产毒真菌基因组研究进展

真菌毒素是产毒真菌产生的次生代谢产物,以木霉、曲霉、毛霉、青霉和根霉为主的丝状真菌是农产品中常见的产毒真菌。阐明农产品中产毒致病微生物的基因组序列信息是揭示真菌特殊遗传性状的基础。截至2013年12月,共有子囊菌门中204个种和担子菌门中62个种的基因组序列已经测序或公布,它们的基因组大小大部分在30-40 Mb。整理了部分已完成基因组测序的具有产毒能力或致病力的真菌基因组信息,并对真菌测序方案、主要产毒真菌及其比较基因组学的研究进展进行了综述。     

Genes encoding longevity: from model organisms to humans

Ample evidence from model organisms has indicated that subtle variation in genes can dramatically influence lifespan. The key genes and molecular pathways that have been identified so far encode for metabolism, maintenance and repair mechanisms that minimize age-related accumulation of permanent damage. Here, we describe the evolutionary conserved genes that are involved in lifespan regulation of model organisms and humans, and explore the reasons of discrepancies that exist between the results found in the various species. In general, the accumulated data have revealed that when moving up the evolutionary ladder, together with an increase of genome complexity, the impact of candidate genes on lifespan becomes smaller. The presence of genetic networks makes it more likely to expect impact of variation in several interacting genes to affect lifespan in humans. Extrapolation of findings from experimental models to humans is further complicated as phenotypes are critically dependent on the setting in which genes are expressed, while laboratory conditions and modern environments are markedly dissimilar. Finally, currently used methodologies may have only little power and validity to reveal genetic variation in the population. In conclusion, although the study of model organisms has revealed potential candidate genetic mechanisms determining aging and lifespan, to what extent they explain variation in human populations is still uncertain.     

Plenty more fish in the sea: comparative and functional genomics using teleost models.

Biology has collaborated with evolution to create an enormous repertoire of animal variation. This in turn has provided experimental biologists with models that can be used in the lab to simulate more complex systems. Amongst the organisms that have been used in this way are fish, where a large number of species have been utilised in a variety of different ways. Fish possess the smallest genomes of any vertebrate, making them ideal as models for genome analysis and gene discovery. Fish are also easy to maintain in a laboratory environment and can be bred easily. Fish often have well-defined physiology and respond well to many experimental procedures. Finally, fish are of great economic importance in their own right, as one of the world's largest sources of protein. In this review, the relationship between fish species is examined along with the role of different fish models in a wide range of biological disciplines.     

Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomic analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood‐decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens and trunk pathogen Porodaedalea pini. Many gene families of lignin‐degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3‐beta‐glucan synthases in P. noxius, which may account for its fast‐growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole‐genome sequencing showed this multinucleate species contains abundant poly‐allelic single nucleotide polymorphisms with atypical allele frequencies. Different patterns of intra‐isolate polymorphism reflect mono‐/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.     

Adaptive sequence divergence forged new neurodevelopmental enhancers in humans

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The real cost of sequencing: higher than you think!

Advances in sequencing technology have led to a sharp decrease in the cost of ''data generation''. But is this sufficient to ensure cost-effective and efficient ''knowledge generation''?     

Genetics on the Fly: A Primer on the Drosophila Model System

Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly’s tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism’s natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.     

功能基因组学的研究内容与方法

基因组学的研究已从结构基因组学转向功能基因组学.综述了功能基因组学研究的内容和方法,主要包括应用微点阵、基因表达系列分析(SAGE)、蛋白质组、生物信息学等方法来研究基因组表达概况、基因组多样性、模式生物体等.     

Through a genome, darkly: comparative analysis of plant chromosomal DNA

Plant nuclear genomes encompass a wide range of variation in size and nucleotide composition with diverse arrangements of chromosomal segments, repetitive sequences and distribution of genes. Comparative genomic analysis may be undertaken at different levels of organisation, which are reflected in this review, together with a focus on the genetic and functional significance of the observed variation. Patterns of genome organisation have been revealed which reflect the different underlying mechanisms and constraints driving change. Thus comparative issues of genome size, nucleotide sequence composition and genome heterogeneity are provided as a background to understanding the different levels of segmental and repetitive sequence duplication and distribution of genes. The extent of synteny and collinearity revealed by recent genetic and sequence comparisons is discussed, together with a consideration of problems associated with such analyses. The possible origins and mechanisms of variation in genome size and organisation are covered, including the prevalence of duplication at different levels of organisation. The likely genetic, functional and adaptive consequences of replicated loci are discussed with evidence from comparative studies. The scope for comparative analysis of epigenetic plant genome variation is considered. Finally, opportunities for applying comparative genomics to isolating genes and understanding complex crop genomes are addressed.     

The Drosophila phenotype gap - and how to close it.

Functional genomics (the elucidation of gene function in the context of a sequenced genome) depends critically on functional biology. Genetic model organisms have hitherto not attracted much physiological input, however. This skills mismatch, termed the phenotype gap, can be quantified by analysis of the annotations of sequenced genomes. This is illustrated in the context of Drosophila. In this case, it seems as if a shift from developmental biology to transport physiology and metabolism will be required to provide a more balanced skills base for post-genomics.     

Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species

Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.     

A negative relationship between mutation pleiotropy and fitness effect in yeast

It is generally thought that random mutations will, on average, reduce an organism's fitness because resulting phenotypic changes are likely to be maladaptive. This relationship leads to the prediction that mutations that alter more phenotypic traits, that is, are more pleiotropic, will impose larger fitness costs than mutations that affect fewer traits. Here we present a systems approach to test this expectation. Previous studies have independently estimated fitness and morphological effects of deleting all nonessential genes in Saccharomyces cerevisiae. Using datasets generated by these studies, we examined the relationship between the pleiotropic effect of each deletion mutation, measured as the number of morphological traits differing from the parental strain, and its effect on fitness. Pleiotropy explained approximately 18% of variation in fitness among the mutants even once we controlled for correlations between morphological traits. This relationship was robust to consideration of other explanatory factors, including the number of protein-protein interactions and the network position of the deleted genes. These results are consistent with pleiotropy having a direct role in affecting fitness.     

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat,Homotherium latidens

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菲律宾海盆沉积物可培养真菌及其温度、盐度适应性初步研究

真菌在海洋生态系统的碳氮循环过程中扮演重要角色。近年来,有关深海真菌研究逐渐增多,丰富了人们对海洋真菌多样性与分布特点的认知。本研究从菲律宾海盆深度约5 000m处采集沉积物样品16份,基于传统培养方法调查真菌多样性,并对部分菌株的生物学特性开展初步研究。共获得132个真菌菌株,隶属于2个门、10个纲、16个目、27个属和32个已知种;在属级水平上,青霉属、枝孢属、曲霉属是优势真菌。温度、盐度适应性实验表明,受测的16株真菌中,有7株菌表现出嗜盐性,即在45‰-60‰盐度条件下生长良好。酵母菌Udeniomyces megalosporus（OUCMBII₁₇0060）在30‰盐度和5℃条件下细胞增殖最快,表现出良好的耐低温与耐盐特性。本研究进一步丰富了深海真菌资源及其多样性的认知,获得的特殊菌株为后续生理生化、遗传进化以及开发利用提供宝贵资源。     

Towards an understanding of the genetics of human male infertility: lessons from flies

It has been argued that about 4–5% of male adults suffer from infertility due to a genetic causation. From studies in the fruitfly Drosophila, there is evidence that up to 1500 recessive genes contribute to male fertility in that species. Here we suggest that the control of human male fertility is of at least comparable genetic complexity. However, because of small family size, conventional positional cloning methods for identifying human genes will have little impact on the dissection of male infertility. A critical selection of well-defined infertility phenotypes in model organisms, combined with identification of the genes involved and their orthologues in man, might reveal the genes that contribute to human male infertility.