On the origin of mitochondria: a genomics perspective

The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.     

Comparative genomics in the Brassicaceae: a family-wide perspective

Comparative genomics of Arabidopsis relatives has great potential to improve our understanding of molecular function and evolutionary processes. Recent studies of phylogenetic relationships within Brassicaceae and the publication of a new tribal classification scheme provide an important framework for comparative genomics research. Comparative linkage mapping and chromosome painting in the close relatives of Arabidopsis have inferred an ancestral karyotype of these species. In addition, comparative mapping to Brassica has identified genomic blocks that have been maintained since the divergence of the Arabidopsis and Brassica lineages. Several analyses of conserved non-coding regions have identified putative cis-regulatory sequences, and have highlighted the need for comparative sequencing at greater evolutionary distances. The development of new model species with novel physiological and ecological traits allows analysis of phenotypes that are not available in A. thaliana. Looking towards the future, we suggest a prioritized research agenda for comparative genomics in the Brassicaceae.     

Comparative genomics - a perspective

The rapidly emerging field of comparative genomics has yielded dramatic results. Comparative genome analysis has become feasible with the availability of a number of completely sequenced genomes. Comparison of complete genomes between organisms allow for global views on genome evolution and the availability of many completely sequenced genomes increases the predictive power in deciphering the hidden information in genome design, function and evolution. Thus, comparison of human genes with genes from other genomes in a genomic landscape could help assign novel functions for un-annotated genes. Here, we discuss the recently used techniques for comparative genomics and their derived inferences in genome biology.     

Bacillus thuringiensis: a genomics and proteomics perspective

Bacillus thuringiensis (Bt) is a unique bacterium in that it shares a common place with a number of chemical compounds which are used commercially to control insects important to agriculture and public health. Although other bacteria, including B. popilliae and B. sphaericus, are used as microbial insecticides, their spectrum of insecticidal activity is quite limited compared to Bt. Importantly, Bt is safe for humans and is the most widely used environmentally compatible biopesticide worldwide. Furthermore, insecticidal Bt genes have been incorporated into several major crops, rendering them insect resistant, and thus providing a model for genetic engineering in agriculture.This review highlights what the authors consider the most relevant issues and topics pertaining to the genomics and proteomics of Bt. At least one of the authors (L.A.B.) has spent most of his professional life studying different aspects of this bacterium with the goal in mind of determining the mechanism(s) by which it kills insects. The other authors have a much shorter experience with Bt but their intellect and personal insight have greatly enriched our understanding of what makes Bt distinctive in the microbial world. Obviously, there is personal interest and bias reflected in this article notwithstanding oversight of a number of published studies. This review contains some material not published elsewhere although several ideas and concepts were developed from a broad base of scientific literature up to 2010.     

Avianbase: a community resource for bird genomics

Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.Access to complete genome sequences provides the first step towards the understanding of the biology of organisms. It is the template that underpins the phenotypic characteristics of individuals and ultimately separates species due to the accumulation and fixation of mutations over evolutionary timescales. In terms of the available genomic datasets for species, birds, as our more distant relatives, have been historically underrepresented. The high cost of sequencing and annotation in the past led to a bias towards accumulating data for species that are either established model organisms or economically significant (that is, chicken, turkey and duck, representing two sister orders within the Galloanseriformes clade from the large and diverse phylogeny of birds). The recent release of genome assemblies and initial predictions of protein-coding genes [1-4] for 44 bird species, including representatives from all major branches of the bird phylogeny, is, therefore, highly significant.One of the major challenges with the release of this number of newly sequenced genomes and the many more to come [5] is how to make these available to the various research communities in a way that supports basic research. Providing access to the sequences and initial annotations in the format of text files will limit the potential usage of the data as they require significant resources, including bioinformatics personnel and computer infrastructure in place to access and mine - for example, searching for genes belonging to certain protein families or searching for orthologous genes. These overheads pose a serious bottleneck that can hinder research and requires concerted action by the relevant research communities.Once genomes are submitted to public databases, genome-wide annotations are frequently generated and released either via the Ensembl project [6] or by the National Center for Biotechnology Information [7] and sequence and annotation are then made visually available online in integrated views via the Ensembl or the University of California Santa Cruz (UCSC) genome browsers [8]. These systems provide search facilities, sequence alignment tools like BLAT/BLAST and various analysis tools to facilitate subsetting and computational retrieval of the data, including UCSC’s Table Browser or Ensembl’s Perl and REST APIs and BioMart system.While these systems have become almost indispensable for research, not all sequenced genomes are annotated and displayed in genome browsers. Full genome annotation remains time consuming and resource intensive: a full evidence-based Ensembl genebuild takes approximately 4 months. Thus, the list of species represented is currently limited and depends on various factors, including the completeness of the assembled genome sequence and the overall demand in the scientific community for the resources, including whether the species is a model organism (for example, human or mouse), economically important (for example, farmed animals) or of specific phylogenetic interest. Many of the recently sequenced bird genomes do not obviously fall within these categories.     

MaizeDB - a functional genomics perspective

MaizeDB (http://www.agron.missouri.edu/) has existed since the early 90's as a genomespecific database that is grounded in genetic maps, their documentation and annotation. The database management system is robust and has continuously been Sybase. In this brief review we provide an introduction to the database as a functional genomics tool and new accesses to the data: 1) probe tables by bin location 2) BLAST access to map data 3) cMap, a comparative map graphical tool.     

Adaption to extreme environments: a perspective from fish genomics

Reviews in Fish Biology and Fisheries - Fishes exhibit greater species diversity than any other group of vertebrates. They are found in most bodies of water, including those that pose extreme...     

Activation of nuclear receptors: a perspective from structural genomics

Crystal structures of more than two dozen different nuclear receptor ligand binding domains have defined a simple paradigm of receptor activation, in which agonist binding induces the activation function-2 (AF-2) helix to form a charge clamp for coactivator recruitment. Recent structural studies present a surprising contrast. Activation of the mouse LRH-1 receptor is independent of a bound agonist despite its large ligand binding pocket, whereas the activation of the Drosophila DHR38 receptor is dependent on ecdysteroids even though the receptor lacks a ligand binding pocket. These new findings shed light on the diverse structural mechanisms that nuclear receptors have evolved for activation, and have important implications in their respective signaling pathways.     

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Background

Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species.

Results

We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes.

Conclusions

This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.     

RNA structure: Merging chemistry and genomics for a holistic perspective

The advent of deep sequencing technology has unexpectedly advanced our structural understanding of molecules composed of nucleic acids. A significant amount of progress has been made recently extrapolating the chemical methods to probe RNA structure into sequencing methods. Herein we review some of the canonical methods to analyze RNA structure, and then we outline how these have been used to probe the structure of many RNAs in parallel. The key is the transformation of structural biology problems into sequencing problems, whereby sequencing power can be interpreted to understand nucleic acid proximity, nucleic acid conformation, or nucleic acid‐protein interactions. Utilizing such technologies in this way has the promise to provide novel structural insights into the mechanisms that control normal cellular physiology and provide insight into how structure could be perturbed in disease.     

First steps: bovine genomics in historical perspective

The vision of Morris Soller was instrumental in launching the field of bovine genomics. This study is a review of the early years of bovine gene mapping leading up to the sequencing and assembly of the bovine genome in 2009. A historical perspective of parasexual, linkage and physical mapping is provided with a focus on the contribution of these maps to the eventual assignment and orientation of genes and sequence to cattle chromosomes.     

Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria

Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed ‘diazotrophs'') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.     

Plant genomics: present state and a perspective on future developments.

The year 2001 may well be called the Year of the Human Genome. Less in the limelight, but equally exciting for plant scientists, is the rapid progress in plant genomics. With relatively modest resources, a lot has been achieved. The Arabidopsis genomic sequence (125 megabases [Mb]) is essentially finished, and rice sequencing is progressing rapidly. For many species, expressed sequence tag (EST) resources are plentiful, allowing broad inter-specific comparisons. At the same time, development of integrated physical-genetic maps for large-genome crop species is not progressing as rapidly as desired, while resources for the complete sequencing of these crops are not likely to become available. Some important plant genomes are so large that their complete sequencing may not be practical for many years. Significant plant genome research is concentrated in industry, and not freely available, creating some frustration in the academic community. Growing interest is anticipated in the development of metabolic profiling technologies, RNA profiling, proteomics and integrated systems approaches to plant biology.     

Hitchhiking mapping--functional genomics from the population genetics perspective

Several statistical tests based on population genetic theory are used to identify genes that have recently acquired a beneficial mutation. Here, I describe the extension of these tests to a multilocus approach for a genome-wide survey for genes that have been under recent positive selection. As this strategy could potentially identify genes with weak phenotypic effects, it will be very useful in population genetic approaches aimed at understanding adaptation processes in natural populations. Furthermore, this 'hitchhiking mapping' could also help in the functional characterization of genomes.     

Madness and care in the community: a medieval perspective.

Care in the community for insane people today is more a matter of expert provision than communal support. In consequence, although they are no longer confined to hospital, mentally ill people largely remain marginalised in a society that does not have the resources, nor often the inclination, to take responsibility for their care. The experience of insane people in medieval England seems to have been of a different order, as shown by a particularly well documented case dating from 1383. From the late 13th century congenital idiots were protected by law. Care of lunatics, by contrast, was primarily the responsibility of the family. However, where the family could not or was unwilling to provide, provision was made by the crown. Through the instrument of the inquisition, the diagnosis and social circumstances of each case were determined by commissioners in consultation with a local jury and all interested parties, including the subject himself or herself. The best interests of the subject remained a prime concern, and the settlement that was ordained was tried and enforced in law. The process was confined to those with real or personal estate, but it encompassed poor as well as rich and proved, through the close identity of the local community with the process, to be a sophisticated and effective mechanism for maintaining and sustaining insane people. Unlike today, care in the community was a communal activity that ensured a truly public provision for those who could not look after themselves.     

Fruits and flies: a genomics perspective of an invertebrate model organism.

The increasing number of species for which a full genome sequence is available offers rich pickings for geneticists, but comparative analysis and assembly of information gathered across species does not always lead to answers about the function of a particular gene. This paper aims to place the invertebrate model system--the fly Drosophila melanogaster--into this playing field and to discuss how the organism arrived at its position in functional genetic analysis. Indeed, despite the wealth of knowledge on how a fly lives, breathes and flies, this organism is likely to remain a player in the analysis of biological, disease and pharmaceutical processes. The fast genetics Drosophila offers, combined with a well-annotated genome and a wealth of techniques facilitating gene function discovery, will ensure its place in functional genomics for some time to come. Although the fly cannot speak, it certainly can tell a tale.