Latest Articles

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  Section: Infections ; Topics: Agricultural sciences, Plant biology

  CMV can spread through plant to plant contact: implications for experimental practices

  Chateau, Lola; Szadkowski, Marion; Théodore, Jérémy; Rimbaud, Loup  

  10.24072/pcjournal.675 - Peer Community Journal, Volume 6 (2026), article no. e8

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  Cucumber mosaic virus (CMV) is a major plant pathogen with a worldwide distribution and the widest host range among all known plant viruses. It affects numerous crop species and can cause symptoms that significantly reduce yield. CMV is primarily transmitted by aphids and more sporadically through seeds. It is frequently studied in laboratory settings with the aim of developing effective control strategies. In many experiments, infected plants are placed in direct contact with healthy ones assuming that CMV cannot be transmitted in this way. However, this has not been formally demonstrated. Therefore, this study aimed to assess whether CMV can be transmitted through plant-to-plant contact. Infected plants were first rubbed against healthy ones and then left in contact for 28 days. Target plants were subsequently tested using DAS-ELISA to detect potential transmission. We applied this protocol in two separate experiments totalizing 15 combinations of plant species including pepper (Capsicum annuum) and five weed species commonly found in Espelette pepper fields (Capsella bursa-pastoris, Cerastium glomeratum, Stellaria media, Stachys arvensis and Trifolium repens). We found that CMV could be transmitted through contact between pepper and all tested weed species except T. repens. These findings highlight the importance of verifying whether a virus is capable of contact transmission before carrying out experiments in conditions that could lead to such contacts. In case of transmission, appropriate precautions will be crucial to avoid unintended transmissions.

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  Section: Evolutionary Biology ; Topics: Evolution, Computer sciences

  Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

  Lafond, Manuel;   Scornavacca, Celine  

  10.24072/pcjournal.674 - Peer Community Journal, Volume 6 (2026), article no. e7

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  Gene trees play an important role in various areas of phylogenomics. However, their reconstruction often relies on limited-length sequences and may not account for complex evolutionary events, such as gene duplications, losses, or incomplete lineage sorting (ILS), which are not modeled by standard phylogenetic methods. To address these challenges, it is common to first infer gene trees using fast algorithms for conventional models, then refine them through species tree-aware correction methods. Recently, it has been argued that such corrections can lead to overfitting and force gene trees to resemble the species tree, thereby obscuring genuine gene-level variation caused by ILS. In this paper, we challenge and refute this hypothesis, and we demonstrate that, when applied carefully, correction methods can offer significant benefits, even in the presence of ILS.

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  Section: Zoology ; Topics: Genetics/genomics

  Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences: a case study of Niphargus amphipods

  Salussolia, Alice;   Lecoquierre, Ninon; Stoch, Fabio;   Flot, Jean-François  

  10.24072/pcjournal.671 - Peer Community Journal, Volume 6 (2026), article no. e6

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  With over 430 species currently described, the amphipod genus Niphargus Schiödte, 1849 is the most species-rich crustacean genus in subterranean waters. Previous phylogenetic studies of this genus have relied mainly on mitochondrial COI and nuclear 28S sequences, which do not resolve all the nodes in its phylogeny. As a first step towards a mitogenome-based phylogeny of niphargids, we present here the first complete mitogenome sequence of Niphargus. To obtain high-accuracy mitogenome sequences and annotations, genome skimming of three individuals of Niphargus dolenianensis Lorenzi, 1898 was performed using both short, accurate reads (Illumina) and long, noisier reads (nanopore). Whereas the direct assembly of Illumina sequences yielded structurally incorrect mitogenome sequences, the assembly of nanopore reads produced highly accurate sequences that were corroborated by the mapping of Illumina reads. Polishing the nanopore consensus using Illumina reads corrected a handful of errors at the homopolymer level. The resulting mitogenome sequences ranged from 14,956 to 15,199 bp and shared the same arrangement of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. Phylogenetic analyses based on protein-coding genes confirmed that the Niphargidae family is sister to Pseudoniphargidae, resolving their relationships with other amphipod families. This highlights the utility of mtDNA genome sequences for studying the evolution of this groundwater genus, and the refinement of new methodological approaches, such as nanopore sequencing, is promising for the study of its origin and diversification.

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  Section: Forest & Wood Sciences ; Topics: Applied biological sciences, Environmental sciences, Plant biology

  Comparative responses of legume vs. non-legume tropical trees to biochar additions

  Thomas, Sean C.;   Halim, M. A.;   Ali, Syed Tuhin  

  10.24072/pcjournal.668 - Peer Community Journal, Volume 6 (2026), article no. e5

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  Nitrogen-fixing plants in the legume family (Fabaceae) may show particularly large positive responses to biochar additions due to their capacity to potentially compensate for reduced N in biochar-amended soils. Prior studies also suggest that biochar may have specific developmental effects on legumes, including increased root nodulation and altered morphology. We examined the growth and morphometric responses of legume and non-legume tropical trees to biochar additions in a common garden pot trial experiment. Four legume species (Acacia auriculiformis, A. mangium, Delonix regia, and Pterocarpus santalinus) and four non-legumes (Eucalyptus alba, Melia azedarach, Swietenia macrophylla, and Syzygium cumini) were compared in terms of sapling responses to additions of a wood-feedstock biochar applied at 10 and 20 t/ha. Overall, strong positive effects of biochar additions on sapling performance were observed, with an average increase of 30% in total biomass and a notable increase in height relative to diameter growth. Species showed pronounced differences in responses, with strong interactive effects of species and biochar treatments on growth metrics. Legume species showed an average increase somewhat greater than non-legumes; however, responses were variable among species, with the two Acacia species showing the largest responses, resulting in a non-significant pattern. A literature-based meta-analysis of tropical and subtropical trees likewise suggests greater biochar responses in legumes, but the analysis also falls short of statistical significance. In addition, experimental results indicate large interactive effects of species and biochar on soil pH and other soil properties. Large growth responses of certain taxa of legumes (and other taxa) to biochar, and pronounced species-specific effects on soil properties, may reflect evolved responses to fire disturbance that can be leveraged in the context of forest restoration and enhanced carbon sequestration in degraded tropical landscapes.