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Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a ‘one health’ approach, for a better comprehension and surveillance of humans, plants or animals’ health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to ‘omics’ data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated ‘Galaxy KaruBioNet’ platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html.

Sexual dimorphism of aquaculture traits is common for farmed fish. The Nile tilapia is the second most important farmed species with a production 6 million tons in 2020. Intensive farming relies on the production of all-males due to males' higher growth rate, and as a way to avoid uncontrolled reproductions. Currently the large majority of the all-male productions are obtained through androgen treatments. We aim to use more sustainable procedures to produce all-males such as the use of YY males. Until now, the use of YY males has not been reliable. This is because sex determination in Nile tilapia is complex and controlled by several factors. Although sex determinism follows an XX/XY system, the linkage group (LG) carrying the major sex determinant gene has been assigned to either LG1 or LG23, depending on the domesticated strain. Minor parental factors can also be implicated and in addition, high temperatures can override the genetic determinism. It is not clear to what extent these differences in sex determination are due to natural diversity in the mechanisms of sex determination or due to processes of domestication. It is therefore necessary to better understand the genetic basis of sex determinism in order to use this approach to generate all-males. For this, we decided to work on wild populations in Africa that have not suffered domestic manipulations. We underwent a study of sex determination in several wild populations from West (Lake Volta, Lake Kou) and East Africa (Lake Koka and Lake Hora). We used complementary genomic approaches of ddRAD, whole genome sequencing and long Nanopore reads. We were able to determine that the amh region present on LG23 is the major sex-determining region in most of these populations. Nevertheless, our results also show that there is high polymorphism in this SD region. Furthermore, there are populations that lack the male-specific amh duplication on LG23. Hence, there are no universal Y markers for Nile tilapia. It is necess

In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.