Insights into social insects from the genome of the honeybee Apis mellifera

Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A+T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A. mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A. mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.     

The cost of inbreeding in Arabidopsis

Population geneticists have long sought to estimate the distribution of selection intensities among genes of diverse function across the genome. Only recently have DNA sequencing and analytical techniques converged to make this possible. Important advances have come from comparing genetic variation within species (polymorphism) with fixed differences between species (divergence). These approaches have been used to examine individual genes for evidence of selection. Here we use the fact that the time since species divergence allows combination of data across genes. In a comparison of amino-acid replacements among species of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, we find evidence for predominantly beneficial gene substitutions in Drosophila but predominantly detrimental substitutions in Arabidopsis. We attribute this difference to the Arabidopsis mating system of partial self-fertilization, which corroborates a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations owing to their reduced effective population size.     

Protein interaction maps for complete genomes based on gene fusion events

A large-scale effort to measure, detect and analyse protein-protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.     

The immune response of Drosophila

Drosophila mounts a potent host defence when challenged by various microorganisms. Analysis of this defence by molecular genetics has now provided a global picture of the mechanisms by which this insect senses infection, discriminates between various classes of microorganisms and induces the production of effector molecules, among which antimicrobial peptides are prominent. An unexpected result of these studies was the discovery that most of the genes involved in the Drosophila host defence are homologous or very similar to genes implicated in mammalian innate immune defences. Recent progress in research on Drosophila immune defence provides evidence for similarities and differences between Drosophila immune responses and mammalian innate immunity.     

Complete replacement of mitochondrial DNA in Drosophila

The introduction of foreign mitochondria or mitochondrial DNA into a cell is a useful technique for clarifying the molecular mechanisms responsible for the maintenance of mitochondria. Novel combinations of mitochondrial and nuclear genomes have been studied in mammalian cells in culture and in yeast. In Drosophila, we have recently constructed heteroplasmic flies possessing both endogenous mitochondrial DNA and foreign mitochondrial DNA by intra- and interspecific transplantation of germ plasm. During the maintenance of these heteroplasmic lines, flies of D. melanogaster are produced that no longer possess their own mitochondrial DNA but retain the foreign mitochondrial DNA from D. mauritiana. .These flies are fertile and the foreign mitochondrial DNA is stably maintained in their offspring. Here we report the complete replacement of endogenous mitochondrial DNA with that from another multicellular species. Molecular and genetic analysis of this replacement in Drosophila should provide new insight into the functional interaction between nuclear and organelle genomes.     

果蝇分子群体遗传研究分析方法概述

果蝇属物种长期以来被作为基础生物学、特别是群体和进化遗传学的模式物种,来探讨生物学中的一些基本问题,如物种形成的遗传机制、新基因的起源及其方式、适应性进化的遗传机制等.群体遗传的方法贯穿于遗传学、生态学、古生物学、系统发育学等领域之中,已渐成为基础生物学研究的重要方法.围绕果蝇群体遗传研究中的3个主要问题,即起源地、群体历史动态和群体遗传结构,就当前用于分析上述问题的方法进行了概述,并强调了发展适用于多个座位数据的分析方法是将来的一个重要发展方向.     

Initial sequence of the chimpanzee genome and comparison with the human genome

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.     

The Drosophila melanogaster Genetic Reference Panel

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.     

Activation of a C. elegans Antennapedia homologue in migrating cells controls their direction of migration.

Anterior-posterior patterning in insects, vertebrates and nematodes involves members of conserved Antennapedia-class homeobox gene clusters (HOM-C) that are thought to give specific body regions their identities. The effects of these genes on region-specific body structures have been described extensively, particularly in Drosophila, but little is known about how HOM-C genes affect the behaviours of cells that migrate into their domains of function. In Caenorhabditis elegans, the Antennapedia-like HOM-C gene mab-5 not only specifies postembryonic fates of cells in a posterior body region, but also influences the migration of mesodermal and neural cells that move through this region. Here we show that as one neuroblast migrates into this posterior region, it switches on mab-5 gene expression; mab-5 then acts as a developmental switch to control the migratory behaviour of the neuroblast descendants. HOM-C genes can therefore not only direct region-specific patterns of cell division and differentiation, but can also act within migrating cells to programme region-specific migratory behaviour.     

Unexpected features of Drosophila circadian behavioural rhythms under natural conditions

Circadian clocks have evolved to synchronize physiology, metabolism and behaviour to the 24-h geophysical cycles of the Earth. Drosophila melanogaster's rhythmic locomotor behaviour provides the main phenotype for the identification of higher eukaryotic clock genes. Under laboratory light-dark cycles, flies show enhanced activity before lights on and off signals, and these anticipatory responses have defined the neuronal sites of the corresponding morning (M) and evening (E) oscillators. However, the natural environment provides much richer cycling environmental stimuli than the laboratory, so we sought to examine fly locomotor rhythms in the wild. Here we show that several key laboratory-based assumptions about circadian behaviour are not supported by natural observations. These include the anticipation of light transitions, the midday 'siesta', the fly's crepuscular activity, its nocturnal behaviour under moonlight, and the dominance of light stimuli over temperature. We also observe a third major locomotor component in addition to M and E, which we term 'A' (afternoon). Furthermore, we show that these natural rhythm phenotypes can be observed in the laboratory by using realistic temperature and light cycle simulations. Our results suggest that a comprehensive re-examination of circadian behaviour and its molecular readouts under simulated natural conditions will provide a more authentic interpretation of the adaptive significance of this important rhythmic phenotype. Such studies should also help to clarify the underlying molecular and neuroanatomical substrates of the clock under natural protocols.     

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.     

林木分子育种研究的基因组学信息资源述评

分子育种是指利用与性状相关的DNA标记进行选育,也称标记辅助选择或标记辅助育种,广义上还包括基因工程育种和基因组学辅助育种。林木分子育种为早期选择和加速育种提供了极具潜力的高效手段。笔者对林木分子育种研究的基因组学信息资源进行了进展综述和前景展望。近30年来,林木分子标记技术从早期的低通量方法发展到目前基于微阵列芯片和新一代测序的高通量技术,如测序分型、转录组测序、重测序、扩增子测序和外显子组测序等,并广泛用于连锁作图、关联分析和基因组选择等林木性状相关的DNA变异检测研究。随着2006年毛果杨基因组序列的发表,已有50余个树种完成了基因组测序。基于连锁作图和关联研究检测了林木10余个属生长、材性和抗逆及非木质产品品质等性状相关的大量基因组位点,主要趋势表现为：① 表型广泛,涵盖经济性状、生理指标和代谢成分等;②标记数量成千上万甚至上百万,覆盖全基因组;③转录组和降解组等多组学的分子变异开始应用;④ 利用大群体以提高位点检测的精度;⑤ 重视环境的影响,大田试验设置多个地点,解析QTL与环境、年份的互作效应;⑥ 结合参考基因组序列和/或转录组差异表达基因进一步挖掘性状相关的候选基因,建立了桉属、松属和云杉属等主要造林树种的基因组选择模型。此外,积累了泛基因组、相关软件和算法、功能基因、基因组编辑技术及网站和数据库等其他信息资源。林木分子育种面临的挑战主要包括：① 如何获得稳定性好的性状相关基因组位点和基因组选择（GS）模型;② 缺乏自动化、无损和高通量的表型测定技术;③对大基因组的针叶树和一些多倍体树种,仍难获得高质量的基因组序列;④ 标记辅助选择增加了常规育种之外的费用,且存在不确定性;⑤多数树种的加速育种仍较困难。后基因组时代的林木分子育种将有效结合到常规育种程序中,显著促进遗传增益的提高。     

Fly and frog homoeo domains show homologies with yeast mating type regulatory proteins

Homoeotic genes in the bithorax and Antennapedia complexes of Drosophila melanogaster appear to specify the developmental fate of segments of the fly. Some of these genes (Ultrabithorax, Antennapedia and fushi tarazu) share homology due to their conservation of a 'homoeo domain'1,2 consisting of 60 amino acids. Cross-hybridization and cloning experiments show that the homoeo domain is conserved in a frog (Xenopus laevis) gene expressed in early development and may also be present in earthworm, beetle, chicken, mouse and human genomes. The extreme conservation found in the amino acid sequences between the Drosophila and Xenopus domains suggests that the domain has a vital function in the control of early development. Here we report the results of a search made in the Dayhoff sequence bank, which reveals a lesser but apparently significant homology between the homoeo domain and the amino acids coded from parts of the a 1 and alpha 2 mating type genes of the yeast Saccharomyces cerevisiae.     

基于基因组学的栎树生物学研究进展

栎树(Quercus spp.)是北半球重要的经济与生态树种。夏栎(Q. robur)、加州白栎(Q. lobata)、麻栎(Q. acutissima)等树种基因组的公布,对栎树生物学研究产生了深刻的影响。近5年来,栎树生物学出现了包括系统进化与物种鉴定、基因渐渗与适应进化、景观基因组学与生态保育、生物共存与互作机制、次生代谢与生长发育、DNA甲基化与表观遗传调控及基因与长寿机制等方面的研究热点。虽然基于基因组学的栎树生物学若干研究前沿已经形成,但尚处于起步阶段,笔者预期未来会向4个方面深入:①强调栎树基因组资源的深度应用。应用景观基因组学途径,探究栎树的杂交渐渗与适应进化;联合基因组、转录组、蛋白组等多组学技术,探究栎树生长发育与胁迫响应过程中的基因调控网络与信号通路;优化体细胞发生和遗传转化体系,攻克栎树遗传改良和基因资源开发技术瓶颈。②促进栎树研究体系的广度拓展。随着壳斗科其他树种全基因组序列的公布,基于从分子到群落的不同生物层次的模式系统,将对欧亚大陆和北美不同区域的栎树,包括白栎组、红栎组、冬青栎组、麻栎组等不同栎树类群,以及壳斗科其他属树种基因组生物学研究产生深远影响。③关注栎树资源利用的遗传与发育主题。用栎树基因组资源对其结构的、代谢的和农艺性状的差异及其优化加以解析,全基因组关联研究(GWAS)也将应用于栎树,从而为阐释木材发育和木栓形成的机制奠定基础。④聚焦栎林保育的生态与进化主题。在全球气候变化背景下,通过增加耐受胁迫的基因型,以缓解气候变化对森林生态系统的影响。同时维持和保护栎树在自然生态系统中的生态与进化过程,阐明栎树多样性、迁移与适应、趋异与趋同生态适应等方面进化成功的机制。     

Role of transposable elements in heterochromatin and epigenetic control

Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.