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Nous présentons dans cette note le protocole d'obtention d'animaux triploïdes par choc thermique chez la truite arc-en-ciel, ainsi que quelques indications sur l'intérêt et les caractéristiques zootechniques de ces animaux.

L'utilisation de populations monosexes peut permettre d'accroître la rentabilité économique, lorsque la reproduction est trop rapide (aquaculture extensive dans les pays tropicaux) ou dans le cas d'espèces où l'un des sexes est plus avantageux (meilleure vitesse de croissance ou maturation plus tardive). Nous avons analysé dans ce papier quatre méthodes permettant la production de populations monosexes. Si l'inversion sexuelle par traitement hormonal ou (a gynogenèse induite (dans le cas d'une homogamétie femelle) ne semblent pas directement exploitables, on peut attendre du sexage génétique qui combine ces deux méthodes, des résultats prometteurs. L'hybridation interspécifique peut également conduire à une descendance monosexe dans des cas particuliers.

Author(s): D. Chourrout (corresponding author) [1]; F. Delsuc [2]; P. Chourrout [3]; R. B. Edvardsen [1]; F. Rentzsch [1]; E. Renfer [1]; M. F. Jensen [1]; B. Zhu [4]; P. [...]

Oikopleura dioica is a protochordate with a remarkably short generation time (5 days) that can be bred in the laboratory. Due to high fecundity and transparency, Oikopleura has considerable potential for genetics and embryology. We have examined the overall genome organization in Oikopleura. Flow cytometry has revealed the smallest genome known in the chordate phylum (70 Mb). We have cloned and annotated 400 small and 5 larger genomic fragments, including a 145-kb-long BAC insert. A combination of BLAST search and gene finding programs has revealed a very high gene density (1 gene per 4 kb), which correlates with the presence of very short intergenic sequences and introns. Intron positions indicate major rearrangements of gene structures during the divergence between vertebrates and Oikopleura and also during the late diversification of tunicates. The distribution of predicted genes appears rather uniform and most gene predictions have been confirmed by cloning and sequencing of corresponding cDNAs. Oikopleura is therefore a very attractive model organism for genome-based developmental studies.

Pressure treatment has up to now been the best method to inhibit the disjunction of chromosomes during the first mitosis of salmonid embryos. We have determined the optimum conditions to maximize the yield of tetraploid embryos (fertilization with normal sperm), and the yield of diploid mitotic gynogens (insemination with irradiated sperm). This study has provided two major results: the replacement of gamma-rays by ultraviolet rays, in order to inactivate the sperm for gynogenesis, markedly increases the yield of viable mitotic gynogens, probably because they reduce the risk of any ‘toxic’ partial paternal transmission. The optimal pressure levels for mitotic inhibition are higher than those we had indicated in an earlier study. We interpret this discrepancy as an error of calibration of the pressure apparatus which had been used. [ABSTRACT FROM AUTHOR]

Abstract Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). Results Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP) genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Conclusions Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.

Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factor genes expressed during early OE patterning. Among these are two Pax3/7 copies that we named pax37A and pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 plays a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica pax37A and pax37B in the development of the OE, by using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals. We found that pax37B but not pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supported a neuroepithelial-like or a preplacodal ectoderm transcriptional signature in these cells. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features. This is supported by a fragmented gene regulatory network involved in their development that also operates in ascidian epidermal neurons., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

A fascinating variety of adult body plans can be found in the Tunicates, the closest existing relatives of vertebrates. A distinctive feature of the larvacean class of pelagic tunicates is the presence of a highly specialized surface epithelium that produces a cellulose test, the "larvacean house". While substantial differences exist between the anatomy of larvacean families, most of the ontogeny is derived from the observations of a single genus, Oikopleura. We present the first study of Fritillaria development based on the observation of individuals reproduced in the laboratory. Like the other small epipelagic species Oikopleura dioica, the larvae of Fritillaria borealis grow rapidly in the laboratory, and they acquire the adult form within a day. We could show that major morphological differences exhibited by Fritillaria and Oikopleura adults originate from a key developmental stage during larval organogenesis. Here, the surface epithelium progressively retracts from the posterior digestive organs of Fritillaria larvae, and it establishes house-producing territories around the pharynx. Our results show that the divergence between larvacean genera was associated with a profound rearrangement of the mechanisms controlling the differentiation of the larval ectoderm., (© 2022. The Author(s).)

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.

An overwhelming majority of eukaryotic introns have GT/AG ends, whose identities play a critical role for their recognition and removal by the U2 spliceosome, a well-conserved complex of protein and RNAs. Introns with other splice sites exist at very low frequencies in various genomes, and some of them are processed by the U12 spliceosome. Here, we show that, in the chordate Fritillaria borealis, the majority of old introns have been lost and replaced by introns with highly divergent splice sites. The new introns of F. borealis are exceptionally diverse, though more frequently AG/AC or AG/AT, and features of thousands of them support an origin from transposons. They cannot be processed in human cells, but their splicing is rescued by mutating terminal dinucleotides to GT/AG. With lariat sequencing and splicing inhibitor assays, we show that F. borealis introns are spliced by the U2 spliceosome, which thus evolved to a different selectivity, with neither novel U1 small nuclear RNA (snRNA) types nor major remodeling of its protein and snRNA complements. This genome-wide recolonization by non-canonical introns emphasizes the importance of transposons as a resource of novel introns in a context of massive intron loss. An evolution of the spliceosome may also permit to neutralize harmful transposons through their conversion into introns., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

In eukaryotes, genome size correlates little with the number of coding genes or the level of organismal complexity (C-value paradox). The underlying causes of variations in genome size, whether adaptive or neutral, remain unclear, although several biological traits often covary with it [1-5]. Rapid increases in genome size occur mainly through whole-genome duplications or bursts in the activity of transposable elements (TEs) [6]. The very small and compact genome of Oikopleura dioica, a tunicate of the larvacean class, lacks elements of most ancient families of animal retrotransposons [7, 8]. Here, we sequenced the genomes of six other larvaceans, all of which are larger than that of Oikopleura (up to 12 times) and which increase in size with greater body length. Although no evidence was found for whole-genome duplications within the group of species, the global amount of TEs strongly correlated with genome size. Compared to other metazoans, however, the TE diversity was reduced in all species, as observed previously in O. dioica, suggesting a common ancestor with a compacted genome. Strikingly, non-autonomous elements, particularly short interspersed nuclear elements (SINEs), massively contributed to genome size variation through species-specific independent amplifications, ranging from 3% in the smallest genome up to 49% in the largest. Variations in SINE abundance explain as much as 83% of interspecific genome size variation. These data support an indirect influence of autonomous TEs on genome size via their ability to mobilize non-autonomous elements., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The mechanisms driving innovations that distinguish large taxons are poorly known and essentially accessible via a candidate gene approach. A spectacular acquisition by tunicate larvaceans is the house, a complex extracellular filtration device. Its components are secreted by the oikoplastic epithelium which covers the animal trunk. Here we describe the development of this epithelium in larvae through the formation of specific cellular territories known to produce distinct sets of house proteins (Oikosins). It involves cell divisions and morphological differentiation but very limited cell migration. A diverse set of homeobox genes, most often duplicated in the genome, are transiently and site-specifically expressed in the trunk epithelium at early larval stages. Using RNA interference, we show that two prop duplicates are involved in the differentiation of a region on and around the dorsal midline, regulating morphology and the production of a specific oikosin. Our observations favor a scenario in which multiple homeobox genes and most likely other developmental transcription factors were recruited for this innovation. Their frequent duplications probably predated, but were not required for the emergence of the house., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Classical non-homologous end joining (c-NHEJ), a fundamental pathway that repairs double-strand breaks in DNA, is almost universal in eukaryotes and involves multiple proteins highly conserved from yeast to human [1]. The genes encoding these proteins were not detected in the genome of Oikopleura dioica, a new model system of tunicate larvaceans known for its very compact and highly rearranged genome [2-4]. After showing their absence in the genomes of six other larvacean species, the present study examined how O. dioica oocytes and embryos repair double-strand DNA breaks (DSBs), using two approaches: the injection of linearized plasmids, which resulted in their rapid end joining, and a newly established CRISPR Cas9 technique. In both cases, end joining merged short microhomologous sequences surrounding the break (mainly 4 bp long), thus inducing deletions larger than for the tunicate ascidian Ciona intestinalis and human cells. A relatively high frequency of nucleotide insertions was also observed. Finally, a survey of genomic indels supports the involvement of microhomology-mediated repair in natural conditions. Overall, O. dioica repairs DSBs as other organisms do when their c-NHEJ pathway is experimentally rendered deficient, using another mode of end joining with the same effect as alternative NHEJ (a-NHEJ) or microhomology-mediated end joining (MMEJ) [5-7]. We discuss how the exceptional loss of c-NHEJ and its replacement by a more mutation-prone mechanism may have contributed to reshaping this genome and even been advantageous under pressure for genome compaction., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Background: Germ cell formation has been investigated in sessile forms of tunicates. This process involves the release of a subset of maternal transcripts from the centrosome-attracting body (CAB) in the progenitor cells of the germ line. When germ-soma segregation is completed, CAB structures are missing from the newly formed primordial germ cells (PGCs). In free-swimming tunicates, knowledge about germ cell formation is lacking. In this investigation, comparative gene expression and electron microscopy studies were used to address germ cell formation in Oikopleura dioica (O. dioica)., Results: We found that the RNA localization pattern of pumilio (pum1) is similar to the pattern described for a subset of maternal transcripts marking the posterior end of ascidian embryos. Transcripts marking the posterior end are called postplasmic or posterior-end mark (PEM) transcripts. We found no localization of vasa (vas) transcripts to any sub-region within the germ-line precursor cells. Expression of vas4 was detected in the newly formed PGCs. Electron microscopy studies confirmed the presence of structures with similar morphology to CAB. In the same cytoplasmic compartment, we also identified pum1 transcripts and an epitope recognized by an antibody to histone H3 phosphorylated on serine 28., Conclusions: Our findings support that a CAB-like structure participates in the segregation of maternal pum1 transcripts during germ-soma separation in O. dioica.

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.