文昌鱼特异的基因倍增

进化生物学和发育生物学的结合产生了一门新兴学科——进化发育生物学,近年来该领域研究取得了丰硕的成果。头索动物文昌鱼是现存生物中最近似于脊椎动物直接祖先的生物,在与脊椎动物分化后形态改变很小,其基因组未曾经历大规模的基因组倍增,在一定程度上反映了脊椎动物祖先型基因组的特征,但在漫长的独立进化历程中基因组自身还是经历了一些变化。本文介绍了在几例在文昌鱼支系中独立发生的基因倍增事件(Hox; Evx; HNF-3; Calmodulin-like),有力地揭示了文昌鱼虽然与脊椎动物直接祖先极其接近,但其基因组有其自身特性,不能简单地将之等同于脊椎动物直接祖先。Abstract: The union of the two complementary disciplines, developmental biology and evolutionary biology resulted in a new division of evolutionary developmental biology, namely “Evo-Devo”. Recently, the research on this field has been fruitful in understanding the origin and development of vertebrates. The cephalochordate amphioxus, which remains in relatively invariant morphology since the divergence from the vertebrate lineage, is the closest living relative to vertebrates. The vertebrate-like simple body plan and preduplicative genome provide amphioxus genes the privilege to serve as key landmark to understand morphological evolution. However, the amphioxus genome has not escaped evolution. In this paper several examples of independent gene (Hox; Evx; HNF-3 and Calmodulin-like) duplications in the cephalochordate lineage were summarized. These particularities and oddities remind the fact that amphioxus is not an immediate ancestor of the vertebrates but ‘only’ the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.     

小麦及其近缘种中基因组特异性DNA重复序列的研究进展

本文对小麦族植物中基因组特异性DNA重复序列的分类、基本特征、分离和鉴定方法、在小麦遗传改良中的应用以及未来研究的发展趋势进行了简述。综合已有的研究结果可以看出基因组特异性DNA重复序列是小麦族植物基因组特异性形成的重要构成部分。对基因组特异性DNA重复序列的研究是认识小麦族植物基因组的有效途径之一,基因组特异性DNA重复序列的应用将进一步促进小麦族植物分子细胞遗传学和普通小麦遗传改良研究的进展。 Advances in Studies of Genome-Specific Repetitive DNA Sequences in Wheat and Related Species BAI Jian-rong1,2,JIA Xu1,WANG Dao-wen1 1.The State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,The Chinese Academy of Sciences,Beijing 100101,China; 2.Crop Genetics Institute,Shanxi Academy of Agricultural Sciences,Taiyuan 030031,China Abstract:In this paper we review recent advances in studies of several aspects of genome specific repetitive DNA sequences in wheat and related species.The available results demonstrate that genome specific repetitive DNA sequences are important components of genome specificity in wheat and related species.Research on genome specific repetitive DNA sequences is essential to the elucidation of genome function.The application of genome specific repetitive DNA sequences will aid molecular cytogenetic studies in wheat and related species and contributes to genetic improvement of common wheat. Key words：wheat;genome specific repetitive DNA sequence;chromosome     

水稻基因组测序的研究进展

水稻是最重要的粮食作物之一,世界上大约有一半的人口以水稻为主要粮食.作为基因组研究的模式植物,水稻基因组的测序工作已在世界范围内展开.此项研究工作不仅能破译水稻全基因组序列,还将有助于了解其他禾本科植物的基因组信息.本文对水稻基因组测序工作进展作一综述。 Abstract:Because of the importamce of rice as the staple food source for over half of the world population and since rice is a leading model plant for genomic studies,an international effort has now begun to sequence the rice genome.This project eventually will reveal all of the genomic sequence information of rice and be an indispensable aid in understanding the genomics of other grass species.In this paper,the development and research progress in sequencing of rice genome are reviewed.     

Analysis of collinear regions of Oryza AA and CC genomes

Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated -73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences office cultivar, O. sativa ssp.japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.     

Epigenetic Programming： The Challenge to Species Hybridization

In many organisms, the genomes of individual species are isolated by a range of reproductive barriers that act before or after fertilization. Successful mating between species results in the presence of different genomes within a cell （hybridization）, which can lead to incompatibility in cellular events due to adverse genetic interactions. In addition to such genetic interactions, recent studies have shown that the epigenetic control of the genome, silencing of transposons, control of non-additive gene expression and genomic imprinting might also contribute to reproductive barriers in plant and animal species. These genetic and epigenetic mechanisms play a significant role in the prevention of gene flow between species. In this review, we focus on aspects of epigenetic control related to hybrid incompatibility during species hybrid- ization, and also consider key mechanism（s） in the interaction between different genomes.     

Genome size of 14 species of fireflies (Insecta,Coleoptera, Lampyridae)

Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms.In this study,the genome size of 14 species of fireflies (Lampyridae) (two genera in Lampyrinae,three genera in Luciolinae,and one genus in subfamily incertae sedis) were estimated by propidium iodide (PI)-based flow cytometry.The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg,a 3.1-fold span.Genome sizes of the fireflies varied within the tested subfamilies and genera.Lamprigera and Pyrocoelia species had large and small genome sizes,respectively.No correlation was found between genome size and morphological traits such as body length,body width,eye width,and antennal length.Our data provide additional information on genome size estimation of the firefly family Lampyridae.Furthermore,this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.     

Genetic Relationships Among Five Basic Genomes St, E, A, B and D in Triticeae Revealed by Genomic Southern and in situ Hybridization

The St and E are two important basic genomes in the perennial tribe Triticeae （Poaceae）. They exist in many perennial species and are very closely related to the A, B and D genomes of bread wheat （Triticum aestivum L.）. Genomic Southern hybridization and genomic in situ hybridization （GISH） were used to analyze the genomic relationships between the two genomes （St and E） and the three basic genomes （A, B and D） of T. aestivum. The semi-quantitative analysis of the Southern hybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, and relatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion. St and E are the two basic genomes of Thinopyrum ponticum （StStE^eE^bE^x） and Th. intermedium （StE^eE^b）, two perennial species successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of the spontaneous wheat-Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genome and rarely in the B genome. This would develop further use of alien species for wheat improvement, especially those containing St or E in their genome components.     

The revolution of the biology of the genome

Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution. The major mechanisms involved in the increase of genome sizes are polyploidization and gene duplication.Subsequent gene silencing or mutations, preferentially in regulatory sequences of genes, modify the genome and permit the development of genes with new properties. Mechanisms such as lateral gene transfer, exon shuffling or the creation of new genes by transposition contribute to the evolution of a genome, but remain of relatively restricted relevance.Mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences, such as blocks of satellite DNAs, appear to involve the action of RNA interference (RNAi). RNAi mechanisms have been proven to be involved in chromatin packaging related with gene inactivation as well as in DNA excision during the macronucleus development in ciliates.     

Genetic Relationships Among Five Basic Genomes St,E,A,B and D in Triticeae Revealed by Genomic Southern and in situ Hybridization

The St and E are two important basic genomes in the perennial tribe Triticeae (Poaceae). They exist in many perennialspecies and are very closely related to the A, B and D genomes of bread wheat (Triticum aestivum L.). Genomic Southernhybridization and genomic in situ hybridization (GISH) were used to analyze the genomic relationships between the twogenomes (St and E) and the three basic genomes (A, B and D) of T. aestivum. The semi-quantitative analysis of the Southernhybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, andrelatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion.St and E are the two basic genomes of Thinopyrum ponticum (StStE~eE~bE~x) and Th. intermedium (StE~eE~b), two perennialspecies successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of thespontaneous wheat-Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genomeand rarely in the B genome. This would develop further use of alien species for wheat improvement, especially thosecontaining St or E in their genome components.     

定量四联体

文章： J.L. Huppert and S. Balasubramanian, “G-quadruplexes in promoters throughout the human genome[G-四联体遍布人类基因组的启动子区域]。”     

"Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as "ant" and "grasshopper" strategies of resource utilization. Interestingly, a strain may be "ant" in one medium and "grasshopper" in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective.     

Nitration in neurodegeneration: deciphering the "Hows" "nYs"

Recent literature has ushered in a new awareness of the diverse post-translational events that can influence protein folding and function. Among these modifications, protein nitration is thought to play a critical role in the onset and progression of several neurodegenerative diseases. While previously considered a late-stage epiphenomenon, nitration of protein tyrosine residues appears to be an early event in the lesions of amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease. The advent of highly specific biochemical and immunological detection methods reveals that nitration occurs in vivo with biological selectively and site specificity. In fact, nitration of only a single Tyr residue is often sufficient to induce profound changes in the activity of catalytic proteins and the three-dimensional conformation of structural proteins. Presumably, nitration modifies protein function by altering the hydrophobicity, hydrogen bonding, and electrostatic properties within the targeted protein. Most importantly, however, nitrative injury may represent a unifying mechanism that explains how genetic and environmental causes of neurological disease manifest a singular phenotype. In this review and synthesis, we first examine the pathways of protein nitration in biological systems and the factors that influence site-directed nitration. Subsequently, we turn our attention to the structural implications of site-specific nitration and how it affects the function of several neurodegeneration-related proteins. These proteins include Mn superoxide dismutase and neurofilament light subunit in amyotrophic lateral sclerosis, alpha-synuclein and tyrosine hydroxylase in Parkinson's disease, and tau in Alzheimer's disease.     

"Chitin-specific" peroxidases in plants

The activity of various plant peroxidases and the ability of their individual isoforms to bind chitin was studied. Some increase in peroxidase activity was observed in crude extracts in the presence of chitin. Activated peroxidases of some species fell in the fraction not sorbed on chitin and those of other species can bind chitin. Only anionic isoperoxidases from oat (Avena sativa), rice (Oryza sativa), horseradish (Armoracia rusticana), garden radish (Raphanus sativus var. radicula), peanut (Arachis hypogaea), and tobacco (Nicotiana tabacum Link et Otto) were sorbed on chitin. Both anionic and cationic isoforms from pea (Pisum sativum), galega (Galega orientalis), cucumber (Cucumis sativus), and zucchini (Cucurbita pepo L.) were sorbed on chitin. Peroxidase activation under the influence of chitin was correlated to the processes that occur during hypersensitive reaction and lignification of sites, in which pathogenic fungus penetrates into a plant. The role of chitin-specific isoperoxidases in inhibition of fungal growth and connection of this phenomenon with structural characteristics of isoperoxidases are also discussed.