Origins of bilateral symmetry: Hox and dpp expression in a sea anemone

Over 99% of modern animals are members of the evolutionary lineage Bilateria. The evolutionary success of Bilateria is credited partly to the origin of bilateral symmetry. Although animals of the phylum Cnidaria are not within the Bilateria, some representatives, such as the sea anemone Nematostella vectensis, exhibit bilateral symmetry. We show that Nematostella uses homologous genes to achieve bilateral symmetry: Multiple Hox genes are expressed in a staggered fashion along its primary body axis, and the transforming growth factor-beta gene decapentaplegic (dpp) is expressed in an asymmetric fashion about its secondary body axis. These data suggest that bilateral symmetry arose before the evolutionary split of Cnidaria and Bilateria.     

中华仙影海葵早期发育的初步研究

在生物进化研究中,海葵的胚胎和幼体是研究二侧对称动物进化祖先较理想的实验动物。以室内实验方法研究了中华仙影海葵的胚胎、浮浪幼虫及幼海葵的发生、发育过程,对各阶段的变化和形态特点进行了比较详细的描述,并比较了中华仙影海葵与其他3种海葵的早期发育,揭示了中华仙影海葵从性腺成熟到16触手幼海葵各个阶段的变态过程。     

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.     

海葵多肽类神经毒素的结构与药理学功能

海葵以其触手刺细胞中的毒液行使捕食和防御功能,其毒液中富含各种多肽类神经毒素,分子量为3—7kDa之间,分子序列中含多对二硫键以稳定其结构。海葵神经毒素以钠离子通道毒素和钾离子通道毒素为其主要成分,此外还发现有作用于其他离子通道的成分,此外,还有部分海葵毒素目前尚不清楚其分子靶标。不同类型的海葵毒素具有不同的空间结构。海葵毒素多肽的分子多样性使其成为动物毒素研究的一个重要分支,同时海葵多肽毒素对不同离子通道的特异性和高亲和性,使得它们成为神经生理学和药理学研究的一种重要工具。     

Comparative genomics of trypanosomatid parasitic protozoa

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.     

辣椒RWP-RK转录因子分析

RWP-RK基因家族是植物特有的转录因子家族。该家族在植物氮元素信号传导和配子体发育过程中起核心的调控作用。使用公开的中国重要栽培品种遵辣1号及其野生亲本墨西哥辣椒种"Chiltepin"的基因组序列,鉴定出辣椒基因组中含有RWP-RK结构域的基因,并进行系统进化、染色体定位、保守序列和可能功能等分析。遵辣一号基因组中与拟南芥氮代谢重要调控因子AtNLP7同源的是CaZunla01g000097、CaZunla01g004485和CaZunla00g000405。遵辣1号的2个基因Capana03g001990和Capana03g000787与拟南芥卵细胞形成相关转录因子AtRKD1、AtRKD2和AtRKD4同源。这些基因在栽培品种遵辣1号和其野生祖先品种基因组中保持了高度的保守性。此外,辣椒基因组中存在特有的RWP-RK转录因子亚家族。这一亚家族的蛋白质氨基酸序列中含有独特的保守序列。这些序列在拟南芥RWP-RK转录因子中并不存在。辣椒栽培品种遵辣1号中有在其野生祖先"Chiltepin"中不存在的RWP-RK转录因子基因。鉴定出了分别与拟南芥RWP-RK转录因子高度相似、存在重大差异以及辣椒野生种和栽培种之间存在差异的RWP-RK转录因子成员,为后期辣椒RWP-RK转录因子家族的克隆和功能研究提供了重要的信息。对这些基因进行功能研究,会极大的促进辣椒对氮元素匮乏环境响应以及辣椒配子体发育的分子机制研究。     

The Chlamydomonas genome reveals the evolution of key animal and plant functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.     

Characterization of compounds that induce symbiosis between sea anemone and anemone fish

The species-specific partnership between the sea anemone and anemone fish in many parts of the Indo-Pacific region is a well-known phenomenon. Chemicals secreted by the sea anemone to elicit symbiotic behavior of the fish have been studied for two host-guest pairs, Radianthus kuekenthali (sea anemone)-Amphiprion perideraion (anemone fish) and Stoichactis kenti-A. ocellaris. A new pyridinium compound, amphikuemin, which induces characteristic attracted swimming (toward the chemical stimulus) in A. perideraion, has been isolated from R. kuekenthali and characterized. Several other chemicals that elicit characteristic symbiotic movements have also been identified.     

仿刺参β-actin基因的克隆及在各组织中的表达

参考海葵Nematoste Uavectensis在GenBank中的β-actin基因mRNA部分序列（XM_001630533）设计引物,对仿刺参Apostichopusjaponicus进行特异的PCR扩增,将扩增产物测序分析,再根据测序结果设计仿刺参专用β-actin引物ACT1／ACT2,对不同退火温度和循环次数条件下的该基因RT-PCR产物进行了对比。本研究中首次克隆了仿刺参的β-actin基因,为今后仿刺参目的基因表达的半定量分析研究奠定了基础。     

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Previous genome comparisons have suggested that one important trend in vertebrate evolution has been a sharp rise in intron abundance. By using genomic data and expressed sequence tags from the marine annelid Platynereis dumerilii, we provide direct evidence that about two-thirds of human introns predate the bilaterian radiation but were lost from insect and nematode genomes to a large extent. A comparison of coding exon sequences confirms the ancestral nature of Platynereis and human genes. Thus, the urbilaterian ancestor had complex, intron-rich genes that have been retained in Platynereis and human.     

Swimming sea anemones of Puget Sound: swimming of Actinostola new species in response to Stomphia coccinea

Swimming as a response of the sea anemone Actinostola new species can be elicited as a result of contact with the submarginal surface of another swimming sea anemone Stomphia coccinea. However, Stomphia does not swim as a result of contact with Actinostola. In all other known respects, swimming is caused in both species by the same stimuli, including certain starfishes, a nudibranch, and electrical stimuli. No agent that causes Actinostola to swim has been detected in extracts, rubbings, or dried matter from Stomphia.     

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.     

黄海葵解剖学和主要器官组织学的研究

黄海葵Anthopleura xanthogrammica Berkly为二胚层动物,体形辐射对称,主要器官包括皮肤、触手、隔膜、消化道和生殖腺。消化道由口、口道和消化腔组成,无肛门;各器官的上皮组织均是由内皮肌细胞或外皮肌细胞组成,上皮中夹有大量的腺细胞;在其触手、隔膜丝及口道的上皮中还发现了3种结构不同的刺细胞(刺丝囊),分别行使不同的功能;生殖腺为滤泡型,由营养细胞和生殖细胞共同构成。此外,还探讨了海葵主要结构与功能的关系。     

A general method for the chromosomal amplification of genes in yeast

The yeast retrotransposon Ty can be used to insert multiple copies of a gene at new sites in the genome. The gene of interest is inserted into a GALI-Ty fusion construct; the entire "amplification cassette" is then introduced into yeast on a high copy number plasmid vector. Transposition of the Ty element carrying the gene occurs at multiple sites in the genome. Two genes, a bacterial neomycin phosphotransferase gene and the yeast TRPl gene, were amplified in this way. Although the amplified genes were about 1 kilobase in length, they were amplified to about the same extent as a 40-base pair segment. The benefit of this "shotgun" approach is that amplification can be achieved in one set of manipulations.     

潘那利番茄GRF基因家族全基因组鉴定分析

【目的】分析研究潘那利番茄GRF基因家族全基因组鉴定分析。【方法】研究基于生物信息学方法对潘那利GRF基因家族成员进行全基因组鉴定和分析,并对其起源及进化进行了追溯。【结果】潘那利番茄中共鉴定了10个SpGRF成员,不均匀分布在7条染色体上,预测了SpGRFs蛋白的分子量、等电点、亲水性总均值等理化性质。SpGRFs基因可分为6个亚家族。所有SpGRF基因N端都含有1个QLQ和1个WRC结构域,C端则为多种保守基序。共线性结果显示基因组内有3对6个旁系同源基因,全部为片段复制,SpGRFs受自然选择压力下,有共同起源祖先,与拟南芥亲缘关系更近。【结论】鉴定了潘那利番茄中GRF基因家族的基本信息。     

Ancient noncoding elements conserved in the human genome

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.     

正选择驱动褪黑激素受体MT1与MT2基因的分化

【目的】研究褪黑激素受体（melatonin receptor,MTNR）基因的进化模式,为褪黑激素受体基因相关功能的研究提供理论参考。【方法】利用生物信息学的方法和软件对来自11个物种的褪黑激素受体1a（MT1）和褪黑激素受体1b（MT2）基因的系统发生关系、基因相似性、选择压力、选择方向等进行系统地分析。【结果】MT1和MT2基因可能由共同祖先基因通过基因重复产生, MT1可能保持着源基因的功能,MT2为新产生的功能基因。MT1基因在物种间的相似性极显著高于MT2基因（P＜0.01）;MT1基因主要受纯化选择,MT2基因受到显著的正选择;MT1与MT2基因均承受着较强的选择压力,且选择压力在2基因间无显著差异（P＞0.05）。【结论】MT1基因主要受纯化选择可能是MT1基因与动物季节性繁殖关联研究结论不统一的原因,MT2基因受正选择提示正选择可能是驱动MT2与MT1发生分化的重要动力。