Complementing aculiferan mitogenomics: comparative characterization of mitochondrial genomes of Solenogastres (Mollusca, Aplacophora).

Background: With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class of aplacophoran molluscs - Solenogastres (or Neomeniomorpha) - is still neglected.

Results: Here, we present six new mitochondrial genomes from five families of Solenogastres (Amphimeniidae, Gymnomeniidae, Proneomeniidae, Pruvotinidae, Simrothiellidae), including the first complete mitogenomes, thereby now representing three of the four traditional orders.

Capture and return of sexual genomes by hybridogenetic frogs provide clonal genome enrichment in a sexual species.

Hybridogenesis is a reproductive tool for sexual parasitism. Hybridogenetic hybrids use gametes from their sexual host for their own reproduction, but sexual species gain no benefit from such matings as their genome is later eliminated. Here, we examine the presence of sexual parasitism in water frogs through crossing experiments and genome-wide data.

New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships.

Relationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (Tryblidia) to have several plesiomorphic molluscan traits. The phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of Conchifera whereas earlier molecular studies supported a clade of Monoplacophora + Polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora + Cephalopoda.

The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes.

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates.

RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.

The sea urchin larval skeleton offers a simple model for formation of developmental patterns. The calcium carbonate skeleton is secreted by primary mesenchyme cells (PMCs) in response to largely unknown patterning cues expressed by the ectoderm. To discover novel ectodermal cues, we performed an unbiased RNA-Seq-based screen and functionally tested candidates; we thereby identified several novel skeletal patterning cues.

The complete mitochondrial genome of Telmatobufo australis (Amphibia: Anura: Calyptocephalellidae).

The mitochondrial (mt) genome of Telmatobufo australis is a circular molecule of 17,989 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Gene order and content are identical to those previously reported from other neobatrachian mt genomes. Two protein-coding genes (COI and ATP6) presumably used GTG as start codons while COIII possessed an incomplete stop codon.

The nervous system of Xenacoelomorpha: a genomic perspective.

Xenacoelomorpha is, most probably, a monophyletic group that includes three clades: Acoela, Nemertodermatida and Xenoturbellida. The group still has contentious phylogenetic affinities; though most authors place it as the sister group of the remaining bilaterians, some would include it as a fourth phylum within the Deuterostomia. Over the past few years, our group, along with others, has undertaken a systematic study of the microscopic anatomy of these worms; our main aim is to understand the structure and development of the nervous system.

LTR retroelements are intrinsic components of transcriptional networks in frogs.

Background: LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology.

Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis.

The marine mussel Mytilus edulis and its closely related sister species are distributed world-wide and play an important role in coastal ecology and economy. The diversification in different species and their hybrids, broad ecological distribution, as well as the filter feeding mode of life has made this genus an attractive model to investigate physiological and molecular adaptations and responses to various biotic and abiotic environmental factors. In the present study we investigated the immune system of Mytilus, which may contribute to the ecological plasticity of this species.

Acoelomorph flatworms are deuterostomes related to Xenoturbella.

Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes and positioning the Acoelomorpha as the most basally branching bilaterian group(s). Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria.

Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix.

Background: The sea urchin embryo has been an important model organism in developmental biology for more than a century. This is due to its relatively simple construction, translucent appearance, and the possibility to follow the fate of individual cells as development to the pluteus larva proceeds. Because the larvae contain tiny calcitic skeletal elements, the spicules, they are also important model organisms for biomineralization research.

Data integration using scanners with SQL output--the bioscanners project at sourceforge.

There is currently no standardized approach for parsing output that the numerous bioinformatical tools generate. Because the framework approach of the Bio-toolkits has some shortcomings, we searched for alternative approaches. To this end, we evaluated scanner generators for various programming languages with respect to their potential of standalone, small and fast applications that can easily delivered on any modern and many ancient operating system.

Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin.

Background: Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field.

Results: The present report contains the determination of test (shell) and tooth organic matrix phosphoproteomes.

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.

Animal genomes possess highly conserved cis-regulatory sequences that are often found near genes that regulate transcription and development. Researchers have proposed that the strong conservation of these sequences may affect the evolution of the surrounding genome, both by repressing rearrangement, and possibly by promoting duplicate gene retention. Conflicting data, however, have made the validity of these propositions unclear.

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network.

Background: Gene Regulatory Networks (GRNs) control the differentiation, specification and function of cells at the genomic level. The levels of interactions within large GRNs are of enormous depth and complexity. Details about many GRNs are emerging, but in most cases it is unknown to what extent they control a given process, i.

Chordin is required for neural but not axial development in sea urchin embryos.

The oral-aboral (OA) axis in the sea urchin is specified by the TGFbeta family members Nodal and BMP2/4. Nodal promotes oral specification, whereas BMP2/4, despite being expressed in the oral territory, is required for aboral specification. This study explores the role of Chordin (Chd) during sea urchin embryogenesis.

In-depth, high-accuracy proteomics of sea urchin tooth organic matrix.

Background: The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified.

Ca(2+) signaling occurs via second messenger release from intraorganelle synthesis sites.

Cyclic ADP-ribose is an important Ca(2+)-mobilizing cytosolic messenger synthesized from beta-NAD(+) by ADP-ribosyl cyclases (ARCs). However, the focus upon ectocellular mammalian ARCs (CD38 and CD157) has led to confusion as to how extracellular enzymes generate intracellular messengers in response to stimuli. We have cloned and characterized three ARCs in the sea urchin egg and found that endogenous ARCbeta and ARCgamma are intracellular and located within the lumen of acidic, exocytotic vesicles, where they are optimally active.

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes.

Background: The organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level.

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement.

Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate that researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate preduplication genome.

Modeling development: spikes of the sea urchin.

Modeling of specification events during development poses new challenges to biochemical modeling. These include data limitations and a notorious absence of homeostasis in developing systems. The sea urchin is one of the best studied model organisms concerning development and a network, the Endomesoderm Network, has been proposed that is presumed to control endoderm and mesoderm specification in the embryo of Strongy-locentrotus purpuratus.

GOblet: annotation of anonymous sequence data with gene ontology and pathway terms.

The functional annotation of genomic data has become a major task for the ever-growing number of sequencing projects. In order to address this challenge, we recently developed GOblet, a free web service for the annotation of anonymous sequences with Gene Ontology (GO) terms. However, to overcome limitations of the GO terminology, and to aid in understanding not only single components but as well systemic interactions between the individual components, we have now extended the GOblet web service to integrate also pathway annotations.