Background 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. 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. Results 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.
Chang et al. (Wed,) studied this question.