Albert Poustka

• Stiftung Naurschutz Berlin

The molecular processes underlying genome exclusion and clonal gamete formation in the germline of hybridogenetic water frog hybrids are poorly understood. For the first time, we have characterized the coding sequences of 160 gametogenic genes from the European water frog species Pelophylax lessonae (LL) and Pelophylax ridibundus (RR). In addition,...

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...

Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profi...

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 da...

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 C...

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 deutero...

Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic [1, 2]; alternatively, they have been linked to the complex Ambulacraria (echinoder...

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 deutero...

Background Although recent studies have greatly advanced understanding of deep molluscan phylogeny, placement of some taxa remains uncertain as different datasets support competing class-relationships. Traditionally, morphologists have placed Monoplacophora, a group of morphologically simple, limpet-like molluscs as sister group to all other conchi...

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 unde...

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 creating...

The sea urchin larval skeleton offers a simple model for developmental pattern formation. 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 can...

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 G...

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...

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...

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 LT...

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 phy...

Information of sample composition within the different transcriptome runs as well as of sequence data generated with *FLX or Titanium chemistry before and after quality control. Data after quality control were used for the assembly (see table S2). (DOC)

Information about genome sources of the different species used for phylogenetic analysis. (DOC)

Putative M. edulis immune relevant genes identified via BLAST analysis. A) Sequence and domain information. Domain information of M. edulis contigs was deduced by amino-acid sequence investigation using SMART [27] and NCBI dart [28] with default thresholds. B) Comparison with selected species. Putative M. edulis immune genes were compared via tBLAS...

TNF related M. edulis transcripts with conserved TNF or TNFR domains identified by PROSITE. (DOC)

M. edulis contigs with high similarity to LPS induced TNF-alpha factor (LITAF) - like proteins of other organisms. (DOC)

Caspase-like contigs of M. edulis . (DOC)

Conserved motifs in M. edulis big defensin transcripts identified in Mytilus edulis. The amino acid sequence of 5 Mytilus edulis big defensins are compared with big defensin amino acid sequences from Argopecten irradians (AiBD, GenBank accession no. DQ334340) and Venerupis philippinarum (VpBD, GenBank accession no. HM562672). Further the conserved...

Assembly strategy of the Mytilus edulis transcriptome. Cleaned and quality controlled reads were initially assembled with either Celera (1. Assembly) or NEWBLER (2. Assembly). Resulting Contigs (C) and singletons (S) were subsequently further assembled in multiple rounds (R) using TGICL (Cap3) assembler and AMOS. For Run numbers 115–284 see table S...

Antimicrobial peptides identified in M. edulis . (DOC)

Alignment (aln format) used for phylogenetic analysis. (ALN)

Deduced amino acid sequence of NF-κB-like contigs of the blue mussel Mytilus edulis. In mammals the five proteins of the NF-κB transcription factor family (p65 (RelA), RelB, c-Rel, p105/p50 (NF-κB1), p100/52 (NF-κB2)) form distinct transcriptionally active homo- and heterodimeric complexes. The p50/p65 dimer is the most prominent heterodimer in mos...

19 MACPF domain bearing contigs of M. edulis. 5 of these fragments showed similarity to macrophage expressed gene-1, and 3 to apextrin, while 11 fragments could not be annotated. Proteins containing the MACPF domain but lacking other domains of the MAC complex members were reported in several other lower invertebrates (for review see, [108]). Some...

Alignment (phy format) used for phylogenetic analysis. (PHY)

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). Rece...

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, t...

Alignment of CTLLD sequences of matrix proteins. This file shows a ClustalW2 alignment of the sequences of predicted CTLLD enlisted in Table 1 (A) and a tree representation for graphical visualization (B).

Comparison of thombospondins Sp-Thsd7b and Sp-Thsd7b_2.

Selected MS/MS spectra of SM30-D peptides. This file contains a ClustalW2 alignment of SM30-D sequence variants and MaxQuant-annotated MS/MS spectra of unique SM30-D peptides.

Alignment of Sp-Mmp18/19-like sequences.

Compilation of proteins identified in S. purpuratus skeletal elements. The proteins were compiled from proteomic analyses of spicule matrix (this report) and published data of spine, test and tooth proteomes [25-27]. ++, proteins among the 33% most abundant; +, present at lower abundance; (+), tentatively identified; -, not found. P, at least parti...

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 standalon...

Selected spectra of test matrix phosphopeptides (docx-file containing embedded eps-files). For each of the unique peptides one spectrum is supplied. Spectra were saved directly from raw-files and annotated manually using and extending annotations provided by MaxQuant.

Protein data (xlsx-file). This file shows the MaxQuant-derived protein data such as protein scores, number of peptides, and molecular weight. Commonly occurring contaminants, such as human keratins or trypsin, were removed. From left to right the columns show Glean3 entry number (A), protein group number (B; groups may contain several Glean3 entrie...

Test matrix protein phosphorylation sites (xls-file). List of scores, phosphorylation site probabilities, possible kinase target motifs, charge, mass, mass errors and intensity of peptides from test matrix proteins as provided by MaxQuant identification and evaluation software.

Peptide data. This Excel sheet contains unique and razor peptide data. Peptides of common contaminants, such as human keratins or trypsin, were removed. A triple helical hydroxyproline-containing peptide belonging to Glean3:15708 and identified in a MaxQuant run including hydroxylation of proline as a variable modification is included with peptide...

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 pur...

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.e. the grade of completeness is...

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 retenti...

Differential equations of the model. Differential equations as used in the model.

SBML Model. Model in SBML format. Parameter values are set to arbitrary values. Also available on BioModels under ID MODEL2133240427.

Detailed comparison of TPEs and exp. Data. All matches and mismatches between detected TPEs and exp. data. Genes in the network for which no unambiguous expression change due to perturbations could be established from data as of December 2007 are not included.

All detected TPEs. All TPEs for all timepoints and territories.

Robustness to parameter variations. Method used to compute the robustness of gene expression against random parameter variations, results and discussion thereof.

Events used to initiate differential expression. Listing the events used in setting static inputs to initiate differential expression. For the Hill-Kinetics controlling inputs to the network in each territory (formula 9), we set S1 = 1, S2 = 0 at the time given in the respective 'on'-column and we set S1 = 0, S2 = 1 at the time given in the respect...

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. Chd is a secreted BMP inhibito...

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 i...

Proteins tentatively identified in the matrix of intact teeth. Identifications with a single unique peptide showing good quality, manually validated, spectra without MS3 confirmation.

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 thre...

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 unde...

Sequences of unique peptides identified in test matrix. List of sequences of accepted peptides from test matrix.

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 h...

The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Run...

Synteny Analysis. A search for cross-species conserved gene orders was performed as previously described [1]. We compared a larger contig of the FrRunt locus (Ensemble: Scaffold 39) than previously analyzed (Ensemble: Scaffold 835[2]) to the zebrafish genome and detected a synteny region between the 3′ genomic region of the FrRunt gene and chromoso...

Dogfish Primers. Primers employed to amplify and analyze the expression of Runt genes in dogfish. PA: Primary amplification, RA: Reamplification. (0.08 MB DOC)

Hagfish Primers. Primers employed to detect Runt genes and analyze Runt gene expression in hagfish. PA: Primary amplification, RA: Reamplification. (0.07 MB DOC)

Alignment used for Phylogenetic Analysis. Alignment (ClustalW, BioEdit: http://www.mbio.ncsu.edu/BioEdit/bioedit.html) of newly detected Runt genes in hagfish (MgRunxA and B, DQ990008, DQ990009) and dogfish (ScRunx1-3, DQ990010, DQ990012, DQ990014) with other deuterostome Runt genes. The conserved sequence blocks used for the phylogenetic analysis...

EMSA Oligos. Oligos employed for the electrophoretic mobility shift assays. (0.07 MB DOC)

Amphioxus Primers. Primers employed to analyze Sox9, Hedgehog and Runt genes in lancelets. (0.08 MB DOC)

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 an...

Provided is a table summarizing the sequences of the used Q-PCR primers, amplicon size, and melting temperatures.

Provided are WISH images of 88 endomesoderm genes in blastula stage Strongylocentrotus purpuratus embryos (20 hours).

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...

The genome of the sea urchin Strongylocentrotus purpuratus has recently been sequenced because it is a major model system for the study of gene regulatory networks. Embryonic expression patterns for most genes are unknown, however. Using large-scale screens on arrays carrying 50% to 70% of all genes, we identified novel territory-specific markers....

The Receptor Tyrosine kinase (RTK) and TGF-beta signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding...

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associate...

A gzip-compressed FASTA file containing sequences of the 19087 contigs described in this study.

A complete list of sheep genes upregulated in early fracture healing as determined by EST analysis with links to human homologs in UniGene and to the GeneNest database. Additionally, RT-PCR primer sequences and detailed results are shown.

The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relatively little research has been performed into sheep genetics, and DNA sequences are available for only a small number of sheep genes. In this w...

Complete genome doubling has long-term consequences for the genome structure and the subsequent evolution of an organism. It has been suggested that two genome duplications occurred at the origin of vertebrates (known as the 2R hypothesis). However, there has been considerable debate as to whether these were two successive duplications, or whether...

Components of the Wnt signaling pathway are involved in patterning the sea urchin primary or animal-vegetal (AV) axis, but the molecular cues that pattern the secondary embryonic axis, the aboral/oral (AO) axis, are not known. In an analysis of signaling molecules that influence patterning along the sea urchin embryonic axes, we found that members...

We identified a transcription factor of the onecut class in the sea urchin Strongylocentrotus purpuratus that represents an ortholog of the mammalian gene HNF6, the founding member of the onecut class of proteins. The isolated sea urchin gene, named SpOnecut, encodes a protein of 483 amino acids with one cut domain and a homeodomain. Phylogenetic a...

We have identified an NK2 family homeodomain transcription factor, SpNK2.1, in the sea urchin Strongylocentrotus purpuratus whose transcripts are initially detected within the apical plate ectoderm of the hatching blastula and are confined to the apical organ at least through 2 weeks of development. Protein localization studies demonstrate that SpN...

Calcium (Ca(2+)) is a ubiquitous intracellular messenger, controlling a diverse range of cellular processes, including fertilization and development of the embryo. One of the key mechanisms involved in triggering intracellular calcium release is the generation of the second messenger inositol-1,4,5-phosphate (IP(3)) by the phospholipase C (PLC) cla...

Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also amenable to functional studies, the sea urchin system has emerged as one of the leading models for the analysis of the function of genomic regulatory ne...

Runt-homologous molecules are characterized by their DNA binding runt-domain which is highly conserved within bilaterians. The three mammalian runt-genes are master regulators in cartilage/bone formation and hematopoiesis. Historically these features evolved in Craniota and might have been promoted by runt-gene duplication events. The purpose of th...

The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the hypothesized genome duplications. Through the comparison of a gene catalog from amphioxus, the closest living invertebrate relative of vertebrates, to 3453 sing...

Brachyury is a transcription factor that functions in gastrulation and endoderm development throughout the Bilateria. Here, we identify genes that are expressed downstream of brachyury during gastrulation of the sea urchin embryo. Screens with two different complex probes generated by subtractive hybridization were carried out on high-density array...

The first stages in the sea urchin genome project have been reported.

Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 12...

Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 12...

In this article we describe a method for characterization of large cDNA clone libraries based on oligonucleotide fingerprints (OFPs). The main advantage of this technique lies in that, without sequencing, each clone is tagged in an almost unique way, which has a couple of interesting applications, e.g. clustering of clones that belong to the same g...

Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivat...

We describe the use of oligonucleotide fingerprinting for the generation of a normalized cDNA library from unfertilized sea urchin eggs and report the preliminary analysis of this library, which resulted in the establishment of a partial gene catalogue of the sea urchin egg. In an analysis of 21,925 cDNA clones by hybridization with 217 oligonucleo...