Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.European Research Council (ERC) 757451Swedish Research Council 2019-04452, 2018-0597

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Background: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results: We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion:The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.Additional co-authors: Thomas D Kocher, Catherine Ozouf-Costaz, Jean Francois Baroiller and Francis Galiber

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

Background: The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC endsequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species. Results: We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies. Conclusions: Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome. (Résumé d'auteur

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

A História da Alimentação: balizas historiográficas

Os M. pretenderam traçar um quadro da História da Alimentação, não como um novo ramo epistemológico da disciplina, mas como um campo em desenvolvimento de práticas e atividades especializadas, incluindo pesquisa, formação, publicações, associações, encontros acadêmicos, etc. Um breve relato das condições em que tal campo se assentou faz-se preceder de um panorama dos estudos de alimentação e temas correia tos, em geral, segundo cinco abardagens Ia biológica, a econômica, a social, a cultural e a filosófica!, assim como da identificação das contribuições mais relevantes da Antropologia, Arqueologia, Sociologia e Geografia. A fim de comentar a multiforme e volumosa bibliografia histórica, foi ela organizada segundo critérios morfológicos. A seguir, alguns tópicos importantes mereceram tratamento à parte: a fome, o alimento e o domínio religioso, as descobertas européias e a difusão mundial de alimentos, gosto e gastronomia. O artigo se encerra com um rápido balanço crítico da historiografia brasileira sobre o tema

Research in silico of genes potentially linked to sex on the linkage group LG3 on Nile tilapia Oreochromis niloticus

Les tilapias (espèces Oreochromis) sont le second groupe le plus important de poissons dans l'aquaculture mondiale ainsi qu'une des premières sources de protéines animales pour des millions de personnes dans les pays en cours de développement. En effet, Les tilapias ont la plupart des qualités requises dans le monde aquacole comme un taux de croissance important et une résistance aux maladies. Cependant leurs reproductions précoces et continues provoquent une surpopulation des bassins et un nanisme des individus. Pour surmonter ces difficultés, il s'agit de créer de nouvelles méthodes de contrôle du sexe (génétique et température) pour une meilleure compréhension de la détermination du sexe chez le tilapia. La détermination sexuelle chez les tilapias est complexe. En effet, le sexe est influencé par des facteurs génétiques majeurs (XX/XY), des facteurs génétiques mineur (sur les autosomes : LG3, LG23) et la température. Au cours des dernières années, de nombreuses ressources génomiques ont été progressivement développées (Bac End Sequences, Expressed sequence Tag, physical map, RH map…). Dans ce travail de thèse nous avons cherché à identifier, par des approches in silico, des gènes liés au sexe, en nous intéressant, en particulier, à ceux localisés sur LG3. Nous avons divisé notre travail en deux étapes. La première recouvre des travaux préliminaires de collecte et de comparaison d'informations existantes. Elle s'est concrétisée par la création d'une carte physique comparée entre le génome complet de l'épinoche et des BES du tilapia ainsi que d'une carte RH du tilapia. La deuxième étape porte sur l'analyse du chromosome correspondant au LG3 (Chr3). Nous avons pu grâce aux méthodes, outils et données développés lors de la première étape, reconstituer le Chr3, l'annoter et faire une liste de gènes impliqués dans la cascade du sexe chez le tilapia du Nil.Tilapias (Oreochromis spp.) are the second most important fish group in aquaculture and a primary source of animal protein for millions of people in developing countries. Indeed, Tilapias have most of the qualities required in aquaculture such as a good growth-rate and resistance to diseases. Nevertheless, their early and constant reproduction leads to tank overpopulation and dwarfism of individuals. To overcome this, new sex controlling methods (genetics and temperature) are being studied to better understand the sex determination in tilapia. Sex determination in tilapia is complex since sex is influenced by major genetic factors (XX/XY), minor genetic factors (on an autosome: LG3, LG23) and temperature factors. Over the past years a great effort has been done to increase the genomic tools in tilapia by obtaining data on Bac End Sequences (BES), Expressed Sequence tags (EST), physical map, RH map.... The objective of our work is to identify, by in silico approaches, genes associated to sex, especially the ones located on the linkage group LG3. We divided our work in two steps. The first work is to collect heterogeneous and available information existing on tilapia using comparative genomic analyses. This step led to the creation of a comparative physical map between the complete genome of stickleback and the BES of tilapia along with a tilapia RH map. The second step is to analyse the chromosome corresponding to the LG3 (Chr3). Using methods, tools and data developed during the first step, we recreated the Chr3, annotated it and listed the genes involved in the sex cascade in Nile tilapia

An organizational environment for "in silico" experiments in molecular biology

International audienc

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes