# An alternative technique for organelle genome recovery in diatoms using culture-independent, minimal-cell whole genome amplification

## TL;DR

This paper introduces a new method to recover organelle genomes from uncultured diatoms using minimal-cell whole genome amplification, enabling genomic study without lab cultivation.

## Contribution

The novel use of minimal-cell genomics to recover complete chloroplast and mitochondrial genomes from uncultured diatoms.

## Key findings

- Complete chloroplast and mitochondrial genomes were recovered from 8–12 viable cells of two uncultured diatom species.
- C. clypeus has a 143,367 bp chloroplast and 46,274 bp mitochondrial genome.
- P. lepidoptera has a 116,161 bp chloroplast and 49,356 bp mitochondrial genome.

## Abstract

This study presents an alternative method in diatom genomics using two raphid diatoms—Campylodiscus clypeus and Plagiotropis lepidoptera—whose organellar genome characteristics have remained unexplored due to cultivation constraints. Only a small fraction of the estimated 200,000 diatom species has been cultured in the laboratory. This research showcases the use of minimal-cell genomics as a viable alternative for studying diatoms and other eukaryotic microorganisms that do not respond well to traditional laboratory culture methods.

Initial attempts to culture C. clypeus and P. lepidoptera were unsuccessful, hindering the acquisition of genomic data. To overcome these challenges, we employed minimal-cell whole genome amplification (mcWGA) techniques for two uncultured species, followed by metagenomic sequencing and assembly. This enabled direct genomic recovery from minimally isolated and pooled cells, eliminating the need for cultivation.

Using mcWGA approach, we successfully obtained the complete chloroplasts and mitochondrial genomes of C. clypeus and P. lepidoptera using only 8–12 viable cells isolated from fresh environmental samples. The plastome size of C. clypeus was 143,367 bp and mitogenome size was 46,274 bp, while P. lepidoptera has plastome and mitogenome sizes of 116,161 bp and 49,356 bp, respectively. The data generated provides a valuable resource for further research, highlighting the importance of culture-independent techniques in microbial genomics.