Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.     

The duplication of the <Emphasis Type="Italic">Hox</Emphasis> gene clusters in teleost fishes

Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can be used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster. Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of 7 or 8 orthologous Hox gene clusters. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved non-coding sequences provides additional support for the “duplication early” hypothesis that the Hox clusters in teleosts are derived from eight ancestral clusters by means of subsequent gene loss; the data remain ambiguous, however, in particular for the HoxC clusters. Assuming the “duplication early” hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that is still ongoing. A few suggestions on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed. Supplemental material is available at http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/04-006/.     

Neuroectodermal and endodermal expression of the ascidian Cdx gene is separated by metamorphosis

Ascidians are a group of invertebrate chordates that exhibit a biphasic life history, with chordate-specific structures developing during embryogenesis (dorsal neural tube and notochord) and metamorphosis (pharyngeal gill slits and endostyle). Here we characterize the expression of a caudal/Cdx gene homologue, Hec-Cdx, from the ascidian Herdmania curvata. Vertebrate Cdx genes are expressed at gastrulation and in the posterior of the developing neural tube and endoderm. Hec-Cdx expression is initiated at the earliest stages of gastrulation, with peaks in RNA abundance occurring first during neurulation and tailbud extension and then in 3- to 5-day-old juveniles. Hec-Cdx is expressed in a pair of cells in the anterior lip of the blastopore in the late gastrula which form the most posterior portion of the neural plate. During tailbud formation expression is maintained in and solely restricted to these cells. During metamorphosis expression is localized to the intestine of the juvenile. These data, along with data for the H. curvata Otx gene, suggest that the evolution of the novel ascidian biphasic body plan was not accompanied by a deployment of these genes into new pathways but by a temporal separation of tissue-specific expression. Received: 10 October 1999 / Accepted: 1 November 1999     

Evolution of trophic types in emperor fishes ( Lethrinus,Lethrinidae, Percoidei) based on cytochrome B gene sequence variation

Three trophic categories exist within emperor fishes, genus Lethrinus, relating to body form and dentition type. One group contains low-bodied, high speed, stalking predators with conical teeth. Another group comprises high-bodied, slow speed carnivores with molariform teeth capable of crushing hard-shelled benthic prey. A third group is also high-bodied but with conical teeth feeding mostly on small or soft-shelled benthic prey. Inferring the evolution of these trophic types within Lethrinus using morphology is problematic since these characters are typically correlated with feeding mode and are potentially homoplasious. We use mitochondrial DNA sequences, to independently determine a phylogenetic hypothesis for Lethrinus, which are not dependent on morphological characters relating to trophic categories. We analyzed complete cytochrome b gene sequences (1140 bp) for 20 species of Lethrinus, representing the three trophic types, and for 13 outgroup species, including four other representatives of the Lethrinidae. A monophyletic Lethrinidae did not resolve, but the monophyly of Lethrinus is well supported. In addition, two major clades within Lethrinus are well supported. One of these clades exclusively contains low-bodied species with conical teeth while the other clade only comprises the high-bodied species with molariform teeth. A high-bodied species with conical teeth, Lethrinus miniatus, appears most ancestral and sister to all other Lethrinus species. We hypothesize that this generalist trophic type was the evolutionary precursor to both of the other primary trophic types.     

Regulatory elements in the promoter of the vitelline membrane gene VM32E of Drosophila melanogaster direct gene expression in distinct domains of the follicular epithelium

The Drosophila vitelline membrane protein gene VM32E is expressed according to a precise temporal and spatial program in the follicle cells. Results from germ line transformation experiments using different fragments of the −465/−39 VM32E region fused to the hsp/lacZ reporter gene revealed that the region −348/−39 is sufficient to confer the wild-type expression pattern. Within this segment, distinct cis-regulatory elements control VM32E expression in ventral and dorsal follicle cells. The region between −135/−113 is essential for expression of the VM32E gene in the ventral columnar follicle cells. Expression in the dorsal domain requires the two regions −348/−254 and −118/−39. Furthermore, the region −253/−119 appears to contain a negative element that represses gene activity in anterior centripetal cells. We suggest that the expression of the VM32E gene throughout the follicular epithelium is controlled by specific cis-regulatory elements acting in distinct spatial domains and following a precise developmental program. Received: 22 October 1996 / Accepted: 14 November 1996     

Evolution of the vertebrate twist family and synfunctionalization: a mechanism for differential gene loss through merging of expression domains

Twist genes are essential for embryonic development and are conserved from jellyfish to human. To study the vertebrate twist family and its evolution, the entire complement of twist genes was obtained for 9 representative species. Phylogenetic analysis showed that a single protochordate twist gene was duplicated at least twice before the teleost-tetrapod split to give rise to 3 ancestral genes, which were further duplicated or deleted, resulting in fluctuating number of twist paralogs in different vertebrate lineages. To find whether changes in gene copy number were associated with changes in gene function, embryonic expression patterns of twist orthologs were evaluated against the number of twist paralogs in different species. The results showed evidence for both neo- and subfunctionalization, and, in addition, for loss of an ancestral regulatory gene. For example, in Xenopus, twist2 was lost, but the twist1 paralog acquired, and therefore preserved, twist2 function. A general model is proposed to explain the data. In this process, termed synfunctionalization, one paralog acquires the expression domain(s) of another. The merging may lead to function shuffle. Alternatively, it may leave one paralog redundant and thus subject to deletion--while its function is retained by the surviving paralog(s). Synfunctionalization is a mechanism that, together with neo- and subfunctionalization, may work to establish equilibrium in the number of genes that regulate developmental processes; it may regulate the complexity of regulatory regions as well as gene copy number and therefore may play a role in evolution of gene function and the structure of genome.     

Constitutive components and induced gene expression are involved in the desiccation tolerance of Selaginella tamariscina

Selaginella tamariscina, one of the most primitive vascularplants, can remain alive in a desiccated state and resurrectwhen water becomes available. To evaluate the nature of desiccationtolerance in this plant, we compared the composition of solublesugars and saturation ratios of phospholipids (PLs) betweenhydrated and desiccated tissues of S. tamariscina using gaschromatography. In this study, differences in gene expressionand ABA contents were also analyzed during dehydration. Theresults revealed that trehalose (at >130 mg g^–1 DW)was the major soluble sugar, and low saturated fatty acid contentin PLs (0.31) was maintained in both hydrated and desiccatedtissues. In addition, the ABA content of S. tamariscina increased3-fold, and genes involved in ABA signaling and cellular protectionwere up-regulated while photosystem-related genes were down-regulatedduring dehydration. The biochemical and molecular findings suggestthat both constitutive and inducible protective molecules contributeto desiccation tolerance of S. tamariscina.     

Comprehensive analyses of hox gene expression in Xenopus laevis embryos and adult tissues

From whole genome sequencing of an allotetraploid frog, Xenopus laevis, two homeologous sets (L and S) of four Hox clusters A through D (HoxA.L/S, HoxB.L/S, HoxC.L/S, and HoxD.L/S) and 13 paralogous groups (PGs) with 76 genes were identified, allowing us to carry out the first comprehensive analyses of hox gene expression in vertebrates. Expression of all hox genes during development and in adult tissues was analyzed by RNA‐sequencing. The expression levels of most hox genes were similar between homeologs, but in some pairs, large differences were observed and several of these were confirmed by RT‐PCR and whole mount in situ hybridization experiments. These results indicate that subfunctionalization of hox genes may have occurred since allotetraploidization. Furthermore, comprehensive analysis of hox gene expression during early development did not agree with the hypothesis of temporal collinearity especially in genes belonging to PG2 to PG10 .     

The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes

The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement with the well-established phylogeny of cichlid fish. Received: 11 October 2000 / Accepted: 26 February 2001     

A comparison of the response to induced exercise in red- and white-blooded Antarctic fishes

The physiological responses to forced exercise were studied in yellowbelly and marbled rockcod (Notothenia coriiceps and N. rossii), and the haemoglobinless icefish (Chaenocephalus aceratus), from blood samples obtained via indwelling catheters. The maximal exertion tolerable by N. coriiceps was 3–5 min, although N. rossii was not fully exhausted by this effort, and it proved difficult to elicit sustained maximal activity in C. aceratus. Arterial O₂ tension reflected the relative degree of exhaustion, showing a significant fall in the case of N. coriiceps, little change in N. rossii, and even a rise in C. aceratus as a result of hyperventilation. Such changes in the red-blooded species were not caused by altered O₂ carrying capacity, as there was no change in haematocrit. In Notothenia spp. the decrease in arterial pH was better correlated with a rise in arterial CO₂ tension than with blood lactate concentration, which is reflected in a modest net metabolic acid load. In contrast, the icefish showed an attenuated hypercapnia and a more pronounced lactacidosis, but an insignificant net metabolic acid load. Disturbance in ionoregulation following exercise was limited to an elevated [Cl⁻] in Notothenia, while circulating catecholamine levels remained unusually low in all specimens. The response to stress appears to reflect lifestyle and/or endemic speciation, rather than specific adaptations to the stenothermal environment. Accepted: 9 August 1996     

The effect of smectite composition on the catalysis of peptide bond formation

Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80°C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed. Received: 20 February 1996 / Accepted: 26 April 1996     

Towards an explanation of the developmental strategy in leptocephalous larvae of marine teleost fishes

Synopsis Various observations on the morphology, physiology and biochemistry of leptocephalous larvae of different groups of marine teleost fishes have been brought together in order to arrive at a model which attempts to explain the ‘leptocephalous strategy’ of larval development. The observation that basic similarities are found in the developmental pattern of all groups of fishes with a leptocephalus (Superorder: Elopomorpha) forms the basis for proposing a common strategy within the superorder. Circumstantial evidence suggesting that premetamorphic (Phase I) larvae obtain a significant fraction of their nutritional needs by absorbing dissolved organic matter across surface epithelia has been reviewed. It is suggested that this might occur via a Na⁺-mediated transport system similar to that seen in various marine invertebrates. Breakdown of the gelatinous matrix formed during Phase I is assumed to provide the nutrients required for the metamorphic larvae (Phase II). This strategy is then contrasted with the more ‘typical’ form of larval development in marine teleosts and shown to differ in several basic respects.     

Evolution of the mouse polyubiquitin-C gene

The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats with no spacer sequences between individual monomer units. Ubiquitin is one of the most conserved proteins known to date, and the individual units within a number of poly-u genes are significantly more similar to each other than would be expected if each unit evolved independently. It has been proposed that the rather striking similarity among poly-u monomers in some lineages is caused by a series of homogenization events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two mouse strains. Analysis of these sequences, as well as those of the previously reported Chinese hamster and rat poly-u genes, supports the assertion that the homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over events. The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 × 10⁻⁵ events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene.     

The role of exo-(1-->4)-beta-galactanase in the mobilization of polysaccharides from the cotyledon cell walls of Lupinus angustifolius following germination

BACKGROUND AND AIMS: The cotyledons of Lupinus angustifolius contain large amounts of cell wall storage polysaccharide (CWSP) composed mainly of (1-->4)-beta-linked D-galactose residues in the form of branches attached to a rhamnogalacturonan core molecule. An exo-(1-->4)-beta-galactanase with a very high specificity towards (1-->4)-beta-linked D-galactan has been isolated from L. angustifolius cotyledons, and shown to vary (activity and specific protein) in step with CWSP mobilization. This work aimed to confirm the hypothesis that galactan is the main polymer retrieved from the wall during mobilization at the ultrastructural level, using the purified exo-galactanase as a probe. METHODS: Storage mesophyll cell walls ('ghosts') were isolated from the cotyledons of imbibed but ungerminated lupin seeds, and also from cotyledons of seedlings after the mobilization of the CWSP. The pure exo-(1-->4)-beta-galactanase was coupled to colloidal gold particles and shown to be a specific probe for (1-->4)-beta-D-galactan. They were used to localize galactan in ultrathin sections of L. angustifolius cotyledonary mesophyll tissue during CWSP mobilization. KEY RESULTS: On comparing the morphologies of isolated cell walls, the post-mobilization 'ghosts' did not have the massive wall-thickenings of pre-mobilization walls. Compositional analysis showed that the post-mobilization walls were depleted in galactose and, to a lesser extent, in arabinose. When pre-mobilization ghosts were treated with the pure exo-galactanase, they became morphologically similar to the post-mobilization ghosts. They were depleted of approximately 70% of the galactose residues that would have been mobilized in vivo, and retained all the other sugar residues originally present. Sharply defined electron-transparent wall zones or pockets are associated with CWSP mobilization, being totally free of galactan, whereas wall areas immediately adjacent to them were apparently undepleted. CONCLUSIONS: The exo-(1-->4)-beta-galactanase is the principal enzyme involved in CWSP mobilization in lupin cotyledons in vivo. The storage walls dramatically change their texture during mobilization as most of the galactan is hydrolysed during seedling development.