Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.

A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.

Many organisms, when alone, behave differently from when they are among a crowd. Drosophila similarly display social behaviour and collective behaviour dynamics within groups not seen in individuals. In flies, these emergent behaviours may be in response to the global size of the group or local nearest-neighbour density. Here we investigate i) which aspect of social life flies respond to: group size, density, or both and ii) whether behavioural changes within the group are dependent on olfactory support cells. Behavioural assays demonstrate that flies adjust their interactive behaviour to group size but otherwise compensate for density by achieving a standard rate of movement, suggesting that individuals are aware of the number of others within their group. We show that olfactory support cells are necessary for flies to behave normally in large groups. These findings shed insight into the subtle and complex life of Drosophila within a social setting.

Animals interact with each other in species-specific reproducible patterns. These patterns of organization are captured by social network analysis, and social interaction networks (SINs) have been described for a wide variety of species including fish, insects, birds, and mammals. The aim of this study is to understand the evolution of social organization inDrosophila. Using a comparative ecological, phylogenetic, and behavioral approach, the different properties of SINs formed by 20 drosophilids were compared. We investigate whether drosophilid network structures arise from common ancestry, a response to the species’ past climate, other social behaviors, or a combination of these factors. This study shows that differences in past climate predicted the species’ current SIN properties. The drosophilid phylogeny offered no value to predicting species’ differences in SINs through phylogenetic signal tests. This suggests that group-level social behaviors in drosophilid species are shaped by divergent climates. However, we find that the social distance at which flies interact correlated with the drosophilid phylogeny, indicating that behavioral elements of SINs have remained largely unchanged in their evolutionary history. We find a significant correlation of leg length to social distance, outlining the interdependence of anatomy and complex social structures. Although SINs display a complex evolutionary relationship across drosophilids, this study suggests that the ecology, and not common ancestry, contributes to diversity in social structure inDrosophila.

The zebrafish has become a popular model system for the study of vertebrate developmental biology because of its numerous strengths as a molecular genetic and embryological system. To determine the requirement for specific genes during embryogenesis, it is necessary to generate organisms carrying loss-of-function mutations. This can be accomplished in zebrafish through a reverse genetic approach. This review discusses the current techniques for generating mutations in known genes in zebrafish. These techniques include the generation of chromosomal deletions and the subsequent identification of complementation groups within deletions through noncomplementation assays. In addition, this review will discuss methods currently being evaluated that may improve the methods for finding mutations in a known sequence, including screening for randomly induced small deletions within genes and screening for randomly induced point mutations within specific genes.

BackgroundMosquitoes are important pathogen vectors affecting human and other animals. Studies on genetic control of mosquito mediated disease transmission gained traction recently due to mosquito transgenesis technology. Active transposons are considered valuable tools to propagate pathogen resistance transgenes among mosquitoes, rendering the whole population recalcitrant to diseases. A major hurdle in this approach is the inefficient remobilization activity after the integration of heterologous transposon vectors bearing transgenes into chromosomes. Therefore, endogenous active transposons in mosquito genomes are highly desirable.ResultsStarting with the transposable element database of the yellow fever mosquito Aedes aegypti genome, detailed analyses of the members of each TE family were performed to identify sequences with multiple identical copies, an indicator of their latest or current transposition activity. Among a dozen of potentially active TE families, two DNA elements (TF000728 and TF000742 in TEfam) are short and nonautonomous. Close inspection of the elements revealed that these two families were previously mis-categorized and, unlike other known TEs, insert specifically at dinucleotide “AT”. These two families were therefore designated as ATon-I and ATon-II. ATon-I has a total copy number of 294, among which three elements have more than 10 identical copies (146, 61 and 17). ATon-II has a total copy number of 317, among which three elements have more than 10 identical copies (84, 15 and 12). Genome wide searches revealed additional 24 ATon families in A. aegypti genome with nearly 6500 copies in total. Transposon display analysis of ATon-1 family using different A. aegypti strains suggests that the elements are similarly abundant in the tested mosquito strains.ConclusionATons are novel mobile genetic elements bearing terminal inverted repeats and insert specifically at dinucleotide “AT”. Five ATon families contain elements existing at more than 10 identical copies, suggesting very recent or current transposition activity. A total of 24 new TE families with nearly 6000 copies were identified in this study.

Freely available on the web at http://labs.csb.utoronto.ca/yang/TE_Displayer.

Cultural norms, collective decisions, reproductive behaviour, and pathogen transmission all emerge from interaction patterns within animal social groups. These patterns of interaction support group-level phenomena that can influence an individual's fitness.The aim of this study is to understand the evolution of social organization in Drosophila.Using a comparative ecological, phylogenetic and behavioural approach, we studied the different properties of social interaction networks (SINs) formed by 20 drosophilids and the different ways these species interact. We investigate whether animal network structures arise from common ancestry, a response to the species' past ecological environment, other social behaviours, or a combination of these factors. We demonstrate that differences in past climate predicted the species' current SIN properties. The drosophilid phylogeny offered no value to predicting species' differences in SINs through phylogenetic signal tests. This suggests group-level social behaviours in drosophilid species are shaped by divergent climates. However, we find that the distance at which flies interact correlated with the drosophilid phylogeny, indicating that behavioural elements that comprise SINs have remained largely unchanged in their recent evolutionary history. We find a significant correlation of leg length to social distance, outlining the interdependence of anatomy and complex social structures.Although SINs display a complex evolutionary relationship across drosophilids, this study provides evidence of selective pressures acting on social behaviour in Drosophila.We speculate that conserved molecular mechanisms may be shared across drosophilids deep in their evolutionary history, similar to other pervasive mechanisms, like biological clocks.