scholarly journals Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248054
Author(s):  
Jaqueline Raquel de Almeida ◽  
Diego Mauricio Riaño Pachón ◽  
Livia Maria Franceschini ◽  
Isaneli Batista dos Santos ◽  
Jessica Aparecida Ferrarezi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Transmembrane Protein ◽  
Genome Structure ◽  
Rust Fungi ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
The Core ◽  
Mtdna Sequence ◽  
Austropuccinia Psidii

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

scholarly journals Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

2019 ◽  
Author(s):  
Shaun D. Jackman ◽  
Lauren Coombe ◽  
René L. Warren ◽  
Heather Kirk ◽  
Eva Trinh ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Active Sites ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Sitka Spruce ◽  
Physical Structure ◽  
Picea Sitchensis ◽  
Mitochondrial Genomes ◽  
Long Reads ◽  
Branching Points

AbstractPlant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), the largest complete mitochondrial genome of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

scholarly journals Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod

2022 ◽  
Vol 9 (1) ◽  
Author(s):  
William S. Pearman ◽  
Sarah J. Wells ◽  
James Dale ◽  
Olin K. Silander ◽  
Nikki E. Freed
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Dna Sequencing ◽  
Recent Work ◽  
Genome Structure ◽  
Mitochondrial Genomes ◽  
Short Read ◽  
Mitochondrial Structure ◽  
Evolutionary Origins ◽  
Long Read

Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda , species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda . Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus , but confirm the presence of two asymmetrical sites recently reported in two other isopod species.

Epilogue

2019 ◽  
pp. 244-248
Author(s):  
Geoffrey E. Hill
Keyword(s):  
Sexual Selection ◽  
Mitochondrial Genome ◽  
21St Century ◽  
Evolutionary Ecology ◽  
Early Years ◽  
Mitochondrial Genomes ◽  
Respiratory Enzymes ◽  
The Core ◽  
The Past ◽  
Full Consideration

Evolutionary ecology is at the precipice of a paradigm shift. For many years and through the early years of the 21st century, mitochondrial genomes were dismissed as unimportant to the evolution of complex life. Variation within mitochondrial genomes was proposed to be functionally neutral. These conceptions about mitochondrial genomes and mitonuclear genomic interactions have begun to change within the past decade, but currently accepted theories of sexual selection and speciation were proposed before the discovery of the mitochondrial genome. Evolutionary ecology has yet to fully appreciate the fundamental implications of two genomes coding for the core respiratory enzymes of eukaryotes. This chapter promotes a fundamental rethinking of key theories in evolutionary ecology with full consideration of the necessity of coadaptation of mitochondrial and nuclear genes.

The plant mitochondrial genome: homologous recombination as a mechanism for generating heterogeneity

1988 ◽  
Vol 319 (1193) ◽  
pp. 149-163 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Homologous Recombination ◽  
Mitochondrial Genome ◽  
Higher Plants ◽  
Genome Structure ◽  
Rapid Evolution ◽  
Mitochondrial Genomes ◽  
Base Sequence ◽  
Plant Mitochondrial Genome ◽  
Organelle Genomes

The mitochondrial genomes of higher plants are among the largest and most complex organelle genomes described. They are generally multicircular or partly linear; in some species, extrachromosomal plasmids are present. It is proposed that inter- and intramolecular homologous recombination can account for the diversity of the observed genome organizations. The ability of mitochondria to fuse establishes a panmictic mitochondrial DNA population which is in recombinational equilibrium. It is suggested that this suppresses the base mutation rate, and unequal partitioning of the cytoplasm during cell division can lead to the rapid evolution of mitochondrial genome structure. This contrasts with the observed rates of base-sequence and genome evolution in chloroplasts. This difference can be accounted for solely by the inability of chloroplasts to fuse, thereby preventing chloroplast genome panmixis.

scholarly journals Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod

2021 ◽  
Author(s):  
William S Pearman ◽  
Sarah J Wells ◽  
James Dale ◽  
Olin K Silander ◽  
Nikki E Freed
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Dna Sequencing ◽  
Recent Work ◽  
Genome Structure ◽  
Mitochondrial Genomes ◽  
Short Read ◽  
Mitochondrial Structure ◽  
Evolutionary Origins ◽  
Long Read

Most animal mitochondrial genomes are small, circular, and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long and short read DNA sequencing, suggests that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that a heteroplasmic site previously observed across many species within Isopoda is absent in I. armatus, but confirm the presence of two heteroplasmic sites recently reported in two other isopod species.

scholarly journals Functional Difference of Mitochondrial Genome and Its Association with Traits of Common Complex Diseases in Humans

2017 ◽  
Author(s):  
Young Min Cho ◽  
Kyong Soo Park ◽  
Youngmi Kim Pak ◽  
Masashi Tanaka ◽  
Hong Kyu Lee
Keyword(s):  
Metabolic Syndrome ◽  
Mitochondrial Genome ◽  
Serum Triglyceride ◽  
Complex Diseases ◽  
Human Diseases ◽  
Dna Polymorphisms ◽  
Mitochondrial Genomes ◽  
Functional Difference

AbstractRecent evidence suggests that mitochondrial genomes harboring common mitochondrial DNA polymorphisms might have functional difference and could be associated with common complex human diseases such as metabolic syndrome and cancer that are related to mitochondrial dysfunction. However, there has been no report examining the functional difference of mitochondrial genome in the pathogenesis of such diseases at the cellular or molecular level. In order to examine the effect of mitochondrial genome on metabolic syndrome or cancer without interference from nuclear genes, we analyzed trans-mitochondrial cytoplasmic hybrid cells (cybrids) with common Asian mtDNA haplogroups A, B, D, and F from healthy volunteers. The mitochondrial oxygen consumption rates of cybrids were associated with multiple components of metabolic syndrome such as body mass index, waist circumference, serum triglyceride levels and high-density lipoprotein cholesterol levels. In addition, the cybrids showed varying degree of tumorigenicity both in vitro and in vivo. Especially, the cybrids harboring mtDNA haplogroup D had a significantly slower growth rate. These findings suggest that the phenotypes of common complex diseases in humans can be determined by their mitochondrial genomes. Therefore, not only nuclear genome but also mitochondrial genome should be considered in explaining the genetic pathogenesis of common complex human diseases.

scholarly journals Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

2020 ◽  
Author(s):  
Guohong Cai ◽  
Steven R. Scofield
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Proteins ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Circular Molecule

ABSTRACTPhytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

scholarly journals Mitochondrial genomes ofColumbicolafeather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

2019 ◽  
Author(s):  
Andrew D. Sweet ◽  
Kevin P. Johnson ◽  
Stephen L. Cameron
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Genome Structure ◽  
Mitochondrial Genomes ◽  
Single Chromosome ◽  
Pediculus Humanus ◽  
Feather Lice ◽  
Genome Shotgun Sequence ◽  
Repeated Evolution ◽  
Linear Chromosomes

ABSTRACTMost animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between 9 and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2-3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genusColumbicola(Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling theColumbicolamitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome ofPediculus humanusfrom shotgun sequencing reads, a species known to have minicircles. All three methods indicatedColumbicolaspp. genomes are highly fragmented into 15-17 minicircles between 1,119 and 3,173 bp in length, with 1-4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species ofColumbicolarepresent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

scholarly journals Description of the female, nymph and larva and mitochondrial genome, and redescription of the male, of Ixodes barkeri Barker, 2019 (Acari: Ixodidae) from the short-beaked echidna, Tachyglossus aculeatus, with a consideration of the most suitable subgenus for this tick

2021 ◽  
Author(s):  
Dayana Barker ◽  
Samuel Kelava ◽  
Renfu Shao ◽  
Owen D. Seeman ◽  
Malcolm K. Jones ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Far North ◽  
The Core ◽  
Wet Tropics ◽  
Palpal Segment ◽  
Subgenus Classification ◽  
First Time ◽  
Tachyglossus Aculeatus

Abstract Background Ixodes barkeri, a tick with a distinctive ventrolateral horn-like projection on palpal segment 1, was described in 2019 from two male ticks from the Wet Tropics of Far North Queensland, Australia. However, females lie at the core of the taxonomy and subgenus classification of Ixodes, hence we sought specimens of female ticks, successfully recovering females, plus nymphs and larvae. Mitochondrial genomes are also desirable additions to the descriptions of species of ticks particularly with regard to subgenus systematics. So, we sequenced the mt genomes of I. barkeri Barker, 2019 and the possible relatives of I. barkeri that were available to us (I. australiensis Neumann, 1904, I. fecialis Warburton & Nuttall, 1909, and I. woyliei Ash et al. 2017) with a view to discovering which if any of the subgenera of Ixodes would be most suitable for I. barkeri Barker, 2019. Results The female, nymph, larva, and mitochondrial genome of Ixodes barkeri Barker, 2019 are described for the first time and the male of I. barkeri is redescribed in greater detail than previously. So far, I. barkeri is known only from a monotreme, the short-beaked echidna, Tachyglossus aculeatus (Shaw, 1792), from the highland-rainforests of Far North Queensland, Australia. Conclusions Our phylogeny from entire mitochondrial genomes indicated that I. barkeri, and indeed I. woyliei Ash et al. 2017, another tick that was described recently, are best placed in the subgenus Endopalpiger Schulze, 1935.

scholarly journals Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8759 ◽  
Author(s):  
Andrew D. Sweet ◽  
Kevin P. Johnson ◽  
Stephen L. Cameron
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Genome Structure ◽  
Mitochondrial Genomes ◽  
Single Chromosome ◽  
Pediculus Humanus ◽  
Feather Lice ◽  
Genome Shotgun Sequence ◽  
Repeated Evolution ◽  
Linear Chromosomes

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

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