Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes

The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.     

Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution

Microbiology - Acidobacteria are one of the widespread and numerically abundant groups of prokaryotes in soils and peatlands. The functional potential of these microorganisms remains poorly...     

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes–S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens–and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions.     

基因组编码小分子蛋白质研究进展

不超过50个氨基酸组成的蛋白在所有生物体中表现的特征都不明显.对其相应的基进行确实可靠的注释非常具有挑战性.由从细胞中纯化和鉴定小分子蛋白产物极其困难,难以确切知道细胞内有多少小分子蛋白,更不用说研究它们的生物学功能了.但越来越多的例子表明,小分子蛋白在细胞中分布广泛,而且有着不同的细胞生理学功能.本文即是对小分子蛋白研究进展的简要总结.     

植物细胞壁多糖合成酶系及真菌降解酶系

秸秆类植物细胞壁多糖高效降解转化对我国农业经济的绿色可持续发展具有重要意义,然而植物细胞壁在长期进化过程中形成了复杂结构限制了工业化酶解转化的过程。一方面从植物细胞壁多糖合成酶系的多样性、细胞壁多糖成分的复杂性、超分子结构的异质性等方面综述了形成植物细胞壁抗降解屏障的原因;另一方面从真菌降解植物细胞壁酶系的多样性、不同菌株降解酶组成差异性等分析降解转化植物细胞壁时发挥的不同作用,从而为工业转化合理复配真菌降解酶系,提高秸秆生物质的利用效率提供理论支持。     

植物病毒沉默抑制因子研究进展

RNA沉默是广泛存在于真菌、动物和植物中的一种特异序列降解机制.在植物中,RNA沉默是一种抵抗外界植物病毒入侵的自然机制.但是,植物病毒通常也会采取编码沉默抑制因子的相应机制来抵抗基因沉默,以便能够入侵植物.论述了主要沉默抑制因子的机制、特点和相关确认沉默抑制因子实验,并对沉默抑制因子的研究前景进行了展望.     

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.     

Bioinformatic Characterization of P-Type ATPases Encoded Within the Fully Sequenced Genomes of 26 Eukaryotes

P-type ATPases play essential roles in numerous processes, which in humans include nerve impulse propagation, relaxation of muscle fibers, secretion and absorption in the kidney, acidification of the stomach and nutrient absorption in the intestine. Published evidence suggests that uncharacterized families of P-type ATPases with novel specificities exist. In this study, the fully sequenced genomes of 26 eukaryotes, including animals, plants, fungi and unicellular eukaryotes, were analyzed for P-type ATPases. We report the organismal distributions, phylogenetic relationships, probable topologies and conserved motifs of nine functionally characterized families and 13 uncharacterized families of these enzyme transporters. We have classified these proteins according to the conventions of the functional and phylogenetic IUBMB-approved transporter classification system (, Saier et al. in Nucleic Acids Res 34:181–186, 2006; Nucleic Acids Res 37:274–278, 2009). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

植物基因组比较作图研究进展

基因组比较作图是基因组研究的重要内容。植物比较作图研究表明,在长期的进化过程中,基因的组成表现出高度的保守性。随着植物遗传图谱和物理图谱的迅速发展,为植物比较作图奠定了重要的基础。现就植物基因组遗传图和物理图以及比较作图的最新研究进展作一介绍。     

Studies of Aquatic Fungi. XVIII. Aquatic Fungi in Lake S̀niardwy and Eighteen Neighbouring Lakes

The work was undertaken to investigate the mycoflora of Lake S̀niardwy and eighteen adjacent lakes. Samples of water were collected once a month (1984-1987) for hydrochemical analysis and studies of the fungi content. Forty species of fungi were found in lake S̀niardwy and 60 in other lakes. The following fungi unknown from Poland were found in these lakes: Olpidium endogenum, Olpidium granulatum, Dictyomorpha dioica, Phlyctochytrium aureliae, Rhizophydium planktonicum, Zygorhizidium melosirae, Cladochytrium polystomum, Blastocladia rostrata, Olpidiopsis achlyae, Olpidiopsis pythii, Lagenidium rabenhorstii, Pythiella vernalis, Achlya rodrigueziana, Anguillospora gigantea, Dimorphospora foliicola and Mycocentrospora aquatica.     

Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.     

Molecular Evolution of FtsZ Protein Sequences Encoded Within the Genomes of Archaea,Bacteria, and Eukaryota

The FtsZ protein is a polymer-forming GTPase which drives bacterial cell division and is structurally and functionally related to eukaryotic tubulins. We have searched for FtsZ-related sequences in all freely accessible databases, then used strict criteria based on the tertiary structure of FtsZ and its well-characterized in vitro and in vivo properties to determine which sequences represent genuine homologues of FtsZ. We have identified 225 full-length FtsZ homologues, which we have used to document, phylum by phylum, the primary sequence characteristics of FtsZ homologues from the Bacteria, Archaea, and Eukaryota. We provide evidence for at least five independent ftsZ gene-duplication events in the bacterial kingdom and suggest the existence of three ancestoral euryarchaeal FtsZ paralogues. In addition, we identify FtsZ-like sequences from Bacteria and Archaea that, while showing significant sequence similarity to FtsZs, are unlikely to bind and hydrolyze GTP.     

Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota,Potentially Bridging the Gap between the Prokaryotes and Eukaryotes

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虫生真菌分子致病机理及基因工程改造研究进展

虫生真菌侵染寄主昆虫的复杂过程可分为体表附着、体壁穿透及体内定殖和致死等不同阶段.近年来,以金龟子绿僵茵(Metarhizium anisopliae)和球孢白僵菌(Beauveria bassiana)为代表的基因功能研究取得了长足的进展,从不同角度阐明了虫生真菌的分子致病机理;同时,基因工程技术的应用为昆虫病原真菌的遗传改良和选育高毒力杀虫菌株开辟了新的途径.对近年来昆虫病原真菌侵染寄主的分子对策及基因工程改造的研究进展进行了综述,并就进一步研究虫生真菌的毒力基因及功能进行了探讨.     

虫生真菌分子致病机理及基因工程改造研究进展

虫生真菌侵染寄主昆虫的复杂过程可分为体表附着、体壁穿透及体内定殖和致死等不同阶段。近年来, 以金龟子绿僵菌(Metarhizium anisopliae)和球孢白僵菌(Beauveria bassiana)为代表的基因功能研究取得了长足的进展, 从不同角度阐明了虫生真菌的分子致病机理; 同时, 基因工程技术的应用为昆虫病原真菌的遗传改良和选育高毒力杀虫菌株开辟了新的途径。对近年来昆虫病原真菌侵染寄主的分子对策及基因工程改造的研究进展进行了综述, 并就进一步研究虫生真菌的毒力基因及功能进行了探讨。     

A Model Simulating the Dynamics of Plant Mitochondrial Genomes

Molecular evolution of the plant mitochondrial genome involves rearrangements due to the presence of highly recombining repeated sequences. As a result, this genome is composed of a set of molecules of various sizes that generate each other through recombination. The model presented simulates the evolution of various frequencies of the different types of molecules over successive cell cycles. It considers the mitochondrial genome as a population of circular molecules evolving through recombination, replication and random segregation. The model parameters are the rates of recombination of each sequence, the frequency of each type of recombination, the replication rates of the circles and the total amount of mitochondrial DNA per cell. This model demonstrates that high recombination rates lead to rapid deletions of sequences in the absence of selection. The frequency of deletion is dependent on the simulated reproductive mechanism. The conditions leading to reversible or irreversible rearrangements were also investigated.