Drosophila virilis has long and highly polymorphic microsatellites

Comparative genomics is a powerful approach to inference of the dynamics of genome evolution. Most information about the evolution of microsatellites in the genus Drosophila has been obtained from Drosophila melanogaster. For comparison, we collected microsatellite data for the distantly related species Drosophila virilis. Screening about 0.5 Mb of nonredundant genomic sequence from GenBank, we identified 239 dinucleotide microsatellites. On average, D. virilis dinucleotides were significantly longer than D. melanogaster microsatellites (7.69 repeats vs. 6.75 repeats). Similarly, direct cloning of microsatellites resulted in a higher mean repeat number in D. virilis than in D. melanogaster (12.7 repeats vs. 12.2 repeats). Characterization of 11 microsatellite loci mapping to division 40-49 on the fourth chromosome of D. virilis indicated that D. virilis microsatellites are more variable than those of D. melanogaster.     

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes

Transposable elements (TEs) are indwelling components of genomes, and their dynamics have been a driving force in genome evolution. Although we now have more information concerning their amounts and characteristics in various organisms, we still have little data from overall comparisons of their sequences in very closely-related species. While the Drosophila melanogaster genome has been extensively studied, we have only limited knowledge regarding the precise TE sequences in the genomes of the related species Drosophila simulans, Drosophila sechellia and Drosophila yakuba. In this study we analyzed the number and structure of TE copies in the sequenced genomes of these four species. Our findings show that, unexpectedly, the number of TE insertions in D. simulans is greater than that in D. melanogaster, but that most of the copies in D. simulans are degraded and in small fragments, as in D. sechellia and D. yakuba. This suggests that all three species were invaded by numerous TEs a long time ago, but have since regulated their activity, as the present TE copies are degraded, with very few full-length elements. In contrast, in D. melanogaster, a recent activation of TEs has resulted in a large number of almost-identical TE copies. We have detected variants of some TEs in D. simulans and D. sechellia, that are almost identical to the reference TE sequences in D. melanogaster, suggesting that D. melanogaster has recently been invaded by active TE variants from the other species. Our results indicate that the three species D. simulans, D. sechellia, and D. yakuba seem to be at a different stage of their TE life cycle when compared to D. melanogaster. Moreover, we show that D. melanogaster has been invaded by active TE variants for several TE families likely to come from D. simulans or the ancestor of D. simulans and D. sechellia. The numerous horizontal transfer events implied to explain these results could indicate introgression events between these species.     

缺失Df(3R)Espl3/TM6C基因片段影响黑腹果蝇的睡眠时间

【目的】果蝇的睡眠活动具有生物节律性, 可受到基因的调控。为了寻找影响果蝇睡眠时间的基因, 本研究对与果蝇睡眠时间相关的基因型进行了筛选。【方法】选择黑腹果蝇Drosophila melanogaster基因缺失系5601, 8904, 7061, 7146, 27327, 669, 8103, 691, 9697, 24416, 26525, 5411, 3096, 5877和7682的7日龄成虫和野生CS品系7日龄成虫为研究对象, 利用果蝇活动监测器系统（Drosophila Activity Monitoring System, DAMS）, 记录果蝇的睡眠时间, 累计计算24 h内果蝇睡眠时间, 将测得的各品系果蝇睡眠时间进行对比分析。【结果】与野生型CS品系7日龄成虫相比, 缺失Df(3R)Espl3/TM6C基因片段的 5601品系7日龄成虫睡眠时间明显缩短（P<0.001）。【结论】缺失Df(3R)Espl3/TM6C基因片段与果蝇睡眠有关。本研究结果为揭示影响果蝇睡眠时间的基因提供数据支持, 进而为研究人类睡眠提供线索。     

Comparative and functional studies of Drosophila species invasion by the gypsy endogenous retrovirus.

Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species. gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers. We report here the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster, suggesting that potentially infective gypsy copies able to spread between sexually isolated species can occur. The ability of gypsy to invade the genome of a new species is conditioned by its capacity to be expressed in the naive genome. The genetic basis for the regulation of gypsy activity in D. melanogaster is now well known, and it has been assigned to an X-linked gene called flamenco. We established an experimental simulation of the invasion of the D. melanogaster genome by gypsy elements derived from other Drosophila species, which demonstrates that these non- D. melanogaster gypsy elements escape the repression exerted by the D. melanogaster flamenco gene.     

Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data

We performed a comprehensive analysis of the evolution of the Ty3/GYPSY: group of long-terminal-repeat retrotransposons (also known as METAVIRIDAE:). Exhaustive database searches allowed us to detect novel elements of this group. In particular, the Arabidopsis thaliana and Drosophila melanogaster genome sequencing projects have recently disclosed a large number of new Ty3/GYPSY: sequences. So far, elements of three different Ty3/GYPSY: lineages had been described for A. thaliana. Here, we describe six new lineages, which we have called Tit-for-tat1, Tit-for-tat2, Gimli, Gloin, Legolas, and Little Athila. We confirm that plant Ty3/GYPSY: elements form two main monophyletic groups. Moreover, our results suggest that at least four independent ancestral lineages existed before the monocot-dicot split, about 200 MYA. Twelve sequences from D. melanogaster that may correspond to new elements are also described. Some of these sequences are similar to those of OSVALDO: and Ulysses, two elements of the OSVALDO: clade that had never before been described for D. melanogaster. Comparative analyses of multiple organisms, some of them with completely sequenced genomes, show that the number of lineages of Ty3/GYPSY: elements is very variable. Thus, while only 1 lineage is present in Saccharomyces cerevisiae, at least 6 exist in Caenorhabditis elegans, at least 9 are present in the A. thaliana, and perhaps 20 are present in D. melanogaster. Finally, we suggest that the presence of a chromodomain-containing integrase, a feature of some closely related Ty3/GYPSY: elements of fungi, plants, and animals, may be used to define a new METAVIRIDAE: genus.     

Regulative interactions between cells of wing discs from different dipteran species

The mechanism by which patterns are produced appears to be repeated in each segment of an animal, and it has been proposed that it may even have been conserved in evolution so that different species would have the same system of positional information. This idea has been tested by mixing cells of a defined fragment of the wing disc of Drosophila melanogaster with wing disc fragments of five other dipteran species to assay the ability of these disc fragments to stimulate intercalary regeneration of the D. melanogaster cells. The genetically marked (y; mwh) D. melanogaster fragment was mechanically mixed with wing discs or wing disc fragments of four drosophilids (D. melanogaster as a control, D. virilis, D. hydei, Zaprionus vittiger), of Musca domestica, and of Piophila casei. The mixed aggregates were cultured in vivo for 7 days, then metamorphosed in D. melanogaster larval hosts. The D. melanogaster fragments were only stimulated to regenerate when combined with complementary fragments from D. melanogaster or D. virilis wing discs. In the combination between D. melanogaster and D. hydei, the tissue formed integrated mosaic patterns, but no regeneration ensued. The one positive result (D. melanogaster mixed with D. virilis) shows that positional cues can be exchanged and correctly interpreted between cells of different species. The negative results do not prove that the mechanism for establishing patterns is different in the tested species, but may be due to incompatibilities that are not related to pattern formation.     

Proteome reference map of Drosophila melanogaster head

Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases.     

Population structure in African Drosophila melanogaster revealed by microsatellite analysis

Tropical sub-Saharan regions are considered to be the geographical origin of Drosophila melanogaster. Starting from there, the species colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic scenario, African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, limited information is available on the genetic structure of African populations. We used X chromosomal microsatellite variation to study the population structure of D. melanogaster populations using 13 sampling sites in North, West and East Africa. These populations were compared to six European and one North American population. Significant population structure was found among African D. melanogaster populations. Using a Bayesian method for inferring population structure we detected two distinct groups of populations among African D. melanogaster. Interestingly, the comparison to cosmopolitan D. melanogaster populations indicated that one of the divergent African groups is closely related to cosmopolitan flies. Low, but significant levels of differentiation were observed for sub-Saharan D. melanogaster populations from West and East Africa.     

黑腹果蝇成虫生长过程的脂质组分析

果蝇是一种重要的模式生物,为遗传学研究作出了巨大贡献。近几十年来,在发育生物学、行为生物学、神经生物学等领域也都发挥了十分关键的作用。脂质是构成生命的4大类基本物质之一,但关于果蝇脂质组特征研究并不多,尤其是黑腹果蝇在生长发育过程中的脂质组含量变化尚未见报导。为更全面了解果蝇生长发育的特性,本研究应用脂质组学方法,系统地表征了黑腹果蝇成虫生长过程中的337种脂质分子的变化。结果显示,磷脂总量从152.61 ± 4.92 nmol/mg 降低至112.3 ± 3.87 nmol/mg,其中溶血磷脂酰胆碱含量从0.70 ± 0.03 nmol/mg 升高至0.93 ± 0.11 nmol/mg。而中性脂甘油三酯 (TAG) 和甘油二酯 (DAG) 变化最剧烈,伴随果蝇生长,从356.12 ± 34.05 nmol/mg下降至86.99 ± 13.07 nmol/mg。同时,分析了与细胞膜稳定性有关的膜脂碳链长度、双键数目(DBI)和磷脂酰胆碱(PC)/磷脂酰乙醇胺(PE)比值的变化。结果显示,果蝇成虫在生长阶段早中期（8～15 d）细胞膜最稳定,通过增加膜脂双键数目（10%～20%）和升高PC/PE比值（14%）,增强膜稳定性。黑腹果蝇在成虫生长的不同阶段,其脂质分子组成特征不同,我们所发现的黑腹果蝇成虫生长过程中脂质分子含量变化,一方面为在脂质水平研究黑腹果蝇生长调控奠定了重要基础,另一方面也为黑腹果蝇作为研究模型时控制其正常健康生长提供了参考标准。     

Rates and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda

Comparisons of gene orders between species permit estimation of the rate of chromosomal evolution since their divergence from a common ancestor. We have compared gene orders on three chromosomes of Drosophila pseudoobscura with its close relative, D. miranda, and the distant outgroup species, D. melanogaster, by using the public genome sequences of D. pseudoobscura and D. melanogaster and approximately 50 in situ hybridizations of gene probes in D. miranda. We find no evidence for extensive transfer of genes among chromosomes in D. miranda. The rates of chromosomal rearrangements between D. miranda and D. pseudoobscura are far higher than those found before in Drosophila and approach those for nematodes, the fastest rates among higher eukaryotes. In addition, we find that the D. pseudoobscura chromosome with the highest level of inversion polymorphism (Muller's element C) does not show an unusually fast rate of evolution with respect to chromosome structure, suggesting that this classic case of inversion polymorphism reflects selection rather than mutational processes. On the basis of our results, we propose possible ancestral arrangements for the D. pseudoobscura C chromosome, which are different from those in the current literature. We also describe a new method for correcting for rearrangements that are not detected with a limited set of markers.     

Freeze substitution Hi-C,a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples

Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in High-through chromosome conformation capture(Hi-C) to keep natural chromatin conformation intact. This requirement has impeded the advancement of 3 D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time. Here, we develop a freeze substitution Hi-C(FS-Hi-C) technique that overcomes the need for fresh samples. FS-Hi-C can be used with samples stored in liquid nitrogen(LN2):the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution.After confirming that the FS step preserves the natural chromosome conformation during sample thawing,we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum. Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains, we found that FS-HiC outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-HiC will probably extend the application of 3 D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date.     

Cloning and daily expression of the timeless gene in Aedes aegypti (Diptera:Culicidae)

Molecular approaches for studying biological rhythms in insects have been well investigated in the model Drosophila melanogaster, in which a number of genes have been characterized in terms of sequence, expression, protein interactions and involvement in the control of locomotor activity and eclosion rhythms. However, only scattered information is available for insect vectors of diseases. In this paper, we report the cloning and expression analysis of the clock gene timeless in the mosquito Aedes aegypti, vector of Dengue and Yellow Fever viruses. In Drosophila, timeless has a crucial role in the control of the central pacemaker and the resetting mechanism that allows the clock to synchronize with the environment light-dark cycles. Comparison of the predicted protein sequence encoded by timeless in Ae. aegypti and D. melanogaster demonstrated high similarity in some important domains, suggesting functional conservation. Analysis of the daily expression of timeless in Ae. aegypti shows a peak in mRNA abundance around the light-dark transition.     

The period gene of Drosophila carries species-specific behavioral instructions.

We have analyzed and compared the circadian locomotor activity rhythms of Drosophila melanogaster and D.pseudoobscura. The rhythms of D.pseudoobscura are stronger and the periods shorter than those of D.melanogaster. We have also transformed D.melanogaster flies with a hybrid gene containing the coding region of the D.pseudoobscura period (per) gene. Behavioral assays of flies containing this hybrid gene show that the per protein encoded by the D.pseudoobscura per gene is able to rescue the rhythmic deficiencies of arrhythmic, pero1 D.melanogaster. More important, the rhythms of some of these strains are stronger and the periods shorter than those of D.melanogaster (and those of transformants which carry the equivalent D.melanogaster per gene construct) and hence resemble those of D.pseudoobscura. The results suggest that the primary amino acid sequence of the per gene encodes species-specific behavioral instructions that are detectable when only the per gene is transferred to a different species.     

黑腹果蝇3号染色体裂翅平衡致死位点的发现及2号、3号染色体裂卷翅双平衡染色体的建立

果蝇的平衡染色体在遗传研究中被广泛应用.文章通过分析黑腹果蝇裂翅新突变体与野生型、982紫眼及黑檀体杂交后代裂翅性状情况,首次将裂翅基因定位于3号染色体上,并阐明了裂翅平衡致死、杂合子纯繁的遗传机制,获得了以裂翅为显性标记的3号平衡染色体品系.探索了双平衡染色体显性标记基因聚合的杂交模式,成功建立了以裂翅和卷翅为标记的2号、3号双平衡染色体.裂翅的发现为3号染色体平衡子提供了更加方便识另0的显性翅型标记,同时裂卷翅双平衡体的建立丰富了果蝇常用工具平衡子,可以广泛用于基因定位及突变筛选过程.     

Sequence-based detection and breakpoint assembly of polymorphic inversions

Inversion polymorphisms have occupied a privileged place in Drosophila genetic research since their discovery in the 1920s. Indeed, inversions seem to be nearly ubiquitous, and the majority of species that have been thoroughly surveyed have been found to be polymorphic for one or more chromosomal inversions. Despite enduring interest, however, inversions remain difficult to study because their effects are often cryptic, and few efficient assays have been developed. Even in Drosophila melanogaster, in which inversions can be reliably detected and have received considerable attention, the breakpoints of only three inversions have been characterized molecularly. Hence, inversion detection and assay design remain important unsolved problems. Here, we present a method for identification and local de novo assembly of inversion breakpoints using next-generation paired-end reads derived from D. melanogaster isofemale lines. PCR and cytological confirmations demonstrate that our method can reliably assemble inversion breakpoints, providing tools for future research on D. melanogaster inversions as well as a framework for detection and assay design of inversions and other chromosome aberrations in diverse taxa.     

A high-quality catalog of the Drosophila melanogaster proteome

Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.