1. In silico analysis of phages-nanogen interplay : human gastrointestinal tract microbiota dynamics and clinical perspectivesIhab Malat, Michel Drancourt, B. Henrissat, Ghiles Grine, 2026, original scientific article Abstract: Digestive tract nanoarchaea Nanopusillus massiliensis and Candidatus Nanopusillus phoceensis form symbiotic nanogens with residing methanogens Methanobrevibacter oralis and Methanobrevibacter smithii, preventing their translocation by unknown mechanisms. We found that 0.45% of M. oralis YH nanogen genome encoding 18 proteins and 1.12% of M. smithii KB11 nanogen genome encoding 32 proteins were of Caudoviricetes and NAV1 origin. In block encoded glycosyltransferase and S-adenosyl-methionine-dependent methyltransferase confer nanogens (but not methanogens) a capacity in cell wall glycosylation. This hypothetical deduced cell wall glycosylation could prevent pseudomurein endo-isopeptidase-mediated interactions of nanogens with digestive tract virome and further nanogen translocation. These observations renew understanding of methanogen and nanogen-associated physiology and pathologies in the digestive tract and beyond.
Keywords: Archaeal virome, Methanogens, CRISPR-Spacers, Caudoviricetes, Human microbiome, Microbial diversity, Mobile genetic elements, Nanoarchaea, Nanogen, Methanobrevibacter smithii, Methanobrevibacter oralis
Published in RUP: 18.06.2026; Views: 216; Downloads: 8
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2. Biodiversity genomics research practices require harmonising to meet stakeholder needs in conservationElena Bužan, Christian de Guttry, Chiara Bortoluzzi, Nathaniel R. Street, Kay Lucek, Anna Rosling, Lino Ometto, Alice Mouton, Luísa S. Marins, María José Ruiz-López, José Melo-Ferreira, Elisabet Ottosson, Camila J. Mazzoni, Robert M. Waterhouse, 2025, original scientific article Abstract: Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.
Keywords: best practices, biodiversity genomics, genome-wide genetic diversity, stakeholder engagement, standardisation, whole genome resequencing data
Published in RUP: 16.01.2026; Views: 772; Downloads: 2
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4. Analysis of genetic diversity in Croatian fig (Ficus carica L.) germplasm using SSR markersDanijela Poljuha, Ines Kralj, Marin Krapac, Tatjana Klepo, Mira Radunić, Frane Strikić, Tim Weber, Sezai Ercişli, Alenka Baruca Arbeiter, Matjaž Hladnik, Dunja Bandelj, 2021, published scientific conference contribution Keywords: Ficus carica, germplasm, national collections, genetic diversity, Croatia, microsatellite
Published in RUP: 18.10.2021; Views: 4174; Downloads: 36
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5. First set of microsatellite markers for immortelle (Helichrysum italicum (Roth) G. Don) : a step towards the selection of the most promising genotypes for cultivationAlenka Baruca Arbeiter, Matjaž Hladnik, Jernej Jakše, Dunja Bandelj, 2021, original scientific article Keywords: curry plant, Helichrysum italicum (Roth) G. Don, high-throughput DNA sequencing, genomic SSRs, genetic diversity, DNA fingerprinting
Published in RUP: 06.05.2021; Views: 5227; Downloads: 40
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6. Inferring population history and demography using microsatellites and major histocompatibility complex genes in european roe deerElena Bužan, Luka Duniš, Urška Gerič, Sandra Potušek, Boštjan Pokorny, 2021, published scientific conference contribution abstract Keywords: microsatellites, major histocompatibility complex, next-generation sequencing, spatial genetic diversity, roe deer
Published in RUP: 04.02.2021; Views: 4121; Downloads: 14
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7. The characterisation of Vitis vinifera 'Refošk' with AFLP and SSR molecular markers and ampelographic traitsMatjaž Hladnik, Jernej Jakše, Dunja Bandelj, Irma Tomažič, 2014, original scientific article Keywords: AFLP, genetic diversity, SSR, cultivar identity, morphological traits, germplasm, grapevine, Refošk, Refosco
Published in RUP: 21.12.2015; Views: 6656; Downloads: 394
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8. Genomic and EST microsatellite loci development and use in Olive : molecular tools for genetic mapping and association studiesL. Essalouh, A. Zine El Aabidine, S. Contreras, I. Ben Sadok, S. Santoni, B. Khadari, Jernej Jakše, Dunja Bandelj, 2014, published scientific conference contribution Keywords: Olea europaea L., molecular markers, genetic map, genetic diversity, association mapping
Published in RUP: 15.10.2015; Views: 9662; Downloads: 131
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