scholarly journals Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Alex Z. Zaccaron ◽  
Ioannis Stergiopoulos
Keyword(s):  
Comparative Analysis ◽  
Mitochondrial Genome ◽  
Powdery Mildew ◽  
Nucleotide Composition ◽  
Phytopathogenic Fungi ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Limited Information ◽  
Reverse Transcriptases ◽  
Golovinomyces Cichoracearum

Powdery mildews comprise a large group of economically important phytopathogenic fungi. However, limited information exists on their mitochondrial genomes. Here, we assembled and compared the mitochondrial genomes of the powdery mildew pathogens Blumeria graminis f. sp. tritici, Erysiphe pisi, and Golovinomyces cichoracearum. Included in the comparative analysis was also the mitochondrial genome of Erysiphe necator that was previously analysed. The mitochondrial genomes of the four Erysiphales exhibit a similar gene content and organization but a large variation in size, with sizes ranging from 109800 bp in B. graminis f. sp. tritici to 332165 bp in G. cichoracearum, which is the largest mitochondrial genome of a fungal pathogen reported to date. Further comparative analysis revealed an unusual bimodal GC distribution in the mitochondrial genomes of B. graminis f. sp. tritici and G. cichoracearum that was not previously observed in fungi. The cytochrome b (cob) genes of E. necator, E. pisi, and G. cichoracearum were also exceptionally rich in introns, which in turn harboured rare open reading frames encoding reverse transcriptases that were likely acquired horizontally. Golovinomyces cichoracearum had also the longest cob gene (45 kb) among 703 fungal cob genes analysed. Collectively, these results provide novel insights into the organization of mitochondrial genomes of powdery mildew pathogens and represent valuable resources for population genetics and evolutionary studies.

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 Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8356
Author(s):  
Darrin T. Schultz ◽  
Jordan M. Eizenga ◽  
Russell B. Corbett-Detig ◽  
Warren R. Francis ◽  
Lynne M. Christianson ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Hypothesis Test ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Intergenic Sequence ◽  
Computational Tools ◽  
Protein Coding ◽  
Bayesian Hypothesis Test ◽  
And Function ◽  
Reading Frames

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

scholarly journals Mitochondrial genome evolution of placozoans: gene rearrangements and repeat expansions

2020 ◽  
Author(s):  
Hideyuki Miyazawa ◽  
Hans-Jürgen Osigus ◽  
Sarah Rolfes ◽  
Kai Kamm ◽  
Bernd Schierwater ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gc Content ◽  
Distribution Patterns ◽  
Sister Group ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Group I ◽  
Phylogenomic Analyses

Abstract Placozoans, non-bilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNA are circular chromosomes of 32-43 kbp in size, which encode 12 protein-coding genes, 24 tRNAs, and 2 rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Since P. mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

scholarly journals Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 663
Author(s):  
Alessandro Formaggioni ◽  
Andrea Luchetti ◽  
Federico Plazzi
Keyword(s):  
Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Complete Sequence ◽  
Gene Content ◽  
Mitochondrial Genomes ◽  
Single Chromosome ◽  
Genomic Landscape ◽  
Linear Genomes ◽  
Huge Variation ◽  
General Conservation

Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.

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 Complete mitochondrial genome of the aluminum‐tolerant fungus R hodotorula taiwanensis RS 1 and comparative analysis of B asidiomycota mitochondrial genomes

2013 ◽  
Vol 2 (2) ◽  
pp. 308-317 ◽  
Author(s):  
Xue Qiang Zhao ◽  
Tomoko Aizawa ◽  
Jessica Schneider ◽  
Chao Wang ◽  
Ren Fang Shen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes

scholarly journals Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

2020 ◽  
Vol 145 (2) ◽  
Author(s):  
Fei Ye ◽  
Ting Liu ◽  
Wenbo Zhu ◽  
Ping You
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

scholarly journals The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Lidia Komondy ◽  
Jose Huguet-Tapia ◽  
Marina S. Ascunce ◽  
Ericka E. Helmick ◽  
Erica M. Goss ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Internal Control ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lethal Yellowing ◽  
Primer Sets

Haplaxius crudus Van Duzee is a pest of various economically important palms due to its ability to transmit lethal yellowing, a fatal phytoplasma infection. It is also the putative vector of lethal bronzing in Florida, another lethal phytoplasma disease causing significant economic losses. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. In this study, the complete mitochondrial genome of H. crudus was sequenced, assembled, and annotated from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator. The mitogenome of H. crudus is 15,848 bp long and encodes 37 mitochondrial genes (including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) in addition to a putative noncoding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A/T (44.8 %A, 13.4 %C, 8.5 %G, and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is highly similar to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis based on the entire mitogenome shows H. crudus resolving closely to Delphacidae, the accepted sister taxon of Cixiidae. These data provide a useful resource for developing novel primer sets that could aid in either phylogenetic studies or population genetic studies. As more full mitogenomes become available in the future for other planthopper species, more robust phylogenies can be constructed, giving more accurate perspectives on the evolutionary relationships within this fascinating and economically important group of insects.

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