mitochondrial lncRNAs could be degraded fragments of transient RNAs or random breaks during experimental processing. The high-resolution annotations of mitochondrial genomes can be used to study the phylogenetics and molecular evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

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.

The complete mitochondrial DNA genome of Eremias brenchleyi (Reptilia: Lacertidae) and its phylogeny position within squamata reptiles

2009 ◽  
Vol 30 (1) ◽  
pp. 25-35 ◽  
Author(s):  
Liuwang Nie ◽  
Yuting Wang ◽  
Jinlong Rui
Keyword(s):  
Mitochondrial Dna ◽  
Tandem Repeats ◽  
Bootstrap Support ◽  
Phylogenetic Study ◽  
Mtdna Sequence ◽  
High Bootstrap ◽  
Mitochondrial Sequences ◽  
Relationship Of ◽  
Internal Relationships ◽  
Typical Vertebrate

AbstractSquamata is the most diversified reptilian order that has been traditionally classified into three suborders – Lacertilia, Serpentes and Amphisbaenia in which Lacertilia have about 16-19 families. But the phylogenetic relationships among major groups of Lacertilia remain controversial. In this paper, the complete mitochondrial DNA sequence of Eremias brenchleyi was determined by using long-and-accurate PCR (LA-PCR). The mtDNA sequence is 19 542 bp, making it the longest mitochondrial genome in squamates species reported so far. It shows the typical vertebrate arrangement of genes. The control region of E. brenchleyi was characterized by two conspicuous 65 bp and 56 bp tandem repeats at its 5′ and 3′ terminus respectively. In order to study the higher level relationships of squamates, the phylogenetic study including all currently available squamates mitochondrial sequences was carried out. We obtained a relationship of 16 families of lizards (Lacertidae, Scincidae, Iguanidae, Chameleonidae, Agamidae, Trogonophidae, Bipedidae, Shinisauridae, Helodermatidae, Amphisbaenidae, Gekkonidae, Varanidae, Anguidae, Xantusiidae, Rhineuridae, Cordylidae) and 8 families of Serpentes. The internal relationships within this group yielded high bootstrap support and were more congruent with morphological analyses.

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