Daniel Chourrout

Tunicates and not cephalochordates are the closest living relatives of vertebrates

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.

Genome Regulation by Polycomb and Trithorax Proteins

Polycomb group (PcG) and trithorax group (trxG) proteins are critical regulators of numerous developmental genes. To silence or activate gene expression, respectively, PcG and trxG proteins bind to specific regions of DNA and direct the posttranslational modification of histones. Recent work suggests that PcG proteins regulate the nuclear organization of their target genes and that PcG-mediated gene silencing involves noncoding RNAs and the RNAi machinery.

Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica.

Tunicate embryos and larvae have small cell numbers and simple anatomical features in comparison with other chordates, including vertebrates. Although they branch near the base of chordate phylogenetic trees, their degree of divergence from the common chordate ancestor remains difficult to evaluate. Here we show that the tunicate Oikopleura dioica has a complement of nine Hox genes in which all central genes are lacking but a full vertebrate-like set of posterior genes is present. In contrast to all bilaterians studied so far, Hox genes are not clustered in the Oikopleura genome. Their expression occurs mostly in the tail, with some tissue preference, and a strong partition of expression domains in the nerve cord, in the notochord and in the muscle. In each tissue of the tail, the anteroposterior order of Hox gene expression evokes spatial collinearity, with several alterations. We propose a relationship between the Hox cluster breakdown, the separation of Hox expression domains, and a transition to a determinative mode of development.

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

Ocean Dweller Sequenced The Tunicates, which include the solitary free-swimming larvaceans that are a major pelagic component of our oceans, are a basal lineage of the chordates. In order to investigate the major evolutionary transition represented by these organisms, Denoeud et al. (p. 1381, published online 18 November) sequenced the genome of Oikopleura dioica, a chordate placed by phylogeny between vertebrates and amphioxus. Surprisingly, the genome showed little conservation in genome architecture when compared to the genomes of other animals. Furthermore, this highly compacted genome contained intron gains and losses, as well as species-specific gene duplications and losses that may be associated with development. Thus, contrary to popular belief, global similarities of genome architecture from sponges to humans are not essential for the preservation of ancestral morphologies. A metazoan genome departs from the organization that appears rigidly established in other animal phyla. Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.

Pressure-induced retention of second polar body and suppression of first cleavage in rainbow trout: production of all-triploids, all-tetraploids, and heterozygous and homozygous diploid gynogenetics

Abstract Retention of the second polar body in rainbow trout eggs was induced by 7000 psi early pressure shocks (applied 40 min after insemination) lasting 4 min. This resulted in all-triploid progenies after fertilization with functional sperm, and in high yields of heterozygous diploid gynogenetic fry after insemination with gamma-irradiated sperm. All-tetraploid progenies were produced by 7000 psi late pressure shocks (applied 5 h 50 min after insemination) lasting 4 min, if normal sperm had been used. With eggs activated by gamma-irradiated sperm, these shocks resulted in diploid gynogenetic embryos that were supposed to be homozygous at all their loci because obviously they result from the fusion of two mitotic products. This fact may explain their very low post-hatching survival, but the occurrence of residual chromosome fragments of paternal origin in their cells, demonstrated by an extensive karyological investigation, could also be responsible of the poor yields; such an observation suggests that we abandon the use of gamma irradiation for sperm inactivation. Finally, tetraploid hybrid embryos were produced with similar late pressure shocks applied after heterospecific inseminations.

Production of second generation triploid and tetraploid rainbow trout by mating tetraploid males and diploid females - Potential of tetraploid fish.

SummaryFirst generation tetraploids were produced by hydrostatic pressure treatment before the first cleavage and raised until the adult stage. Their survival and growth were severely depressed when compared to the diploid control: after two years, no ovulated females were found although males produced sperm at 1 and 2 years of age and were mated individually with diploid females. The progenies were consistently normal with high survival rates. They were found to be almost all triploids by karyology, which failed to detect a significant rate of aneuploidies. However, the fertilizing ability of tetraploid males was always low (0 to 97% of the control; average 40%). Several arguments presented here support the hypothesis that diploid spermatozoas, which are wider than haploid ones, would be frequently blocked during their penetration through the micropyle canal. Second generation tetraploids were produced after such matings by heat shocks, causing the retention of the second polar body. Their survival and growth were much more satisfactory than in the first generation, although still lower than in diploid and triploid controls issuing from diploid parents. Performances of second generation triploids were comparable to those of diploids, and slightly better than those of conventional triploids issuing from diploid parents. 94.5% of the second generation tetraploids were male.

Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements

Bilaterian animals have a Hox gene cluster essential for patterning the main body axis, and a ParaHox gene cluster. Comparison of Hox and ParaHox genes has led workers to postulate that both clusters originated from the duplication of an ancient cluster named ProtoHox, which contained up to four genes with at least the precursors of anterior and posterior Hox/ParaHox genes. However, the way in which genes diversified within the ProtoHox, Hox and ParaHox clusters remains unclear because no systematic study of non-bilaterian animals exists. Here we characterize the full Hox/ParaHox gene complements and genomic organization in two cnidarian species (Nematostella vectensis and Hydra magnipapillata), and suggest a ProtoHox cluster simpler than originally thought on the basis of three arguments. First, both species possess bilaterian-like anterior Hox genes, but their non-anterior genes do not appear as counterparts of either bilaterian central or posterior genes; second, two clustered ParaHox genes, Gsx and a gene related to Xlox and Cdx, are found in Nematostella vectensis; and third, we do not find clear phylogenetic support for a common origin of bilaterian Cdx and posterior genes, which might therefore have appeared after the ProtoHox cluster duplication. Consequently, the ProtoHox cluster might have consisted of only two anterior genes. Non-anterior genes could have appeared independently in the Hox and ParaHox clusters, possibly after the separation of bilaterians and cnidarians.

High efficiency gene transfer in rainbow trout (Salmo gairdneri Rich.) by microinjection into egg cytoplasm

Abstract A plasmid containing human growth hormone cDNA sequence was injected into cytoplasm of fertilized rainbow trout ( Salmo gairdneri Rich.) eggs before first cleavage. Survival rates at hatching (stage of analysis) were high (average: 77%; range: 50–100%). Foreign DNA was detected in pooled and individual embryos either by dot blot or by southern electrophoresis procedures using the labelled plasmid as probe; it comigrated with the high molecular weight DNA and was therefore most likely integrated in the trout genome. Transformation yields were higher with linearized than with circular plasmid (75% versus 40%). These data suggest that transgenic trout can be routinely obtained in large proportions.

Spliced-Leader RNA trans Splicing in a Chordate, Oikopleura dioica, with a Compact Genome

ABSTRACT trans splicing of a spliced-leader RNA (SL RNA) to the 5′ ends of mRNAs has been shown to have a limited and sporadic distribution among eukaryotes. Within metazoans, only nematodes are known to process polycistronic pre-mRNAs, produced from operon units of transcription, into mature monocistronic mRNAs via an SL RNA trans-splicing mechanism. Here we demonstrate that a chordate with a highly compact genome, Oikopleura dioica, now joins Caenorhabditis elegans in coupling trans splicing with processing of polycistronic transcipts. We identified a single SL RNA which associates with Sm proteins and has a trimethyl guanosine cap structure reminiscent of spliceosomal snRNPs. The same SL RNA, estimated to be trans-spliced to at least 25% of O. dioica mRNAs, is used for the processing of both isolated or first cistrons and downstream cistrons in a polycistronic precursor. Remarkably, intercistronic regions in O. dioica are far more reduced than those in either nematodes or kinetoplastids, implying minimal cis-regulatory elements for coupling of 3′-end formation and trans splicing.

Sex chromosome polymorphism and heterogametic males revealed by two cloned DNA probes in the ZW /ZZ fish Leporinus elongatus

In order to study the divergence of teleost sex chromosomes, subtractive cloning was carried out between genomic DNA of males and females of the rainbow trout (XX/XY) and of Leporinus elongatus (ZW/ZZ). Inserts cloned in a plasmid vector were individually tested on Southern blots of DNA of males and females for sex specificity. No sex-specific insert was obtained from trout, but two out of ten inserts cloned from L. elongatus showed sex-specific patterns in this species: one corresponds to a sequence present on both Z and W chromosomes, while the other is W specific. Sequences of these two inserts show neither clear homology with other known sequences, nor an open reading frame. They cross-hybridize with the genomic DNA of Leporinus friderici, but without sex-specific patterns. Twenty-four L. elongatus adults were sexed by gonadal observation, chromosomed examination and Southern hybridization with one or the other insert. Ten males and 11 females had chromosomes and hybridization patterns typical of their sex. One ZW female was recognized as a male with the W-specific probe. This was also the case for two unusual ZW males, one having a male hybridization pattern with the other probe. These three atypical individuals may result from single genetic exchanges between four regions of the Z and the W, giving rise to three atypical W chromosomes. Finding males with such atypical heterochromosomes in a female heterogametic species may indicate that a gradual transition occurs between the heterogametic systems.