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#barcoding

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Nina Filippova

#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): gbif.org/dataset/d922b606-6c94

Public
Dezene Huber 🌻

One of the best uses of #DNA 🧬 #barcoding is linking different life stages of single #species that appear different from each other and do different things.

In this paper the authors used barcoding to figure out which #polyp (sedentary) and #medusa (swimming) life stages of several #hydrozoans (related to #sea #jellies and sea #anemones) belong to each other.

🔗: peerj.com/articles/15118/

Title: Odd family reunion: DNA barcoding reveals unexpected relationship between three hydrozoan species

From figure heading (see paper in link): “Figure 4: Morphological characters of Halopsis ocellata. Halopsis ocellata. (A) Colony growing on a polychaete tube. (B, C) Hydrothecae (hy) with polyps. (D, E) Nematothecae (ne). (F) Mastigophore (ma) and Isorhiza (is). (G, H) Adult hydromedusa stage. (I, J) Details of the umbrella margin of the adult hydromedusa including a statocyst (st). Image Credits: Lara M. Beckmann, Fredrik Broms (G–I), Joan J. Soto-Angel.”
Public
Mya Breitbart

Excited to share our new paper - Evaluation of DNA metabarcoding for identifying #fish eggs: a case study on the West #Florida Shelf - published today in PeerJ
peerj.com/articles/15016
#Fisheries #Barcoding #DNA #oceanography #science #IABO #USFCMS @PeerJ

PeerJEvaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida ShelfA critical factor in fisheries management is the protection of spawning sites for ecologically and economically important fish species. DNA barcoding (i.e., amplification and sequencing of the mitochondrial cytochrome c oxidase I (COI) gene) of fish eggs has emerged as a powerful technique for identifying spawning sites. However, DNA barcoding of individual fish eggs is time-consuming and expensive. In an attempt to reduce costs and effort for long-term fisheries monitoring programs, here we used DNA metabarcoding, in which DNA is extracted and amplified from a composited sample containing all the fish eggs collected at a given site, to identify fish eggs from 49 stations on the West Florida Shelf. A total of 37 taxa were recovered from 4,719 fish eggs. Egg distributions on the West Florida Shelf corresponded with the known habitat types occupied by these taxa, which included burrower, coastal pelagic, epipelagic, mesopelagic, demersal, deep demersal, commensal, and reef-associated taxa. Metabarcoding of fish eggs was faster and far less expensive than barcoding individual eggs; however, this method cannot provide absolute taxon proportions due to variable copy numbers of mitochondrial DNA in different taxa, different numbers of cells within eggs depending on developmental stage, and PCR amplification biases. In addition, some samples yielded sequences from more taxa than the number of eggs present, demonstrating the presence of contaminating DNA and requiring the application of a threshold proportion of sequences required for counting a taxon as present. Finally, we review the advantages and disadvantages of using metabarcoding vs. individual fish egg barcoding for long-term monitoring programs.
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