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Author Spotlight: Diatom Testing for Forensic Drowning Examination

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Published on: November 10, 2023

Re-examination of two diatom reference genomes using long-read sequencing.

Gina V Filloramo^1,2, Bruce A Curtis^3,4, Emma Blanche^3,4

¹Department of Biochemistry and Molecular Biology, Dalhousie University, PO Box 15000, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada. gina.filloramo@dal.ca.

|May 25, 2021

Summary

Long-read sequencing improved the quality and contiguity of diatom genomes, revealing new genes and transposable elements. These updated reference genomes offer a more robust foundation for future research on marine diatoms.

Keywords:

Bionano optical mapping Diatom genomics Long-terminal repeat retrotransposons Oxford Nanopore long-read sequencing Phaeodactylum tricornutum Thalassiosira pseudonana

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Area of Science:

Marine biology
Genomics
Molecular evolution

Background:

Marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are key model organisms.
Previous reference genomes (2004, 2008) were based on Sanger sequencing, containing unresolved regions.

Purpose of the Study:

To update and validate the quality and contiguity of T. pseudonana and P. tricornutum genomes using long-read sequencing.
To resolve uncertain genomic regions, characterize structural variation, and re-evaluate repetitive DNA content.
To explore the potential of long-read sequencing and optical mapping for resolving haplotypes.

Main Methods:

Oxford Nanopore Technologies long-read sequencing.
Fine-scale assessment of genome assemblies.
Bionano optical mapping of P. tricornutum chromosomes.

Main Results:

Long-read sequencing resolved previously uncertain genomic regions and characterized structural variation in both diatom genomes.
Identified 1862 new genes in T. pseudonana and 33 novel copia-type LTR-RT insertions in P. tricornutum.
Combined long-read data with optical mapping to explore haplotype resolution.

Conclusions:

Long-read sequencing, while powerful, faces challenges with repetitive DNA in genome assembly.
Revised reference genomes for P. tricornutum and T. pseudonana provide enhanced insight into diatom genome structure and evolution.
These updated genomes serve as a more robust foundation for future diatom research.