Architecture and material properties of diatom shells provide effective mechanical protection

Diatoms are the major contributors to phytoplankton blooms in lakes and in the sea and hence are central in aquatic ecosystems and the global carbon cycle. All free-living diatoms differ from other phytoplankton groups in having silicified cell walls in the form of two 'shells' (the frustule) of manifold shape and intricate architecture whose function and role, if any, in contributing to the evolutionary success of diatoms is under debate. We explored the defence potential of the frustules as armour against predators by measuring their strength. Real and virtual loading tests (using calibrated glass microneedles and finite element analysis) were performed on centric and pennate diatom cells. Here we show that the frustules are remarkably strong by virtue of their architecture and the material properties of the diatom silica. We conclude that diatom frustules have evolved as mechanical protection for the cells because exceptional force is required to break them. The evolutionary arms race between diatoms and their specialized predators will have had considerable influence in structuring pelagic food webs and biogeochemical cycles.     

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Diatoms dominate the biomass of phytoplankton in nutrient-rich conditions and form the basis of some of the world's most productive marine food webs. The diatom nuclear genome contains genes with bacterial and plastid origins as well as genes of the secondary endosymbiotic host (the exosymbiont), yet little is known about the relative contribution of each gene group to diatom metabolism. Here we show that the exosymbiont-derived ornithine-urea cycle, which is similar to that of metazoans but is absent in green algae and plants, facilitates rapid recovery from prolonged nitrogen limitation. RNA-interference-mediated knockdown of a mitochondrial carbamoyl phosphate synthase impairs the response of nitrogen-limited diatoms to nitrogen addition. Metabolomic analyses indicate that intermediates in the ornithine-urea cycle are particularly depleted and that both the tricarboxylic acid cycle and the glutamine synthetase/glutamate synthase cycles are linked directly with the ornithine-urea cycle. Several other depleted metabolites are generated from ornithine-urea cycle intermediates by the products of genes laterally acquired from bacteria. This metabolic coupling of bacterial- and exosymbiont-derived proteins seems to be fundamental to diatom physiology because the compounds affected include the major diatom osmolyte proline and the precursors for long-chain polyamines required for silica precipitation during cell wall formation. So far, the ornithine-urea cycle is only known for its essential role in the removal of fixed nitrogen in metazoans. In diatoms, this cycle serves as a distribution and repackaging hub for inorganic carbon and nitrogen and contributes significantly to the metabolic response of diatoms to episodic nitrogen availability. The diatom ornithine-urea cycle therefore represents a key pathway for anaplerotic carbon fixation into nitrogenous compounds that are essential for diatom growth and for the contribution of diatoms to marine productivity.     

Gene transfer to the nucleus and the evolution of chloroplasts

Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information contained within single genes. Among the 210 different protein-coding genes contained in the completely sequenced chloroplast genomes from a glaucocystophyte, a rhodophyte, a diatom, a euglenophyte and five land plants, we have now identified the set of 45 common to each and to a cyanobacterial outgroup genome. Phylogenetic inference with an alignment of 11,039 amino-acid positions per genome indicates that this information is sufficient--but just rarely so--to identify the rooted nine-taxon topology. We mapped the process of gene loss from chloroplast genomes across the inferred tree and found that, surprisingly, independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more that 4:1. We identified homologues of 44 different plastid-encoded proteins as functional nuclear genes of chloroplast origin, providing evidence for endosymbiotic gene transfer to the nucleus in plants.     

Copepod hatching success in marine ecosystems with high diatom concentrations

Diatoms dominate spring bloom phytoplankton assemblages in temperate waters and coastal upwelling regions of the global ocean. Copepods usually dominate the zooplankton in these regions and are the prey of many larval fish species. Recent laboratory studies suggest that diatoms may have a deleterious effect on the success of copepod egg hatching. These findings challenge the classical view of marine food-web energy flow from diatoms to fish by means of copepods. Egg mortality is an important factor in copepod population dynamics, thus, if diatoms have a deleterious in situ effect, paradoxically, high diatom abundance could limit secondary production. Therefore, the current understanding of energy transfer from primary production to fisheries in some of the most productive and economically important marine ecosystems may be seriously flawed. Here we present in situ estimates of copepod egg hatching success from twelve globally distributed areas, where diatoms dominate the phytoplankton assemblage. We did not observe a negative relationship between copepod egg hatching success and either diatom biomass or dominance in the microplankton in any of these regions. The classical model for diatom-dominated system remains valid.     

Photosynthetic architecture differs in coastal and oceanic diatoms

Diatoms are a key taxon of eukaryotic phytoplankton and a major contributor to global carbon fixation. They are ubiquitous in the marine ecosystem despite marked gradients in environmental properties, such as dissolved iron concentrations, between coastal and oceanic waters. Previous studies have shown that offshore species of diatoms and other eukaryotic algae have evolved lower iron requirements to subsist in iron-poor oceanic waters, but the biochemical mechanisms responsible for their decreased iron demand are unknown. Here we show, using laboratory-cultured model species, a fundamental difference between a coastal and an oceanic diatom in their photosynthetic architecture. Specifically, the oceanic diatom had up to fivefold lower photosystem I and up to sevenfold lower cytochrome b6f complex concentrations than a coastal diatom. These changes to the photosynthetic apparatus markedly decrease the cellular iron requirements of the oceanic diatom but not its photosynthetic rates. However, oceanic diatoms might have also sacrificed their ability to acclimate to rapid fluctuations in light intensity--a characteristic of dynamic and turbid coastal waters. We suggest that diatoms, and probably other eukaryotic algal taxa, exploited this difference in the underwater light climate between oceanic and coastal waters, enabling them to decrease their iron requirements without compromising photosynthetic capacity. This adaptation probably facilitated the colonization of the open ocean by diatoms, and contributes to their persistence in this iron-impoverished environment.     

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.     

Identification and bioinformatics analysis of pseudogenes from whole genome sequence of Phaeodactylum tricornutum

Pseudogenes share sequence similarities with functional genes, but in general they have lost their protein-coding ability. The identification of pseudogenes is a very important step in genome annotation. Phaeodactylum tricornutum is a marine diatom that is rich in polyunsaturated fatty acids (PUFAs). The genome of P. tricornutum has been completely sequenced. To identify pseudogenes in P. tricornutum, we developed a pipeline to discover and characterize pseudogenes. We identified a total of 1654 ‘true’ processed pseudogenes, 714 duplicated pseudogenes and 4729 pseudogene fragments. The results of the bioinformatics analysis indicated that the genome sequence of P. tricornutum contained many pseudogenes and pseudogene fragments.     

Yeast genome duplication was followed by asynchronous differentiation of duplicated genes

Gene redundancy has been observed in yeast, plant and human genomes, and is thought to be a consequence of whole-genome duplications. Baker's yeast, Saccharomyces cerevisiae, contains several hundred duplicated genes. Duplication(s) could have occurred before or after a given speciation. To understand the evolution of the yeast genome, we analysed orthologues of some of these genes in several related yeast species. On the basis of the inferred phylogeny of each set of genes, we were able to deduce whether the gene duplicated and/or specialized before or after the divergence of two yeast lineages. Here we show that the gene duplications might have occurred as a single event, and that it probably took place before the Saccharomyces and Kluyveromyces lineages diverged from each other. Further evolution of each duplicated gene pair-such as specialization or differentiation of the two copies, or deletion of a single copy--has taken place independently throughout the evolution of these species.     

Vast laminated diatom mat deposits from the west low-latitude Pacific Ocean in the last glacial period

Diatoms are one of the predominant contributors to global carbon fixation by accounting for over 40% of total oceanic primary production and dominate export production. They play a significant role in marine biogeochemistry cycle. The diatom mat deposits are results of vast diatoms bloom. By analysis of diatom mats in 136°00′--140°00′E, 15°00′--21°00′N, Eastern Philippines Sea, we identified the species of the diatoms as giant Ethmodiscus rex （Wallich） Hendey. AMS 14C dating shows that the sediments rich in diatom mats occurred during 16000--28600 a B.P., which means the bloom mainly occurred during the last glacial period, while there are no diatom mat deposits in other layers. Preliminary analysis indicates that Antarctic Intermediate Water （AAIW） expanded northward and brought silicate-rich water into the area, namely, silicon leakage processes caused the bloom of diatoms. In addition, the increase of iron input is one of the main reasons for the diatom bloom.     

The medaka draft genome and insights into vertebrate genome evolution

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.     

同源重组敲除三角褐指藻基因的研究

为探索应用基因敲除技术研究三角褐指藻基因功能的研究体系,本文以三角褐指藻甘油激酶基因作为靶基因,构建了同源重组基因敲除载体,利用微弹轰击法将该载体成功转化至三角褐指藻中,经100μg/mL Zeocin筛选和PCR验证获得了34个阳性转基因藻株;并进一步对三角褐指藻甘油激酶基因敲除转基因藻株的甘油激酶表达量和生长两方面进行分析,结果显示胞外甘油兼养不影响转基因藻细胞生长,甘油激酶不表达或表达量降低.本文通过构建敲除载体,完成了遗传转化,筛选获得阳性转基因藻,并进一步研究了转基因藻的性状,最终建立了应用同源重组基因敲除技术靶向研究三角褐指藻基因功能的研究体系.     

海洋硅藻多样性与生态作用研究

硅藻是海洋浮游植物的主要类群,也是海洋生态系统中的主要初级生产者,在海洋生态系统的物质循环和能量流动中起着极其重要的作用,但人们对海洋硅藻多样性和生态作用的认识还很有限.在叙述海洋硅藻多样性、生态作用及硅藻分类学与系统学的国内外研究动态和最新进展的基础上,概述了厦门大学硅藻课题组近年来在海洋硅藻分类学与系统学、多样性与生态分布、硅藻数据库与计算机自动识别、微型硅藻与硅藻隐形种、硅藻遗传地理差异、硅藻对环境和气候变化的响应机制、硅藻细胞硅吸收与硅质壁形成机制等方面的主要研究进展和取得的主要成果.     

海洋浮游植物休眠期的生态学研究

休眠期是甲藻和硅藻抵御外界不利环境条件的一种有效的生理反应机制，也是许多赤潮藻生活史中的一个重要生活阶段．从生态分布、生态作用尤其是在赤潮生消过程中的作用等角度简述了海洋浮游甲藻和硅藻休眠期的生态学的研究情况，并对二者的生态学特征进行比较．甲藻孢囊和硅藻休止细胞在海洋沉积物中的丰度有明显差别，前者较后者具有更明显的季节性萌发能力．温度和光照是影响二者萌发的重要生态因子，温度是甲藻孢囊萌发不可或缺的因素，而光照是硅藻休止细胞萌发的触发因子．二者在种源策略和生态特征上的差异导致了不同的群落演替模式和引发藻华的机制．     

Genome evolution in yeasts

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.     

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.     

夏季南极长城湾沿岸海域浮游硅藻群落定量分析

对南极硅藻进行定量研究较有必要,以客观准确地了解它的组成和分布特征。在南极长城湾沿岸海域共设置6个采样点,每个采样点定量采集3个浮游硅藻样本。结果显示:长城湾海域共发现浮游硅藻31种。浮游硅藻群落的优势种为Cocconesi fasciolata(18.5%)、Amphora holsatica(13.6%)。次优势种为Cocconeis costata(7.1%)、Cocconeis imperatrix(6.8%)、Thalassiosira antarctica(6.4%)、Rhoicosphenia genuflexa(6.1%)、Licmophora antarctica(5.1%)。各样点浮游硅藻细胞密度总平均值为1.92×10~5ind·L~(-1),变幅为1.44×10~5~2.56×10~5ind·L~(-1)。浮游硅藻的分布从湾心到湾口呈现出一定趋势:浮游硅藻的物种丰度,湾心处共15种,湾口处共25种;浮游硅藻的细胞密度,湾心处平均为2.51×10~5ind·L-1,湾口处平均为1.48×10~5ind·L~(-1)。通过相关性分析结果可知,浮游硅藻由湾心到湾口,物种丰度和硅藻细胞密度呈负相关。     

Unicellular C4 photosynthesis in a marine diatom

Nearly 50 years ago, inorganic carbon was shown to be fixed in microalgae as the C3 compound phosphoglyceric acid. The enzyme responsible for C3 carbon fixation, ribulose-1,5-bisphosphate carboxylase (Rubisco), however, requires inorganic carbon in the form of CO2 (ref. 2), and Rubisco enzymes from diatoms have half-saturation constants for CO2 of 30-60 microM (ref. 3). As a result, diatoms growing in seawater that contains about 10 microM CO2 may be CO2 limited. Kinetic and growth studies have shown that diatoms can avoid CO2 limitation, but the biochemistry of the underlying mechanisms remains unknown. Here we present evidence that C4 photosynthesis supports carbon assimilation in the marine diatom Thalassiosira weissflogii, thus providing a biochemical explanation for CO2-insensitive photosynthesis in marine diatoms. If C4 photosynthesis is common among marine diatoms, it may account for a significant portion of carbon fixation and export in the ocean, and would explain the greater enrichment of 13C in diatoms compared with other classes of phytoplankton. Unicellular C4 carbon assimilation may have predated the appearance of multicellular C4 plants.     

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.     

DNA sequence and comparative analysis of chimpanzee chromosome 22

Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.     

簸箕柳SPL基因家族分析

【目的】确定SPL基因家族在不同物种之间的选择性保留和丢失情况,为后续研究被子植物花发育提供参考。【方法】通过在拟南芥(Arabidopsis thaliana)、毛果杨(Populus trichocarpa)、簸箕柳(Salix suchowensis)、葡萄(Vitis vinifera)、番木瓜(Carica papaya)、水稻(Oryza sativa)6种被子植物基因组中查找SPL结构域,寻找6个物种的SPL同源序列。对所找到的SPL序列进行BLASTN比对鉴定同源基因类型。使用自编Perl脚本结合KaKs_Calculator计算SPL同源基因的非同义突变(K_a)以及同义突变(K_s)值,采用共线性分析确定该基因家族的复制和扩张方式。【结果】在6种被子植物基因组中,共发现120个SPL基因。根据种内和种间旁系同源、直系同源基因以及这些同源基因选择压的计算显示:杨柳科SPL同源基因最多,共有旁系同源基因24对,直系同源基因50对; 番木瓜没有旁系同源基因。6个物种中,木本植物比草本植物直系同源基因更多,双子叶植物比单子叶植物直系同源基因更多; 所有旁系同源和直系同源基因的K_a/K_s值均小于1。系统发育树的分析结果与基因同源性分析基本吻合,证明了这两种分析方法具有较高的可靠性。此次研究选取了簸箕柳同一植株上开花和不开花的枝条进行了转录组测序分析,差异表达分析发现了1个SPL基因(willow_GLEAN_10025160)在两种枝条的转录组中表达差异显著(P≤0.01),其在开花枝条中的表达量显著高于未开花枝条,该基因被选为SPL基因家族中参与簸箕柳开花调控的候选基因。【结论】通过对6个物种SPL基因家族的分析,发现6个物种中所有直系同源和旁系同源基因都经历了纯化选择(K_a/K_s<1),基因功能保守。这6个物种除了经历过全基因组复制事件,还发生过大规模的基因丢失或者通过其他方式产生的基因扩张,阐明了它们在进化历史上的复制事件及SPL基因在不同物种中的选择性保留与丢失情况,为进一步研究其在调控簸箕柳开花中的作用提供了有力证据。