Domestication relaxed selective constraints on the yak mitochondrial genome

Wild yaks roaming in the high-altitude Qinghai-Tibetan plateau have to maintain high metabolic efficiency. However, domestic yaks do not require such high efficiency because of their limited activity. Hence, domestication may have caused the relaxation of selective constraints on the yak mitochondrial genome because mitochondrial mutations are extremely sensitive to energy-related selective pressures. We have tested this hypothesis by analyzing the mitochondrial genomes of 51 domestic yaks and 21 wild yaks. The results show that the ratio of nonsynonymous/synonymous substitutions in mitochondrial protein-coding genes is significantly higher in domestic yak lineages than those of wild yaks. This genetic difference suggests that the relaxation of selective constraints following the domestication in addition to bottlenecks has allowed faster accumulation of nonsilent substitutions in the yak mitochondrial genome, despite its short domestication history.     

Instability of the mitochondrial genome

A number of manifestations of mitochondrial DNA instability have been reviewed. Differences in organization of mitochondrial genomes of different origin have been regarded as well as variability concerning the genetic code. Examples of molecular heterogeneity of mtDNA and among them insertions and optional introns in Saccharomyces cerevisiae are given. Specific mutations in ascomycets and higher plants have been discussed as an aspect of instability since they cause the appearance of mitochondrial plasmids and episomes. One can regard the rate of mtDNA evolution particularly the high frequency of molecular rearrangement as connected with the fact that some of its regions behave as "egoistic" DNA. According to the Doolittle-Crick concept phenotypical selection always supports any useful function of that DNA, emerging by chance. Therefore we admit that some of the optional insertions into mt genes in S. cerevisiae have the adaptive function. It is also possible that in the course of evolution some higher plants "have learned" to use the DNA's ability to generate plasmids and episomes in order to create new means of gene activity regulation.     

Deciphering signature of selection affecting beef quality traits in Angus cattle

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A–H and A–J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A–H) and five (A–J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.     

The signals of selective constraints on the mitochondrial non-coding control region: insights from comparative mitogenomics of Clupeoid fishes

Genetica - The vertebrate mitochondrial genome is characterized by an exceptional organization evolving towards a reduced size. However, the persistence of a non-coding and highly variable control...     

犬科动物线粒体基因组特征分析

在基因组水平上,分析了已知犬科动物线粒体基因组的特征。结果表明：其基因排列顺序相同;具有AT含量高,G含量最低的碱基偏好性;存在基N间隔和基N重叠;CUA（Leu）,Auu（Ile）,AUA（Met）等密码子使用率最高,密码子第3位G使用率最低;轻链复制起点序列组成和二级结构高度保守;在犬、狼、郊狼控制区存在10bp的相似重复序列,赤狐序列差异较大。     

Positive and negative selection on the mitochondrial genome

Several recent studies have confirmed that mitochondrial DNA variation and evolution are not consistent with the neutral theory of molecular evolution and might be inappropriate for estimating effective population sizes. Evidence for the action of both positive and negative selection on mitochondrial genes has been put forward, and the complex genetics of mitochondrial DNA adds to the challenge of resolving this debate. The solution could lie in distinguishing genetic drift from 'genetic draft' and in dissecting the physiology of mitochondrial fitness.     

Human evolution and the mitochondrial genome

The use of mitochondrial DNA (mtDNA) continues to dominate studies of human genetic variation and evolution. Recent work has re-affirmed the strict maternal inheritance of mtDNA, yielded new insights into the extent and nature of intra-individual variation, supported a recent African origin of human mtDNA, and amply demonstrated the utility of mtDNA in tracing population history and in analyses of ancient remains.     

Chemical synthesis of the mouse mitochondrial genome

We describe a one-step, isothermal assembly method for synthesizing DNA molecules from overlapping oligonucleotides. The method cycles between in vitro recombination and amplification until the desired length is reached. As a demonstration of its simplicity and robustness, we synthesized the entire 16.3-kilobase mouse mitochondrial genome from 600 overlapping 60-mers.     

Adaptive evolution of the Homo mitochondrial genome

Adaptive evolution of 12 protein-coding mitochondrial genes in members of genus Homo (Denisova hominin (H. sp. Altai), Neandertals (H. neanderthalensis) and modern humans (H. sapiens)) has been evaluated by assessing the pattern of changes in the physicochemical properties of amino acid replacements during the primate evolution. It has been found that in the Homo molecular adaptation (positive destabilizing selection) become apparent in the form of 12 radical amino acid replacements accompanied by statistically significant (P < 0.001) changes of physicochemical properties that probably had the functional consequences. These replacements have occurred on the stage of a common ancestor of the Homo (in CO2 and CytB genes) as well as with the appearance of the common ancestor of Neandertals and modern humans (in CO1 and ND5 genes). Radical amino acid replacements were mainly revealed in the cytochrome c oxidase complex IV and cytochrome bc1 complex III, thus coinciding with general trend of increasing of non-synonymous changes in mtDNA genes coding subunits of complexes III and IV proteins in anthropoid primates.     

The mitochondrial genome of protists

The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.     

var1 Gene on the mitochondrial genome of Torulopsis glabrata

We have cloned and sequenced a region of the Torulopsis glabrata mitochondrial genome homologous to the Saccharomyces cerevisiae var1 gene (var1Sc). An open reading frame that could encode a protein of 339 amino acids was found with 72.7% amino acid and 85.3% nucleotide sequence homology to the S. cerevisiae var1 gene. The T. glabrata gene (var1Tg) is transcribed yielding two stable RNAs, a more abundant 13.5 S RNA and a less abundant 18 S species. We have also identified a candidate for a T. glabrata var1 protein among mitochondrial translation products labeled in isolated mitochondria. The var1Tg gene is even more A + T-rich (93%) than var1Sc (89.6%) and has conserved the strong codon bias of var1Sc. Major differences between the two sequences were found. Significant among these are that no GC clusters are found in var1Tg and the sequences surrounding each of the sites where known polymorphisms exist in var1Sc have deletions at the corresponding sites in var1Tg. These data are discussed with respect to possible origins of these var1 genes and translocation of GC clusters in S. cerevisiae mitochondrial DNA.     

线粒体基因组的遗传与进化研究进展

线粒体基因组是当前生命科学的热门话题之一。文章根据国内外有关线粒体DNA的结构、表达过程和遗传特征方面的最新研究成果,重点介绍线粒体基因组与核基因组关系、线粒体遗传密码及基因组的进货线索等问题,并简要说明了线粒体基因组遗传分析的要点。     

Presence of a latent mitochondrial targeting signal in gene on mitochondrial genome

Organelles, such as mitochondria and chloroplasts, are derived from endosymbionts. Gene transfer events from organelles to the nucleus have occurred over evolutionary time. In the case that a transferred gene in the nucleus needs to go back to the original organelle, it must obtain targeting information for sorting its protein to that organelle. Here, we reveal that the genes for the ribosomal proteins L2 and S4 in the Arabidopsis thaliana mitochondrial (mt) genome contain information for protein targeting into the mitochondria. Similarly, the genes for the ribosomal proteins L2 and S19 in the Oryza sativa mt genome contain information for protein targeting into mitochondria. These results suggest that targeting information already existed in each gene in the plant mt genome before the transfer event to the nucleus occurred. We provide new insights into the timing of the appearance of targeting signals in evolution.     

Linkage disequilibrium as a signature of selective sweeps

The hitchhiking effect of a beneficial mutation, or a selective sweep, generates a unique distribution of allele frequencies and spatial distribution of polymorphic sites. A composite-likelihood test was previously designed to detect these signatures of a selective sweep, solely on the basis of the spatial distribution and marginal allele frequencies of polymorphisms. As an excess of linkage disequilibrium (LD) is also known to be a strong signature of a selective sweep, we investigate how much statistical power is increased by the inclusion of information regarding LD. The expected pattern of LD is predicted by a genealogical approach. Both theory and simulation suggest that strong LD is generated in narrow regions at both sides of the location of beneficial mutation. However, a lack of LD is expected across the two sides. We explore various ways to detect this signature of selective sweeps by statistical tests. A new composite-likelihood method is proposed to incorporate information regarding LD. This method enables us to detect selective sweeps and estimate the parameters of the selection model better than the previous composite-likelihood method that does not take LD into account. However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms.     

Unusual mitochondrial genome structures throughout the Euglenozoa

Mitochondrial DNA of Kinetoplastea is composed of different chromosomes, the maxicircle (bearing 'regular' genes) and numerous minicircles (specifying guide RNAs involved in RNA editing). In trypanosomes [Kinetoplastea], DNA circles are compacted into a single dense body, the kinetoplast. This report addresses the question whether multi-chromosome mitochondrial genomes and compacted chromosome organization are restricted to Kinetoplastea or rather occur throughout Euglenozoa, i.e., Kinetoplastea, Euglenida and Diplonemea. To this end, we investigated the diplonemid Rhynchopus euleeides and the euglenids Petalomonas cantuscygni, Peranema trichophorum and Entosiphon sulcatum, using light and electron microscopy and molecular techniques. Our findings together with previously published data show that multi-chromosome mitochondrial genomes prevail across Euglenozoa, while kinetoplast-like mtDNA packaging is confined to trypanosomes.     

Mitochondrial fusion and inheritance of the mitochondrial genome

Although maternal or uniparental inheritance of mitochondrial genomes is a general rule, biparental inheritance is sometimes observed in protists and fungi, including yeasts. In yeast, recombination occurs between the mitochondrial genomes inherited from both parents. Mitochondrial fusion observed in yeast zygotes is thought to set up a space for DNA recombination. In the last decade, a universal mitochondrial fusion mechanism has been uncovered, using yeast as a model. On the other hand, an alternative mitochondrial fusion mechanism has been identified in the true slime mold Physarum polycephalum. A specific mitochondrial plasmid, mF, has been detected as the genetic material that causes mitochondrial fusion in P. polycephalum. Without mF, fusion of the mitochondria is not observed throughout the life cycle, suggesting that Physarum has no constitutive mitochondrial fusion mechanism. Conversely, mitochondria fuse in zygotes and during sporulation with mF. The complete mF sequence suggests that one gene, ORF640, encodes a fusogen for Physarum mitochondria. Although in general, mitochondria are inherited uniparentally, biparental inheritance occurs with specific sexual crossing in P. polycephalum. An analysis of the transmission of mitochondrial genomes has shown that recombinations between two parental mitochondrial genomes require mitochondrial fusion, mediated by mF. Physarum is a unique organism for studying mitochondrial fusion.