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.

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 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 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 Primer designing strategy for amplification and sequencing of the complete mitochondrial genome of Semnopithecus hypoleucos

2021 ◽  
Author(s):  
Vipin Hiremath ◽  
Chandrakant Jadhav ◽  
Gulab Khedkar
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Primate Species ◽  
Mitochondrial Genomes ◽  
Evolutionary Analysis ◽  
Closely Related Species ◽  
Design And Optimization ◽  
Genome Data ◽  
Phylogenetic Studies ◽  
Conserved Gene

Abstract The mitochondrial genome is highly informative for evolutionary analysis of organism lineages and phylogenetic studies. The availability of robust primers for amplifying complete mitochondrial genomes is a crucial step in current mitogenome studies. However, organism specific characteristics such as variable transition to transversion substitution ratios seen in some groups pose challenges for the development of universal, or at least broadly applicable, primer pairs for this purpose. This study reports on a strategy of primer design and optimization (PDO) where regions of known mtDNA genescan be used for choosing primers for amplification, sequencing and assembly of entire mitochondrial genomes of several closely-related species. In brief, taking advantage of the circular organization of mtDNA, primers are first designed for amplification of “long” products using the 5’ region of one conserved gene and a 3’region from another conserved gene. Additional primers are then used to amplify “short” regions to fill in gaps to allow for complete assembly of the genome. We show how we were able to use this approach to successfully amplify entire mitochondrial genomes from a non-human primate species (Semnopithecus hypoleucos), and also how this provided data useful for annotation of the assembled genome data.

scholarly journals The mitochondrial genomes of the acoelomorph worms Paratomella rubra and Isodiametra pulchra

2017 ◽  
Author(s):  
Helen E Robertson ◽  
François Lapraz ◽  
Bernhard Egger ◽  
Maximilian J Telford ◽  
Philipp H. Schiffer
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Large Degree ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Long Branch Attraction ◽  
Protein Coding ◽  
Simple Body ◽  
Mitochondrial Sequences ◽  
Marine Worms

AbstractAcoels are small, ubiquitous, but understudied, marine worms with a very simple body plan. Their internal phylogeny is still in parts unresolved, and the position of their proposed phylum Xenacoelomorpha (Xenoturbella+Acoela) is still debated.Here we describe mitochondrial genome sequences from two acoel species: Paratomella rubra and Isodiametra pulchra. The 14,954 nucleotide-long P. rubra sequence is typical for metazoans in size and gene content. The larger I. pulchra mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome.Mitochondrial sequences for both P. rubra and I. pulchra have a unique genome organisation in comparison to other published metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap in P. rubra, with little non-coding sequence making the genome compact. Conversely, the I. pulchra mitochondrial genome has many long non-coding sequences between genes, likely driving the genome size expansion. Phylogenetic trees inferred from concatenated alignments of mitochondrial genes grouped the fast-evolving Acoela and Tunicata, almost certainly due to the systematic error of long branch attraction: a reconstruction artefact that is probably compounded by the fast substitution rate of mitochondrial genes in this taxon.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

2021 ◽  
Author(s):  
Shu-Tong Dai ◽  
Dian-Xing Feng ◽  
Da-Peng Sun
Keyword(s):  
Mitochondrial Genome ◽  
Species Identification ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

scholarly journals Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1306 ◽  
Author(s):  
St. John
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Genome ◽  
Cell Fate ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Epigenetic Regulators ◽  
And Function ◽  
Effective Function

It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.

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

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5914 ◽  
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 Suhpalacsa longialata (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 Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

scholarly journals A battle for transmission: the cooperative and selfish animal mitochondrial genomes

Open Biology ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 180267 ◽  
Author(s):  
Anna Klucnika ◽  
Hansong Ma
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Energy Production ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Cellular Processes ◽  
Mitochondrial Replacement Therapy ◽  
Mtdna Evolution ◽  
Organismal Fitness

The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.

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