Phylogeny of the Eisenia nordenskioldi complex based on mitochondrial genomes

AbstractmtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes.

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Mitochondrial genome evolution in pelagophyte algae

Genome Biology and Evolution ◽

10.1093/gbe/evab018 ◽

2021 ◽

Author(s):

Shannon J Sibbald ◽

Maggie Lawton ◽

John M Archibald

Keyword(s):

Mitochondrial Genome ◽

Harmful Algal Blooms ◽

Algal Blooms ◽

23S Rrna ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Unique Region ◽

Long Read ◽

Genomic Studies ◽

Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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Not Frozen in the Ice: large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

Genome Biology and Evolution ◽

10.1093/gbe/evab017 ◽

2021 ◽

Author(s):

Chiara Papetti ◽

Massimiliano Babbucci ◽

Agnes Dettai ◽

Andrea Basso ◽

Magnus Lucassen ◽

...

Keyword(s):

Gene Order ◽

Hot Spot ◽

Mitochondrial Gene ◽

Antarctic Fish ◽

Purifying Selection ◽

Compositional Bias ◽

Mitochondrial Genomes ◽

Notothenioid Fish ◽

Antarctic Notothenioids ◽

The Antarctic

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

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Complete mitochondrial genomes of Epeorus carinatus and E. dayongensis (Ephemeroptera: Heptageniidae): Genomic comparison and phylogenetic inference

Gene ◽

10.1016/j.gene.2021.145467 ◽

2021 ◽

Vol 777 ◽

pp. 145467

Author(s):

Wei Zhang ◽

Ran Li ◽

Changfa Zhou

Keyword(s):

Phylogenetic Inference ◽

Mitochondrial Genomes ◽

Genomic Comparison ◽

Complete Mitochondrial Genomes

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A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae)

Mitochondrial DNA Part A ◽

10.3109/19401736.2015.1028049 ◽

2015 ◽

Vol 27 (4) ◽

pp. 2401-2404 ◽

Cited By ~ 9

Author(s):

Elaine Françoso ◽

Fernando Gomes ◽

Maria Cristina Arias

Keyword(s):

Mitochondrial Genomes

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Harmful mutation load in the mitochondrial genomes of cattle breeds

BMC Research Notes ◽

10.1186/s13104-021-05664-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Sankar Subramanian

Keyword(s):

Population Size ◽

Artificial Selection ◽

Deleterious Mutation ◽

Genetic Diseases ◽

Mitochondrial Genomes ◽

Deleterious Mutations ◽

Founder Population ◽

Mutation Load ◽

Effective Population ◽

Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

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