Detlef Bernhard

CREx: inferring genomic rearrangements based on common intervals

SUMMARY We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders. AVAILABILITY CREx is freely available at http://pacosy.informatik.uni-leipzig.de/crex

Phylogenetic analysis of complete small subunit ribosomal RNA coding region of Myxidium lieberkuehni: evidence that Myxozoa are Metazoa and related to the Bilateria.

Summary: The phylogenetic position of Myxozoa relative to other eukaryotes has been controversialDuring their complex life cycles they show both protist and metazoan charactersIn contrast to their general classification as protists, phylogenetic comparisons of the complete 16Slike rRNA sequence of the myxosporean Myxidium lieberkuehni with other, unicellular and metazoan sequences show that Myxozoa share a common evolutionary history with Metazoa and are most closely related to the Bilateria

Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) Reconstructed with Nuclear Small Subunit rRNA Gene Sequences: Discrepancies and Accordances with Morphological Data

ABSTRACT. The Stichotrichia, known as an especially various and taxonomically difficult group, were intensely studied with morphological, morphogenetic, and molecular methods in the last years. Nevertheless, a consistent classification is lacking and several important questions about the phylogenetic relationships within this group remain unsolved. In order to gain deeper insights into these relationships, the nuclear small subunit rRNA genes of seven species of the Stichotrichia, representatives of the families Oxytrichidae, Amphisiellidae, and Pseudourostylidae, were phylogenetically analysed. Although our analyses resulted in a poor resolution of the phylogenetic relationships, some conclusions can be drawn. Firstly, following the current classification systems the Oxytrichidae as well as their subfamilies seem to be paraphyletic and the basic 18 FVT cirral pattern has been modified several times independently. Secondly, sequence analyses of several Oxytricha species resulted in a high molecular diversity, which does not support monophyly of this genus. Thirdly, several families of the order Urostylida (Urostylidae, Pseudokeronopsidae, and Pseudourostylidae) also do not form monophyletic groups.

The freshwater turtle genus Mauremys (Testudines, Geoemydidae) — a textbook example of an east–west disjunction or a taxonomic misconcept?

Barth, D. Bernhard, D. Fritzsch, G. & Fritz, U. (2004): The freshwater turtle genus Mauremys— a textbook example of an east–west disjunction or a taxonomic misconcept? —Zoologica Scripta, 33, 213–221.

EVOLUTION OF HISTONE H4 AND H3 GENES IN DIFFERENT CILIATE LINEAGES

Abstract. The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4 genes including the intergenic region.The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences. The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones.The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.

Evolution of 16S-like ribosomal RNA genes in the ciliophoran taxa litostomatea and phyllopharyngea

Summary Complete small subunit (16S-like rRNA) gene sequences were determined for two litostome ( Homalozoon vermiculare and Loxophyllum utriculariae ) and two phyllopharyngean ciliates ( Discophrya collini and Trithigmostoma steini ). Six of the eight ciliate classes are now represented in the 16S-like rRNA data base. Phylogenetic reconstructions identify Blepharisma americanum as the first ciliate branch but the heterotrichs B. americanum and Metopus palaeformis do not appear to be closely related. Later branching ciliate lineages are represented by the litostomes, spirotrichs and a heterogeneous group that includes colpodid, oligohymenophoran, and phyllopharyngean ciliates. The relatively simple cytostomal organization of litostomes and phyllopharyngeans should not be regarded as primitive states. Using the rRNA phylogenies as framework to understand the evolution of non-molecular features, the low complexity of their oral structures can be interpreted as a secondary adaptation — possibly caused by a shift towards macro-phagous feeding behavior.

Evolution of Mitochondrial Gene Orders in Echinoderms

A comprehensive analysis of the mitochondrial gene orders of all previously published and two novel Antedon mediterranea (Crinoidea) and Ophiura albida (Ophiuroidea) complete echinoderm mitochondrial genomes shows that all major types of rearrangement operations are necessary to explain the evolution of mitochondrial genomes. In addition to protein coding genes we include all tRNA genes as well as the control region in our analysis. Surprisingly, 7 of the 16 genomes published in the GenBank database contain misannotations, mostly unannotated tRNAs and/or mistakes in the orientation of tRNAs, which we have corrected here. Although the gene orders of mt genomes appear very different, only 8 events are necessary to explain the evolutionary history of echinoderms with the exception of the ophiuroids. Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions.

Phylogenetic Relationships of the Nassulida Within the Phylum Ciliophora Inferred from the Complete Small Subunit rRNA Gene Sequences of Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius

ABSTRACT. Using comparisons of complete small subunit rRNA sequences from the ciliated protozoans Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius we inferred the phylogenetic position of the Nassulida (Class Nassophorea) within the Ciliophora. In distance matrix analyses the Nassulida share a common ancestry with the colpodean ciliate Colpoda inflata. Distance matrix and parsimony methods convincingly demonstrate that the Nassulida plus Colpodida are members of a complex ciliate assemblage that also includes the oligohymenophorans and phyllopharyngeans. These phylogenetic inferences are largely congruent with recent analyses of 23S‐like rRNA gene sequences and morphogenetic features. Groups traditionally thought to represent ancestral lineages now appear as highly derived ciliates. In contrast, heterotrichs which were considered to represent a highly evolved group, diverge at the base of the ciliates.

Fructose-1,6-bisphosphatase genes in animals

A comparison of the amino acid sequences of the liver and muscle fructose-1,6-bisphosphatase (FbPase) isoforms in primates and rodents suggested an ancient duplication event leading to the corresponding genes. We investigated the presence of both genes in the rabbit (order lagomorphs) and in species belonging to further distantly related metazoan taxa. By an analysis of the available complete genomes and proteomes of the nematode Caenorhabditis elegans and of Drosophila melanogaster only one sequence homologous to known FbPases was found in each species. The corresponding mRNAs were characterized by cDNA sequencing. We then carried out reverse transcription-polymerase chain reactions to amplify central fragments of the FbPase cDNAs from liver and muscle of Gallus gallus, Xenopus laevis, and Esox lucius, respectively. Their sequencing revealed that (i) the livers of chicken, frog, and fish contain mRNAs which are closely related to mammalian liver FbPase mRNAs, (ii) chicken muscle contains an mRNA which is most homologous to mammalian muscle FbPase mRNAs, (iii) frog muscle contains both a liver-type and a muscle-type FbPase mRNA, while (iv) in fish muscle no FbPase mRNA could be detected by our approach despite the doubtless presence of the enzyme in this organ. An alignment of the partial amino acid sequences of the different FbPases showed that the residues that are thought to be in contact with the substrate, fructose-2,6-bisphosphate, and Mg(2+) are totally conserved, while some amino acids having contact with adenosine monophosphate were found to vary among several species. The question of what might be the advantage of having more than one gene coding for FbPase per haploid genome is discussed.

Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata

The genome architecture and amino acid sequences of six new complete mitochondrial genomes were determined from representatives of Hemichordata (1), Ophiuroidea (3), Echinoidea (1) and Holothuroidea (1) and were analysed together with previously known sequences. Phylogenetic analyses recovered three lineages within echinoderms, Crinoidea, Ophiuroidea and a group comprising Holothuroidea, Echinoidea, and Asteroidea. In contrast to previous analyses of mitochondrial genomes the increased data set recovered the classical echinoderm phylogeny of Eleutherozoa and Echinozoa in Maximum Likelihood and Bayesian analyses using hemichordate out-group representatives. However, an inconsistent ramification appeared with vertebrate out-groups and in Maximum Parsimony and Neighbour Joining reconstructions. The basal (consensus) gene orders of all three lineages could be derived from a hypothetical ancestral crinoid gene order by one single rearrangement in each lineage. The genome architecture was highly conserved in Echinoidea, whereas the highest gene order differences and large amounts of unassigned sequences (UAS) were detected in Ophiuroidea, supporting a higher evolutionary rate than in any other echinoderm lineage. The variability in gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events.