Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0729-7) contains supplementary material, which is available to authorized users.     

基于基因本体论的模式生物分子功能分布异同

基因本体论是关于基因和蛋白质知识的标准词汇,也是今后实现各种与基因相关的数据统一、数据转换、数据挖掘的基础。本文通过分子功能基因本体论比较了不同模式生物基因产物分子功能分布的异同。结果发现:在动物类、植物类以及真菌类模式生物中,大部分已知功能基因的分布比例是基本一致的,存在一定的同源性;但在动物中结合类基因数量较多而在植物与真菌中反而催化类基因数量较多,信号传导相关基因在动物中的分布数量多间接证明了动物在进化上的高等性,而植物中特有的大分子传递相关编码基因,可能与植物的养分、水分在机体种的传输相关。     

恢复及演替过程中的土壤生态学考虑

 人类社会的日益扩张,导致人类加速占据地球表面景观,并胁迫地球上生态系统提供不断增长的资源需求和废物吸收能力。所以保护尚未“开放”的自然生态系统及恢复退化的生态系统成为人类长期生存的重要保证。该文着重讨论了恢复过程中的土壤生态学问题。土壤是所有陆地生态系统的结构与功能基础。土壤微生物与动物的种群变化,土壤有机质的积累,及主要元素地球化学循环的改变是恢复生态的重要环节。生态恢复与演替有许多共性,所以演替理论对于认识生态系统恢复中的结构与功能变化有着很大帮助。与自然演替不同的是,人的积极参与在生态恢复中占有中心位置。从最初样地的确立与物种的选择,到后续的灌溉与施肥管理,人的选择影响着土壤的演化,生态系统的发展方向,和最终恢复生态的结果。为保障恢复生态系统的可持续性,短期的工作目标,如提供养分促进植物生长,务必与长期的工作目标,如土壤的恢复相结合。植物与土壤的相互反馈是生态恢复成功的重要标志。成功的生态恢复不仅是对现有生态学理论的“试金检验”,也是推动生态学学科发展的重要原动力。     

Energy-efficient growth of phage Q Beta in Escherichia coli

The role of natural selection in the optimal design of organisms is controversial. Optimal forms, functions, or behaviors of organisms have long been claimed without knowledge of how genotype contributes to phenotype, delineation of design constraints, or reference to alternative designs. Moreover, arguments for optimal designs have been often based on models that were difficult, if not impossible, to test. Here, we begin to address these issues by developing and probing a kinetic model for the intracellular growth of bacteriophage Q beta in Escherichia coli. The model accounts for the energetic costs of all template-dependent polymerization reactions, in ATP equivalents, including RNA-dependent RNA elongation by the phage replicase and synthesis of all phage proteins by the translation machinery of the E. coli host cell. We found that translation dominated phage growth, requiring 85% of the total energy expenditure. Only 10% of the total energy was applied to activities other than the direct synthesis of progeny phage components, reflecting primarily the cost of making the negative-strand RNA template that is needed for replication of phage genomic RNA. Further, we defined an energy efficiency of phage growth and showed its direct relationship to the yield of phage progeny. Finally, we performed a sensitivity analysis and found that the growth of wild-type phage was optimized for progeny yield or energy efficiency, suggesting that phage Q beta has evolved to optimally utilize the finite resources of its host cells.     

Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae)

Amplifying microbial DNA by the polymerase chain reaction (PCR) from single phytoseiid mites has been difficult, perhaps due to the low titer of bacteria and to interference by the relatively larger amounts of mite genomic DNA. In this paper we evaluate the efficiency of standard and high-fidelity PCR protocols subsequent to amplification of the whole genome by a multiple displacement amplification (MDA) procedure developed by Dean et al. DNA from the phytoseiid Phytoseiulus persimilis (Athias-Henriot) was tested because it lacks a Cytophaga-like organism (CLO) and we could add known amounts of a plasmid containing a cloned 16S rRNA gene fragment from a CLO from Metaseiulus occidentalis (Nesbitt). P. persimilis genomic DNA was mixed with the serially diluted plasmid and amplified using MDA followed by either standard or high-fidelity PCR. MDA followed by high-fidelity PCR was most efficient and successfully amplified an expected 1.5-kb band from as little as 0.01fg of the plasmid, which is equivalent to about 1 copy. MDA followed by high-fidelity PCR also consistently amplified Wolbachia- or CLO-specific products from naturally infected single females or eggs of M. occidentalis, which will allow detailed studies of infection frequency and transmission of several microorganisms associated with this predatory mite.     

Intragenic codon bias in a set of mouse and human genes

To better conceptualize the mechanism underlying the evolution of synonymous codons, we have analysed intragenic codon usage in chosen "regions" of some mouse and human genes. We divided a given gene into two regions: one consisting of a trinucleotide repeat (TNR) and the other consisting of the "rest of the coding region" (RCR). Usually, a TNR is composed of a repetitive single codon, which may reflect its frequency in a gene. In contrast, a non-random frequency of a codon in the RCR versus TNR (or vice versa) of a gene should indicate a bias for that codon within the TNR. We examined this scenario by comparing codon frequency between the RCR and the cognate TNR(s) for a set of human and mouse genes. A TNR length of six amino acids or more was used to identify genes from the Genbank database. Twenty nine human and twenty one mouse genes containing TNRs coding for nine different amino acid runs were identified. The ratio of codon frequency in a TNR versus the corresponding RCR was expressed as "fold change" which was also regarded as a measure of codon bias (defined as preferential use either in TNR or in RCR). Chi-square values were then determined from the distribution of codon frequency in a TNR vs. the cognate RCR. At p<0.001, 22% and 27%, respectively, of human and mouse TNRs showed codon bias. Greater than 40% of the TNRs (29 out of 69 in human, and 18 of 42 in mouse) showed codon bias at p<0.05. In addition, we identify eight single-codon TNRs in mouse and ten in human genes. Thus, our results show intragenic codon bias in both mouse and human genes expressed in diverse tissue types. Since our results are independent of the Codon Adaptation Index (CAI) and starvation CAI, and since the tRNA repertoire in a cell or in a tissue is constant, our data suggest that other constraints besides tRNA abundance played a role in creating intragenic codon bias in these genes.     

生命科学研究中常用模式生物

模式生物是生命科学研究的重要材料,目前公认的用于生命科学研究的常见模式生物有噬菌体、大肠杆菌、酵母、线虫、果蝇、斑马鱼、小鼠、拟南芥等.这8种常用模式生物对生命现象的揭密和人类疾病治疗的探索等都所做出了重大贡献,对其在生命科学研究中的历史轨迹、各自优势、技术手段、热点研究、发展前景等系统而又简要的了解,有助于具体而又生动地体察到模式生物在今天生命科学发展中的重要地位和推动生命科学及医学进步的不可替代的巨大潜力.     

Species specificity of barnacle settlement-inducing proteins

We previously isolated a larval settlement-inducing protein complex (SIPC) from adult extracts of the barnacle, Balanus amphitrite using a nitrocellulose membrane settlement assay. In the present study, we found that the extracts of other adult barnacles, Megabalanus rosa and Balanus eburneus, also induced the settlement of B. amphitrite cyprids although the inductive activity was slightly lower than that of conspecific extracts. Furthermore, we examined reactivity to anti-SIPC antibody in adult extracts from six species of Japanese barnacles other than B. amphitrite, brine shrimp and eight marine sessile organisms besides barnacles. The results showed that all barnacles examined contained SIPC-like proteins with slightly different molecular weight, while the other animals did not react to the antibody by immunoblot analysis. These findings suggest that species specificity in settlement-inducing proteins of barnacles is not so strict, but these proteins are characteristic to barnacle species.