Biology subjects

Manzanilla, V.

Publications and source records attributed to Manzanilla, V..

7 recordsLinked to original sources

bioRxiv2025

Delayed identification of long-overlooked Aedes (Aedimorphus) vexans in Tahiti Island, French Polynesia

Aedes (Aedimorphus) vexans (Meigen, 1830) is a globally distributed mosquito species commonly associated with temporary flooded habitats, including those in the South Pacific region. While its presence has been documented in several Pacific archipelagos, its occurrence on Tahiti island had remained unconfirmed. A retrospective examination of historical mosquito collections held at the Institut de Recherche pour le Developpement (IRD, France) and the Institut Louis Malarde (ILM, Tahiti) revealed evidence of Ae. vexans on Tahiti dating back as early as 1993. This historical detection was corroborated by targeted field surveys conducted between 2023 and 2025, which confirmed the species presence at multiple sites, particularly in the southern part of the island. To support these observations, COI gene sequences from newly collected specimens were analyzed alongside reference Ae. vexans sequences from GenBank. The Tahitian specimens fall unambiguously within the Pacific clade of Ae. vexans and show no genetic divergence that would support their assignment to Ae. nocturnus or Ae. nipponii. Similarly, sequences published under these names in GenBank do not form distinct lineages within Ae. vexans. This study provides the first confirmed record of Ae. vexans on Tahiti, based on both morphological identification and molecular evidence. The findings underscore the need to integrate molecular tools into entomological monitoring to improve species detection and prevent misidentifications in island environments where vector diversity is often underestimated.

zoology↗

bioRxiv2025

Contrasting temporal patterns and associations in Hyalomma marginatum microbial communities: key insights for the development of novel tick and tick-borne diseases control tools

BackgroundHyalomma marginatum is an invasive tick species in southern mainland France that can carry several pathogens of human and animal interest. Because the tick microbiota represents a major factor that can potentially modulate the pathogen acquisition and transmission and might become a new control tool against ticks and tick-borne diseases, it is more than essential to identify the composition of the H. marginatum microbiota, its temporal dynamics and interactions (statistical association) between members of the tick microbiota. MethodsFrom monthly tick samplings performed in the same site between February to September 2022, 281 adult ticks H. marginatum were collected from horses. The microbiota composition was characterised using a high throughput sequencing approach. Different statistical analyses allowed us to assess the influence of several factors (month, season, tick sex) on the H. marginatum microbial communities and reveal potential interactions among members of these communities. ResultsApart of known obligate endosymbionts Francisella and Midichloria, and the hypothesised facultative endosymbiont (Rickettsia) that dominated the microbiota of H. marginatum, we detected Staphylococcus, Corynebacterium, Williamsia and Mycobacterium, usually described as commensal and/or environmental bacteria. The microbiota composition and bacterial networks differed between males and females, with males being more diverse and composed of more environmental bacteria. We reported several temporal shifts for both males and females into the microbiota composition and bacterial networks. The temporal shifts observed for females were more chaotic in terms of movements among nodes, compared to the male microbial communities that exhibited a more organised and stable dynamics. ConclusionsThe influence of tick sex and time on the holobiont H. marginatum underlines the importance of the scale at which the study is conducted. HighlightsO_LIObligate endosymbionts dominate the Hyalomma marginatum microbiota C_LIO_LIEnvironnemental bacteria are abundant in Hyalomma marginatum microbiota C_LIO_LIBoth the bacterial composition and associations differed according to the tick sex C_LIO_LIBoth the bacterial composition and associations were marked by many temporal shifts for both males and females C_LIO_LIKeystone taxa in tick microbiota were highly variable from one month to another C_LI

microbiology↗

bioRxiv2024

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

We developed a python package called mbctools, designed to offer a cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle the most common tasks in metabarcoding pipelines such as paired-end merging, primer trimming, quality filtering, sequence denoising, zero-radius operational taxonomic unit (ZOTU) filtering, and has the capability to process multiple genetic markers simultaneously. mbctools is a menu-driven program that eliminates the need for expertise in command-line skills and ensures documentation of each analysis for reproducibility purposes. The software, designed to run in a console, offers an interactive experience, guided by keyboard inputs, assisting users along the way through data processing and hiding the complexity of command lines by letting them concentrate on selecting parameters to apply in each step of the process. In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon-based Next-Generation Sequencing data. This software is a versatile open-source tool for processing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. It provides functions for various tasks such as dereplication, clustering, chimera detection, and taxonomic assignment. VSEARCH is thus very efficient in retrieving the overall diversity of a sample. To adapt to the diversity of projects in metabarcoding, we facilitate the reprocessing of datasets with the possibility to adjust parameters. mbctools can also be launched in a headless mode, making it suited for integration into pipelines running on High-Performance Computing environments. mbctools is available at https://github.com/GuilhemSempere/mbctools, https://pypi.org/project/mbctools/.

bioinformatics↗

bioRxiv2019

Tracking the global supply chain of herbal medicines with novel genomic DNA barcodes

AO_SCPLOWBSTRACTC_SCPLOWThe promotion of responsible and sustainable trade in biological resources is widely proposed as one solution to mitigate currently high levels of global biodiversity loss. Various molecular identification methods have been proposed as appropriate tools for monitoring global supply chains of commercialized animals and plants. We demonstrate the efficacy of target capture genomic barcoding in identifying and establishing the geographic origin of samples traded as Anacyclus pyrethrum, a medicinal plant assessed as globally vulnerable in the IUCN Red List of Threatened Species. Samples collected from national and international supply chains were identified through target capture sequencing of 443 low-copy nuclear makers and compared to results derived from genome skimming of plastome, standard plastid barcoding regions and ITS. Both target capture and genome skimming provided approximately 3.4 million reads per sample, but target capture largely outperformed standard plant DNA barcodes and entire plastid genome sequences. Despite the difficulty of distinguishing among closely related species and infraspecific taxa of Anacyclus using conventional taxonomic methods, we succeeded in identifying 89 of 110 analysed samples to subspecies level without ambiguity through target capture. Of the remaining samples, we determined that eleven contained plant material from other genera and families and ten were unidentifiable regardless of the method used. Furthermore, we were able to discern the geographical origin of Anacyclus samples collected in Moroccan, Indian and Sri Lankan markets, differentiating between plant materials originally harvested from diverse populations in Algeria and Morocco. With a recent drop in the cost of analysing samples, target capture offers the potential to routinely identify commercialized plant species and determine their geographic origin. It promises to play an important role in monitoring and regulation of plant species in trade, supporting biodiversity conservation efforts, and in ensuring that plant products are unadulterated, contributing to consumer protection.

genetics↗

bioRxiv2019

Hidden Rice Diversity in the Guianas

Traditional crop varieties are an important source of genetic diversity for crop adaptation and modern breeding. Landraces of Asian (Oryza sativa) and African (Oryza glaberrima) rice have been well studied on the continents where they were domesticated. However, their history of cultivation in northern South America is poorly understood. Here we reveal the rice diversity that is maintained by Maroons, descendants of enslaved Africans who fled to the interior forests of the Guianas ca. 300 years ago. We interviewed subsistence farmers who practice shifting cultivation along the Maroni and Lawa rivers that form the natural border between French Guiana and Suriname, and used ethnobotanical and morphological methods to identify around 50 varieties, of which 15 were previously undocumented. The genetic origin of these varieties was explored using the Angiosperms-353 universal probe set. Despite the large distances between sites and relative inaccessibility of the area, phenotypic and genetic diversity did not display any geographic structure, which is consistent with knowledge of seed exchange among members of the same ethnolinguistic group. Although improved US cultivars were introduced in Maroon villages in the 1940s, these have not displaced the traditional landraces, which are cherished for their taste and nutritious qualities and for their importance in Maroon spiritual life. The unique agricultural and ritual practices of Maroons confirm their role as custodians of rice diversity, a role that is currently under threat from external pressures and encroaching globalization. We expect that the rice diversity uncovered in this study represents only a fraction of the total diversity in the Guianas and may constitute a large untapped resource that holds promise for future rice improvement. Further efforts to inventory and preserve these landraces will help to protect a precious cultural heritage and local food security.

plant biology↗

bioRxiv2018

Cold shock as a screen for genes involved in cold acclimatization in Neurospora crassa

When subjected to rapid drops of temperature (cold shock), Neurospora responds with a dramatic, but temporary shift in its branching pattern. While the cold shock response has been described morphologically, it has yet to be examined genetically. This project aims to begin the genetic characterization of the cold shock response and the associated acclimatization to cold environments. We report here the results of a screen of mutants from the Neurospora knockout library for alterations in their morphological response to cold shock and thus, their ability to acclimatize to the cold. Three groups of knockouts were selected to be subject to this screen: genes previously suspected to be involved in hyphal development as well as knockouts resulting in morphological changes; transcription factors; and genes homologous to E. coli genes known to alter their expression in response to cold shock. Several strains were identified with altered responses. The genes impacted in these mutants are listed and discussed. A significant percentage (81%) of the knockouts of genes homologous to those previously identified in E. coli showed altered cold shock responses in Neurospora - suggesting that the response in these two organisms is largely shared in common.

cell biology↗

bioRxiv2018

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

BackgroundThe economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination.\n\nResultsWe used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus.\n\nConclusionsMBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.

evolutionary biology↗