Sex-limited mitochondrial DNA transmission in the marine mussel Mytilus edulis.

Abstract Mitochondrial DNA (mtDNA) was thought to be inherited maternally in animals, although paternal leakage has been reported in mice and Drosophila. Recently, direct evidence of extensive paternal inheritance of mtDNA has been found in the marine mussel Mytilus. We give evidence that whereas female mussels are homoplasmic for a genome that is transmitted to eggs, male mussels are heteroplasmic for this genome and for a second genome that is transmitted preferentially to sperm. The results provide support for the existence of separate male and female routes of mtDNA inheritance in mussels. The two genomes show a base sequence divergence exceeding 20% at three protein coding genes, consistent with long term maintenance of the heteroplasmic state. We propose that the two genomes differ in fitness in males and females, possibly as a result of interaction with nuclear genes.

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Co-varying Patterns of Physical Activity and Sedentary Behaviors and Their Long-Term Maintenance Among Adolescents

Journal of Physical Activity and Health ◽

10.1123/jpah.7.4.465 ◽

2010 ◽

Vol 7 (4) ◽

pp. 465-474 ◽

Cited By ~ 35

Author(s):

Jihong Liu ◽

Jinseok Kim ◽

Natalie Colabianchi ◽

Andrew Ortaglia ◽

Russell R. Pate

Keyword(s):

Physical Activity ◽

Young Adulthood ◽

Screen Time ◽

Latent Class ◽

Vigorous Physical Activity ◽

Sedentary Behaviors ◽

Logistic Regression Models ◽

Males And Females ◽

Term Maintenance

Background:We examined the covarying patterns of physical activity and sedentary behaviors among adolescents and their long-term maintenance.Methods:Data came from the National Longitudinal Study of Adolescent Health (1995–2002). We used latent class analysis to identify distinct covarying patterns in adolescence. Logistic regression models were used to predict odds of meeting moderate-to-vigorous physical activity (MVPA) recommendations (≥5 bouts/week) and exceeding screen time guidelines (>2 hours/day) 6 years later based on their adolescent class profile.Results:Five classes for each gender were identified and labeled as low physical activity (PA)/low sedentary behaviors (SED), moderate (Mod) PA/high (HI) SED, Mod PA/low SED, HI PA/low SED, and HI PA (except skating/biking)/low SED. Compared with low PA/low SED, males and females in Mod PA/low SED, HI PA/low SED, and HI PA (except skating/biking)/low SED classes had increased odds of meeting MVPA recommendations in young adulthood. Mod PA/HI SED had higher odds of exceeding screen time guidelines in young adulthood (adjusted odds ratio [AOR] for females: 1.67, 95% CI: 1.00−2.81; AOR for males: 3.31, 95% CI: 1.80−6.09).Conclusions:Findings are useful to aid the development of multifactorial interventions that promote physical activity and reduce screen time among adolescents transitioning to adulthood.

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Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus

Nature ◽

10.1038/359412a0 ◽

1992 ◽

Vol 359 (6394) ◽

pp. 412-414 ◽

Cited By ~ 122

Author(s):

Eleftherios Zouros ◽

Kenneth R. Freeman ◽

Amy Oberhauser Ball ◽

Grant H. Pogson

Keyword(s):

Mitochondrial Dna ◽

Direct Evidence ◽

Marine Mussel ◽

Mitochondrial Dna Inheritance

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Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

10.1101/2021.06.05.447185 ◽

2021 ◽

Author(s):

Manu Kumar Gundappa ◽

Thu-Hien To ◽

Lars Grønvold ◽

Samuel A M Martin ◽

Sigbjørn Lien ◽

...

Keyword(s):

Phylogenetic Trees ◽

Sequence Divergence ◽

Meiotic Pairing ◽

Genome Wide ◽

A Genome ◽

Clock Analysis ◽

Multiple Species ◽

Genomic Regions ◽

Genome Assemblies

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent 'explosion' of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial 'wave' of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

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Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus

10.1101/579870 ◽

2019 ◽

Author(s):

Hsin-Han Lee ◽

Huei-Mien Ke ◽

Chan-Yi Ivy Lin ◽

Tracy J. Lee ◽

Chia-Lin Chung ◽

...

Keyword(s):

Size Variation ◽

Sequence Divergence ◽

Mitochondrial Genomes ◽

Intergenic Sequence ◽

Evolutionary Time ◽

Protein Coding ◽

Genetic Lineages ◽

Basidiomycetous Fungus ◽

Mtdna Inheritance

AbstractComparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer (HGT) and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA (mtDNA) inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from two genetic lineages ofPyrrhoderma noxium. Gene order is largely colinear while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high HGT frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes ofP. noxium, mitogenomes’ intraspecific polymorphisms at protein coding sequences are extremely low. Phylogeny based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mtDNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.

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Heterozygosity, Heteromorphy, and Phylogenetic Trees in Asexual Eukaryotes

Genetics ◽

10.1093/genetics/144.1.427 ◽

1996 ◽

Vol 144 (1) ◽

pp. 427-437 ◽

Cited By ~ 13

Author(s):

C William Birky

Keyword(s):

Phylogenetic Trees ◽

Elementary Theory ◽

Chromosomal Rearrangements ◽

Sequence Divergence ◽

Crossing Over ◽

Sequence Evolution ◽

Protein Coding ◽

Mitotic Gene Conversion ◽

Eukaryotic Organisms

Abstract Little attention has been paid to the consequences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic organisms. Some elementary theory shows that the amount of neutral sequence divergence between two alleles of a protein-coding gene in an asexual individual will be greater than that in a sexual species by a factor of 2tu, where t is the number of generations since sexual reproduction was lost and u is the mutation rate per generation in the asexual lineage. Phylogenetic trees based on only one allele from each of two or more species will show incorrect divergence times and, more often than not, incorrect topologies. This allele sequence divergence can be stopped temporarily by mitotic gene conversion, mitotic crossing-over, or ploidy reduction. If these convergence events are rare, ancient asexual lineages can be recognized by their high allele sequence divergence. At intermediate frequencies of convergence events, it will be impossible to reconstruct the correct phylogeny of an asexual clade from the sequences of protein coding genes. Convergence may be limited by allele sequence divergence and heterozygous chromosomal rearrangements which reduce the homology needed for recombination and result in aneuploidy after crossing-over or ploidy cycles.

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High levels of mitochondrial DNA divergence within short-eared rock-wallaby (Petrogale brachyotis) populations in northern Australia

Australian Journal of Zoology ◽

10.1071/zo09119 ◽

2010 ◽

Vol 58 (2) ◽

pp. 104 ◽

Cited By ~ 13

Author(s):

Wendy R. Telfer ◽

Mark D. B. Eldridge

Keyword(s):

Mitochondrial Dna ◽

Gene Flow ◽

Control Region ◽

National Park ◽

Sequence Divergence ◽

Mtdna Control Region ◽

Secondary Contact ◽

Interspecific Hybridisation ◽

Secondary Contact Zone

Most population genetics studies of rock-wallabies conducted to date have examined remnant colonies of threatened species inhabiting southern Australia. In this study we examined the natural pattern of contemporary and long-term gene flow among colonies of the widespread and abundant short-eared rock-wallaby, Petrogale brachyotis, in the relatively unmodified landscapes of Australia’s tropical north. We sampled 105 wallabies from seven colonies 1.2 km to 250 km apart. Mitochondrial DNA (mtDNA) control region sequence analysis was conducted on samples from all colonies and microsatellite analysis (10 loci) on samples from the three largest colonies. The microsatellite data revealed no evidence of inbreeding within colonies, but higher levels of genetic diversity were found in the Kakadu National Park population compared with the smaller, more isolated colonies at Litchfield National Park. Both the mtDNA and microsatellite results showed that populations of P. brachyotis are naturally highly structured even within this relatively intact landscape, with only limited contemporary and long-term gene flow between colonies more than 1.2 km apart. Nine mtDNA control region haplotypes were identified within the seven colonies. There were unusually high levels of sequence divergence (up to 6.9%) within colonies at Litchfield NP. This divergence suggests that multiple taxa may exist within what is currently recognised as P. brachyotis. Alternatively, if current taxonomy is correct, the high levels of divergence raise the possibility of ancestral isolation and divergence of populations in allopatry with subsequent admixture at a secondary contact zone. The possibility that these unusually divergent haplotypes result from introgressive interspecific hybridisation with the sympatric P. concinna appears unlikely.

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Integrate Heterogeneous NGS and TGS Data to Boost Genome-free Transcriptome Research

10.1101/2020.05.27.117796 ◽

2020 ◽

Author(s):

Yangmei Qin ◽

Zhe Lin ◽

Dan Shi ◽

Mindong Zhong ◽

Te An ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Computational Method ◽

Protein Coding ◽

Third Generation Sequencing ◽

A Genome ◽

Amphioxus Genome ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

AbstractIt is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Via integrating ten next generation sequencing (NGS) transcriptome datasets and one third-generation sequencing (TGS) dataset, we built a sequence library of non-redundant expressed transcripts for the amphioxus. The library consisted of overall 91,915 distinct transcripts, 51,549 protein-coding transcripts, and 16,923 novel extragenic transcripts. This substantially improved current amphioxus genome annotation by expanding the distinct gene number from 21,954 to 38,777. We consolidated the library significantly outperformed the genome, as well as de novo method, in transcriptome assembly from multiple aspects. For convenience, we curated the Integrative Transcript Library database of the amphioxus (http://www.bio-add.org/InTrans/). In summary, this work provides a practical solution for most organisms to alleviate the heavy dependence on good quality genome in transcriptome research. It also ensures the amphioxus transcriptome research grounding on reliable data.

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Is there ethological isolation among Drosophila melanogaster strains reared for more than 35 generations on different food?

Archives of Biological Sciences ◽

10.2298/abs0901105p ◽

2009 ◽

Vol 61 (1) ◽

pp. 105-112 ◽

Cited By ~ 5

Author(s):

Sofija Pavkovic-Lucic

Keyword(s):

Drosophila Melanogaster ◽

Sexual Isolation ◽

Multiple Choice Tests ◽

Food Standard ◽

Choice Tests ◽

Cornmeal Agar ◽

Males And Females ◽

Ethological Isolation ◽

Term Maintenance

Ethological isolation among three strains of D. melanogaster reared for more than 35 generations on different food (standard cornmeal-agar-yeast medium, banana, and tomato) was tested in a series of multiple choice tests. Long-term maintenance on different substrates did not contribute to sexual isolation among three 'nutritional strains', as degrees of ethological isolation (Malogolowkin-Cohen's isolation indices) were not statistically significant. Males and females reared on different nutritional resources were equally successful in matings, i.e., significant differences in the number of copulations achieved by males and females from various lines were not observed.

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