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.     

Uncovering historical signature of mitochondrial DNA hidden in the nuclear genome: the biogeography of Schistocerca revisited

Inadvertent coamplification of nuclear mitochondrial pseudogenes (numts) is a serious problem in mitochondrial systematics, but numts can also be a valuable source of information because they represent ancient forms of mtDNA. We present a conceptual framework of numt accumulation, which states that in a given species there can be two types of numts, synaponumts and autaponumts, resulting from integration occurring respectively before and after a speciation event. In a given clade, a species that diverged early can only have its own autaponumts as well as synaponumts that were already present in the genome of the last common ancestor. A species that diverged more recently may, however, have many different synaponumts integrated at each different divergence as well as its own autaponumts. Therefore it is possible to decipher the evolutionary history of a species based on the phylogenetic distribution of numts in a simultaneous analysis of numts and extant mtDNA. In this study, we test this idea empirically in the context of addressing a controversial question regarding the biogeography of the grasshopper genus Schistocerca Stål (Orthoptera: Acrididae), based on numts of the cytochrome c oxidase subunit I (COI) gene. We find that our empirical data can be explained adequately by our conceptual framework, and that the phylogenetic distribution of COI numts reveals intricate evolutionary histories about past speciation events that are otherwise difficult to detect using conventional markers. Our study strongly favours the Old World origin of the desert locust, Schistocerca gregaria and the New World Schistocerca species are descendants from an ancestral gregaria‐like species that colonized the New World via westward transatlantic flight. However, the phylogenetic distribution of S. gregaria numts raises a distinct possibility that there might have been multiple founding events from Africa to America to give rise to the present‐day diversity of the genus. This is a case study for a creative use of numts as molecular fossils, and we demonstrate that numts provide an interesting and powerful phylogenetic signal, much more than what extant mtDNA or nuclear gene sequences might be able to provide.     

The signature of phylogenetic constraints on food-web structure

Understanding the processes underlying food-web structure and organization remains one of the major tasks of ecology. While first attempts were mostly based on niche theory, with body size of species imposing a hierarchical structure for consumer species, it has been recently suggested that phylogenetic constraints may be more fundamental to understand who eats whom in natural communities. Models of food-web structure built on basic evolutionary assumptions are able to adequately reproduce the topology of real food-webs. Here, we analyze different implications of phylogenetic constraints on trophic structure, and present preliminary results. Our exploration of the relationship between trophic and taxonomic similarity in food-webs shows that phylogeny and trophic structure are closely linked. Interestingly, the relationship is stronger for trophic similarity between prey (similarity measured by shared predators species, or predatory similarity) than between consumer species (similarity measured by shared prey species, or dietary similarity). When relating body mass of prey and predators, slopes of major axis regressions within taxonomic groups differ markedly from the global pattern; similar differences between taxonomic levels appear when exploring the relationship between body mass of predators and the range in body mass of their prey, and vice versa. These results are important to understand how evolutionary processes shaping body sizes can affect food-web structure.     

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 Campylobacter jejuni cell surface interactions from the genome sequence

The completion of the Campylobacter jejuni genome sequence is a landmark in Campylobacter research. Discoveries directly arising from these data include the identification of a capsular polysaccharide, extensive capacity for phase variable gene expression and lipo-oligosaccharide structural phase variation. The recent identification of a unique system of general protein glycosylation in C. jejuni, a C. jejuni protein that is translocated into eukaryotic cells, and plasmid-encoded components of a putative type IV secretion system are likely to be significant in terms of the host-pathogen interaction.     

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...     

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.     

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.     

中国3个不同地域藏族群体线粒体ATP6、ATP8和Cyt b基因的比较: 探查自然选择在基因组的印记

线粒体基因组(Mitochondrial DNA, mtDNA)具有区别于核基因组的诸多特性(例如缺乏重组等), 在人类进化历史的研究领域具有巨大的应用价值。文章通过对3个不同地域藏族群体线粒体基因组的ATP6、ATP8和Cyt b 基因约2 kb区域的测序研究发现: 随着海拔的增加, 3个基因的全序列、ATP6和ATP8基因逐渐偏离中性模式, 但未呈现显著性差异; 随着海拔的降低, Cyt b 基因受到纯化选择的作用逐渐增大; ATP6基因可能存在适应性选择, 并且随着海拔的增高呈现出适应性选择增强的趋势; 选择的主要因素应该是该群体所处的特殊的地理环境, 即不同的地理环境具有直接的选择作用。     

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.     

Revisiting the Neurospora crassa mitochondrial genome

The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.     

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 Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants

Mitochondrial genomes of spermatophytes are the largest of all organellar genomes. Their large size has been attributed to various factors; however, the relative contribution of these factors to mitochondrial DNA (mtDNA) expansion remains undetermined. We estimated their relative contribution in Malus domestica (apple). The mitochondrial genome of apple has a size of 396 947 bp and a one to nine ratio of coding to non-coding DNA, close to the corresponding average values for angiosperms. We determined that 71.5% of the apple mtDNA sequence was highly similar to sequences of its nuclear DNA. Using nuclear gene exons, nuclear transposable elements and chloroplast DNA as markers of promiscuous DNA content in mtDNA, we estimated that approximately 20% of the apple mtDNA consisted of DNA sequences imported from other cell compartments, mostly from the nucleus. Similar marker-based estimates of promiscuous DNA content in the mitochondrial genomes of other species ranged between 21.2 and 25.3% of the total mtDNA length for grape, between 23.1 and 38.6% for rice, and between 47.1 and 78.4% for maize. All these estimates are conservative, because they underestimate the import of non-functional DNA. We propose that the import of promiscuous DNA is a core mechanism for mtDNA size expansion in seed plants. In apple, maize and grape this mechanism contributed far more to genome expansion than did homologous recombination. In rice the estimated contribution of both mechanisms was found to be similar.     

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.