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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

BFR2: a curated ribosomal reference dataset for benthic foraminifera.

Maria Holzmann¹, Ngoc-Loi Nguyen², Inès Barrenechea Angeles³

¹Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland. maria.holzmann@unige.ch.

Scientific Data

|November 28, 2024

Summary

A new reference dataset of benthic foraminifera DNA barcodes (BFR2) has been created. This resource aids molecular studies by compiling over 5000 ribosomal DNA sequences from these important environmental indicators.

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Area of Science:

Marine Biology
Protistology
Molecular Ecology

Background:

Benthic foraminifera are key marine protists used as environmental indicators.
Extensive DNA sequencing efforts over three decades have generated numerous genetic data for these organisms.
A comprehensive reference dataset is crucial for advancing molecular research on foraminifera.

Purpose of the Study:

To compile the first curated benthic foraminiferal ribosomal reference dataset (BFR2).
To provide a standardized resource for molecular identification and ecological studies of benthic foraminifera.
To facilitate the discovery of new species and improve taxonomic accuracy.

Main Methods:

Compilation of over 5000 DNA sequences of the 18S rDNA gene fragment from benthic foraminifera.
Curation and organization of sequences representing 279 species, 204 genera, and 91 families.
Inclusion of previously unpublished sequences and identification of potentially novel species.

Main Results:

The BFR2 dataset contains over 5000 18S rDNA sequences from benthic foraminifera.
Sequences represent 279 species, 204 genera, and 91 families, with 45% previously unpublished.
Thirteen percent of sequences are unassigned to described species, suggesting potential new discoveries.

Conclusions:

The BFR2 dataset is a valuable resource for the molecular study of benthic foraminifera.
It enhances taxonomic resolution and aids in identifying new species.
This dataset supports the growing field of molecular foraminiferal research and environmental monitoring.