Latest Articles

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  Section: Animal Science ; Topics: Health sciences

  Evaluation of the Collaborative Process of Public-Private Partnerships in the veterinary domain: the case of the Sanitary Mandate in Tunisia

  Dhaoui, Anissa;   Poupaud, Mariline;   Zargouni , Salma; Dieuzy-Labaye, Isabelle; Ferchiou, Ahmed ; Peyre, Marisa

  10.24072/pcjournal.655 - Peer Community Journal, Volume 6 (2026), article no. e29

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  Public-private partnerships (PPPs) in the veterinary sector are a recent development compared to human health, yet they hold significant potential for strengthening public veterinary services. Recognising this potential, the World Organisation for Animal Health (WOAH) and the French Agricultural Research Centre for International Development (CIRAD) launched the "Public Private Progress" initiative. It aims to study and promote the use of PPPs in national veterinary services. As part of this initiative, CIRAD developed a tool for assessing the quality of PPP processes, which was applied in Tunisia to evaluate the sanitary mandate, a public-private partnership, through a participatory approach. The evaluation, requested by Tunisia's General Directorate of Veterinary Services (DGSV), was conducted jointly by WOAH and CIRAD. It aimed to understand the partnership process and was based on semi-structured interviews (n=9) and group discussions (n=6) with 22 key public and private stakeholders at national and regional levels. It took place both nationally and in two governorates of central Tunisia: Sfax and Sidi Bouzid. This was the first evaluation of the sanitary mandate since its implementation in 2006, and it involved stakeholder mapping, collaborative process analysis, and the partnership’s impacts and benefits identification. The findings highlighted the PPP’s importance in achieving veterinary service strategies. However, it revealed gaps, including misalignment with the current epidemiological context and communication issues. Recommendations included enhancing regional veterinarians’ involvement in decision-making, increasing training frequency and duration, and addressing governance constraints, especially regarding financial dependency on the state for the sanitary mandate's expansion. This study underlines the importance of evaluating PPPs’ collaborative processes through participatory approaches. Such evaluations not only identify functional and organisational limitations but also support evidence-based recommendations for improving partnership performance. Stakeholder engagement in the evaluation enhances the acceptability of findings and reinforces commitment to the veterinary mandate.

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  Section: Genomics ; Topics: Genetics/genomics, Environmental sciences

  Two de novo transcriptome assemblies and functional annotations from juvenile cuttlefish (Sepia officinalis) under various metal and pCO₂ exposure conditions

  Thomas, Sol Dourdin;   Antoine, Minet;   Eric, Pante;   Thomas, Lacoue-Labarthe  

  10.24072/pcjournal.703 - Peer Community Journal, Volume 6 (2026), article no. e28

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  The cuttlefish Sepia officinalis is a precious model in behavioural and neurobiology studies. It is currently facing combined environmental changes related to the anthropogenic global change. However, genomic resources available to support investigations tackling this issue are still scarce. Therefore, we present two annotated de novo transcriptome assemblies from recently hatched (whole body) and one-month old (head) Sepia officinalis juveniles. Both assemblies rely on an important read depth validated by a pseudo-rarefaction analysis, and gathered several individuals from various metal and pCO₂ exposure conditions. After redundancy reduction, assemblies from newly hatched and one-month-old individuals comprised 230,672 and 370,613 transcripts with 35,590 and 44,233 putative ORFs, respectively, and an annotation rate arounf 70%. Assemblies were compared to each other, revealing age-specific transcriptomic landscapes. These two assemblies constitute highly valuable genomic resources complementing reference genome assembly and facilitating the investigation of transcriptomic endpoints in environmental studies considering coleoid cephalopods.

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  Section: Genomics ; Topics: Genetics/genomics ; Conference: JOBIM

  Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework

  Rusakovich, Anastasia;   Corre, Sebastien;   Cadieu, Edouard; Fraboulet, Rose-Marie; Le Bars, Victor;   Galibert, Marie-Dominique;   Derrien, Thomas;   Blum, Yuna  

  10.24072/pcjournal.699 - Peer Community Journal, Volume 6 (2026), article no. e27

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  Circular RNAs (circRNAs) are unique non-coding RNAs with covalently closed loop structures formed through backsplicing events. Their stability, tissue-specific expression patterns, and potential as disease biomarkers have garnered increasing attention. However, their circular structure and diverse size range pose challenges for conventional sequencing technologies. Long-read Oxford Nanopore (ONT) sequencing offers promising capabilities for capturing entire circRNA molecules without fragmentation, yet the effectiveness of bioinformatic tools for analyzing this data remains understudied. This study presents the first comprehensive benchmark comparison of three specialized tools for circRNA detection from ONT long-read data: CIRI-long (Zhang et al., 2021), IsoCIRC (Xin et al., 2021), and circNICK-Irs (Rahimi et al., 2021). To address the lack of standardized evaluation frameworks, we developed a novel computational pipeline, open-source and freely available, to generate realistic simulated circRNA ONT long-read datasets. Our pipeline integrates several molecular features of circRNAs extracted from established databases and real datasets into NanoSim tool (Hafezqorani et al., 2020) and outputs FASTQ reads reflecting therefore biological diversity and technical properties. We systematically assessed tool performance across key metrics, including precision, recall and F1 score. Our analysis revealed distinct performance profiles: while all tools exhibited high specificity, they varied in precision and their ability to detect different circRNA subtypes, often showing limited sensitivity and precision. Notably, the overlap in detected circRNAs among tools was relatively low. Additionally, computational efficiency varied significantly across the tools. This suggests that relying on a single tool might not be ideal, and combining tools or improving algorithms could be necessary for more accurate circRNA detection from ONT data. This benchmark provides valuable insights for researchers selecting appropriate tools for circRNA studies using ONT sequencing. Furthermore, our customizable simulation framework, offering a resource to optimize detection approaches and advance bioinformatic tool development for circRNA research is freely available at: https://gitlab.com/bingo-igdr/nano-circ

   

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  Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics

  Limited directional selection but coevolutionary signals among imprinted genes in A. lyrata

  Le veve, Audrey;   Iltas, Ömer;   Dutheil, Julien;   Lafon Placette, Clement  

  10.24072/pcjournal.702 - Peer Community Journal, Volume 6 (2026), article no. e26

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  Genomic imprinting is a form of gene regulation leading to the unequal expression of maternal and paternal alleles. The main hypothesis invoked to explain the evolution of imprinted genes is the kinship theory, which posits a conflict between parental genomes over resource allocation in progeny. According to this theory, such conflicts select for parent-of-origin–dependent expression of genes involved in resource allocation. How such conflicts translate into signatures of selection at coding or regulatory sequences remains model-dependent and is not explicitly predicted by the kinship theory. However, most studies addressing selection in imprinted genes in flowering plants, particularly those based on population-genomic or phylogenetic analyses, have focused on self-fertilizing species, where conflicts over resource allocation are predicted to be weak. Consequently, the impact of the kinship theory on the evolution of imprinted genes remains largely unexplored in systems where parental conflict is expected to be strong. Furthermore, potential coevolution between antagonistically acting imprinted genes, as proposed in extensions of parental conflict models, has not yet been tested empirically. Using combined phylogenetic and population genomic approaches, we investigated signatures of selection on imprinted genes across the Brassicaceae family and in autogamous and allogamous populations of Arabidopsis lyrata, and searched for evidence of coevolution among imprinted genes. We found that endosperm-expressed genes exhibited signals of balancing selection across Brassicaceae and within allogamous populations, consistent with models of unresolved intralocus conflict. These population-level signals varied with the mating system, in line with expectations that parental conflict is reduced under self-fertilization. Moreover, phylogenetic analyses indicated signatures of purifying (negative) selection acting on imprinted genes. However, the population-level signatures of selection were independent of the mating system and showed limited concordance with kinship predictions, possibly due to stronger selection acting on expression than on coding sequences. Finally, we identified coevolution between imprinted genes, although not at specific sites, suggesting that interactions beyond protein sequence may contribute to this process.