Show threadFrédéric RimetNov 27
and in supp data the logo of diat.barcode ;-) #diatoms #barcoding #eDNA #molecularecology
Frédéric RimetNov 27
Happy to share our new paper presenting a new version of diat.barcode reference #barcoding #dna #library for #diatoms #nature #rivers #water #science #ecology
Gelis, Barry-Martinet, Briand, Chonova, Cochero, Gassiole, Kahlert, Karthick, Keck, Kelly, Kochoska, Mann, Nayak, Pfannkuchen, Servulo, Trobajo, Vasselon, Vidakovic, Viollaz, Wetzel, Zimmermann, Rimet, F. (2025). https://doi.org/10.1051/limn/2025009
Cytology and GeneticsMay 22, 2025
Genetic Diversity of Ukrainian Populations of Invasive Species of the Genus Galinsoga Assessed by ISSR-Markers - #barcoding #biologicaldiversity #geneticpolymorphism #moleculargenomics #interspecieshybridization #molecularmarkers #Ukraine #ISSR #Galinsoga - https://link.springer.com/article/10.3103/S0095452725010141
Genetic Diversity of Ukrainian Populations of Invasive Species of the Genus Galinsoga Assessed by ISSR-Markers - Cytology and Genetics

Abstract Two species of the genus Galinsoga, G. parviflora Cav. and G. quadriradiata Ruiz and Pav., are among the most successful invasive plants causing significant damage to natural- and agroecosystems. Their natural distribution range extends from North to South America, and the adventitious part of the range includes all continents except Antarctica. Despite the practical importance of G. parviflora and G. quadriradiata, the genetic diversity of European populations of these species remains unexplored. In this study, ISSR markers were used to study Ukrainian populations of G. parviflora and G. quadriradiata and compared them with plants from Poland, Lithuania, and Portugal. The results obtained indicate the low genetic diversity (Shannon’s index I = 0.124) of G. quadriradiata populations, which is probably due to the small size of the original population introduced to the Old World from America. In contrast, the genetic diversity in G. parviflora populations is significantly higher (I = 0.254). Some genotypes of G. parviflora have a wide geographical distribution and, at the same time, different genotypes occur in the same area. The data obtained are in good agreement with the hypothesis that the main way of the invasion of Galinsoga species in the Old World was escape from botanical gardens. Among the samples examined, several forms of hybrid nature were identified, probably originating from hybrids between G. parviflora and G. quadriradiata, followed by subsequent backcrossing with one of the parent species.

SpringerLink
CellBioNewsMar 19, 2025

Universal #RNA #barcoding system for tracking #gene_transfer in #bacteria created.

https://phys.org/news/2025-03-universal-rna-barcoding-tracking-gene.html

Universal RNA barcoding system for tracking gene transfer in bacteria created

In the microscopic world of bacteria, gene transfer is a powerful mechanism that can alter cellular function, drive antibiotic resistance and even shape entire ecosystems. Now an interdisciplinary group of researchers at Rice University has developed an innovative RNA "barcoding" method to track these genetic exchanges in microbial communities, providing new insights into how genes move across species. The findings were recently published in Nature Biotechnology.

LaborjournalMar 4, 2025
Die Frage "Was krabbelt denn hier?" ist bei #Spinnen nicht leicht zu beantworten. Yannis Schoeneberg von der Trier möchte samt Kollegen per Multi-Locus-#Barcoding das „taxonomische Rennen“ gewinnen, bevor es zu spät ist … Mehr dazu von Karin Lauschke: https://www.laborjournal.de/editorials/3197.php
Entschlüsselung von Spinnengenomen verbessert Artbestimmung

Spinnen sequenziert ...

Laborjournal
Nina FilippovaJan 21, 2025
#dnaderived #sequences #barcoding #Cortinarius Added another several dozens of sequences to our Fungarium YSU database, which soon will be discoverable though GBIF. Hope to find collaboration through shared barcoding initiatives. Especially like these days Cortinarius spp., they are amazing.
Totally about 1K specimens in our collection have dna-derived data (attached sequences): https://www.gbif.org/dataset/d922b606-6c94-4d51-9277-36c9b03872a7
The Fungarium of Yugra State University

The Fungarium of Yugra State University is a systematic reference collection of fungi organized as a part of the Yugra State University Biological Collection (YSU BC). The main purpose of the Fungarium is to initiate and facilitate systematic studies of fungi in the region. It also serves for education and can be used by specialists in different applied disciplines.The taxonomical structure of the collections currently includes the total number of species represented – about 1.5K, genera represented – about 500, families represented – about 150. The majority of the specimens in the YSU Fungari…

Frédéric RimetMay 16, 2024
Nice presentation of Adriana Radulovici on #iBOL #DNA #dnaquaimg #barcoding @leeselab
20 years after Paul Hebert paper on DNA #barcoding who could expect this wordwide success?
Frédéric RimetApr 18, 2024
Nice presentation of carbon footprint of molecular methods by O Monnier and his student Mathieu.
#footprint #metabarcoding #algae #eDNA #barcoding #carbon
Frédéric RimetMar 27, 2024

Excellent paper from F Keck.

Reference barcoding libraries problems:
(i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. They give possible consequences on the taxonomic assignment process

Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses
https://doi.org/10.1111/1755-0998.13746
#metabarcoding #DNA #bioinfo #barcoding

CellBioNewsFeb 6, 2024

Single degenerated #primer significantly improves #COX1 #barcoding performance in #soil #nematode profiling.

#COIFGED_JB5GED

https://phys.org/news/2024-02-degenerated-primer-significantly-cox1-barcoding.html

Single degenerated primer significantly improves COX1 barcoding performance in soil nematode profiling

Microscopic nematodes play important roles in the soil ecosystem and often serve as bioindicators of soil health. The identification of soil nematodes is often difficult due to their limited diagnostic characters and high phenotypic plasticity. The DNA barcoding and metabarcoding techniques are promising but lack universal primers, especially for mitochondrial COX1 gene.

Phys.org