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Updated: Mar 19, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes.

Jingwen Pan¹, Javier Del Campo¹, Patrick J Keeling¹

¹Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

The Journal of Eukaryotic Microbiology

|June 23, 2016

Summary

This study presents a new database and phylogenetic tree for Labyrinthulomycetes, crucial decomposers in aquatic ecosystems. This resource improves the identification of these microbes in environmental DNA, revealing new ocean-dwelling groups.

Keywords:

18s rRNA amphitremids high-throughput sequencing labyrinthulids phylogeny thraustochytrids

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Area of Science:

Microbiology
Ecology
Bioinformatics

Background:

Labyrinthulomycetes are vital heterotrophic stramenopiles in marine and freshwater decomposition.
Existing Labyrinthulomycetes diversity and phylogenetic data are incomplete, limiting ecological insights.
A comprehensive reference database and phylogeny are needed for accurate environmental studies.

Purpose of the Study:

To create a curated reference database and phylogenetic tree for Labyrinthulomycetes using small subunit ribosomal RNA (SSU or 18S rRNA) data.
To analyze high-throughput environmental sequencing data using the new database.
To improve the identification and ecological distribution analysis of Labyrinthulomycetes subgroups.

Main Methods:

Curated a reference database of Labyrinthulomycetes SSU rRNA sequences.
Constructed an up-to-date phylogenetic tree incorporating known diversity.
Analyzed environmental sequencing data against the curated database.
Compared the curated database with existing tools like PR2 and SILVA.

Main Results:

Developed a comprehensive Labyrinthulomycetes reference database and phylogenetic tree.
Identified numerous previously unknown environmental clades, including widespread ocean-dwelling groups.
The curated database demonstrated higher specificity and fewer misidentifications compared to existing databases.
Revealed new insights into the ecological distribution of various Labyrinthulomycetes subgroups.

Conclusions:

The new phylogenetic framework and database significantly enhance the study of Labyrinthulomycetes diversity and distribution.
This resource offers improved accuracy for identifying environmental sequences, aiding ecological and evolutionary research.
The findings highlight the importance of Labyrinthulomycetes in various aquatic environments, particularly the open ocean.