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de Gregoris T.B.,Northumbria University | Rupp O.,Bielefeld University | Klages S.,Genome Center Cologne at for Plant Breeding Research | Knaust F.,Genome Center Cologne at for Plant Breeding Research | And 7 more authors.
Biofouling | Year: 2011

In order to improve the genetic characterisation of the barnacle Balanus amphitrite, normalised EST libraries for the developmental stages, viz. nauplius (a mix of instars I and II), cyprid and adult, were generated. The libraries were sequenced independently using 454 technologies and 575,666 reads were generated. For adults, 4843 unique isotigs were estimated and 6754 and 7506 in the cyprid and naupliar stage, respectively. It was found that some of the previously proposed cyprid-specific bcs genes were also expressed during the naupliar and adult stage. Furthermore, as lectins have been hypothesised to influence settlement cue recognition in barnacles, the database was searched for lectin-like isotigs. Two proteins, uniquely expressed in either the cyprid or the adult stage, matched a mannose receptor, and their nucleotide sequences were 33% and 31% identical to a lectin (BRA-3) isolated from Megabalanus rosa. Further characterisation of these genes may suggest their involvement in settlement. © 2011 Taylor & Francis. Source

Tine M.,University of Johannesburg | Tine M.,Genome Center Cologne at for Plant Breeding Research
BMC Research Notes | Year: 2015

Background: Phosphoglucose isomerase (PGI) genes are important multifunctional proteins whose evolution has, until now, not been well elucidated because of the limited number of completely sequenced genomes. Although the multifunctionality of this gene family has been considered as an original and innate characteristic, PGI genes may have acquired novel functions through changes in coding sequences and exon/intron structure, which are known to lead to functional divergence after gene duplication. A whole-genome comparative approach was used to estimate the rates of molecular evolution of this protein family. Results: The results confirm the presence of two isoforms in teleost fishes and only one variant in all other vertebrates. Phylogenetic reconstructions grouped the PGI genes into five main groups: lungfishes/coelacanth/cartilaginous fishes, teleost fishes, amphibians, reptiles/birds and mammals, with the teleost group being subdivided into two subclades comprising PGI1 and PGI2. This PGI partitioning into groups is consistent with the synteny and molecular evolution results based on the estimation of the ratios of nonsynonymous to synonymous changes (Ka/Ks) and divergence rates between both PGI paralogs and orthologs. Teleost PGI2 shares more similarity with the variant found in all other vertebrates, suggesting that it has less evolved than PGI1 relative to the PGI of common vertebrate ancestor. Conclusions: The diversification of PGI genes into PGI1 and PGI2 is consistent with a teleost-specific duplication before the radiation of this lineage, and after its split from the other infraclasses of ray-finned fishes. The low average Ka/Ks ratios within teleost and mammalian lineages suggest that both PGI1 and PGI2 are functionally constrained by purifying selection and may, therefore, have the same functions. By contrast, the high average Ka/Ks ratios and divergence rates within reptiles and birds indicate that PGI may be involved in different functions. The synteny analyses show that the genomic region harbouring PGI genes has independently undergone genomic rearrangements in mammals versus the reptile/bird lineage in particular, which may have contributed to the actual functional diversification of this gene family. © 2015 Tine. Source

Stolle E.,Martin Luther University of Halle Wittenberg | Wilfert L.,ETH Zurich | Wilfert L.,University of Cambridge | Schmid-Hempel R.,ETH Zurich | And 5 more authors.
BMC Genomics | Year: 2011

Background: The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level.Results: The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG.Conclusions: This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae. © 2011 Stolle et al; licensee BioMed Central Ltd. Source

Tine M.,Max Planck Institute for Molecular Genetics | Kuhl H.,Max Planck Institute for Molecular Genetics | Jastroch M.,Helmholtz Center for Environmental Research | Reinhardt R.,Genome Center Cologne at for Plant Breeding Research
BMC Evolutionary Biology | Year: 2012

Background: Uncoupling proteins (UCP) are evolutionary conserved mitochondrial carriers that control energy metabolism and therefore play important roles in several physiological processes such as thermogenesis, regulation of reactive oxygen species (ROS), growth control, lipid metabolism and regulation of insulin secretion. Despite their importance in various physiological processes, their molecular function remains controversial. The evolution and phylogenetic distribution may assist to identify their general biological function and structure-function relationships. The exact number of uncoupling protein genes in the fish genome and their evolution is unresolved. Results: Here we report the first characterisation of UCP gene family members in sea bass, Dicentrarchus labrax, and then retrace the evolution of the protein family in vertebrates. Four UCP genes that are shared by five other fish species were identified in sea bass genome. Phylogenetic reconstitution among vertebrate species and synteny analysis revealed that UCP1, UCP2 and UCP3 evolved from duplication events that occurred in the common ancestor of vertebrates, whereas the novel fourth UCP originated specifically in the teleost lineage. Functional divergence analysis among teleost species revealed specific amino acid positions that have been subjected to altered functional constraints after duplications. Conclusions: This work provides the first unambiguous evidence for the presence of a fourth UCP gene in teleost fish genome and brings new insights into the evolutionary history of the gene family. Our results suggest functional divergence among paralogues which might result from long-term and differential selective pressures, and therefore, provide the indication that UCP genes may have diverse physiological functions in teleost fishes. Further experimental analysis of the critical amino acids identified here may provide valuable information on the physiological functions of UCP genes. © 2012 Tine et al.; licensee BioMed Central Ltd. Source

Tine M.,Max Planck Institute for Molecular Genetics | Kuhl H.,Max Planck Institute for Molecular Genetics | Beck A.,Max Planck Institute for Molecular Genetics | Bargelloni L.,University of Padua | Reinhardt R.,Genome Center Cologne at for Plant Breeding Research
Marine Genomics | Year: 2011

This study assessed the relationship between the occurrence and function of intronless or single exon genes (SEG) in the genome of five teleost species and their phylogenetic distance. The results revealed that Takifugu rubripes, Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculeatus and Danio rerio genomes are respectively comprised of 2.83%, 3.42%, 4.49%, 4.35% and 4.02% SEGs. These SEGs encode for a variety of family proteins including claudins, olfactory receptors and histones that are essential for various biological functions. Subsequently, we predicted and annotated SEGs in three European sea bass, Dicentrarchus labrax chromosomes that we have sequenced, and compared results with those of stickleback (G. aculeatus) homologous chromosomes. While the annotation features of three D. labrax chromosomes revealed 78 (5.30%) intronless genes, comparisons with G. aculeatus showed that SEG composition and their order varied significantly among corresponding chromosomes, even for those with nearly complete synteny. More than half of SEGs identified in most of the species have at least one ortholog multiple exon gene in the same genome, which provides insight to their possible origin by retrotransposition. In spite of the fact that they belong to the same lineage, the fraction of predicted SEGs varied significantly between the genomes analyzed, and only a low fraction of proteins (4.1%) is conserved between all five species. Furthermore, the inter-specific distribution of SEGs as well as the functional categories shared by species did not reflect their phylogenetic relationships. These results indicate that new SEGs are continuously and independently generated after species divergence over evolutionary time as evidenced by the phylogenetic results of single exon claudins genes. Although the origin of SEGs cannot be inferred directly from the phylogeny, our results provide strong support for the idea that retrotransposition followed by tandem duplications is the most probable event that can explain the expansion of SEGs in eukaryotic organisms. © 2011 Elsevier B.V. Source

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