Abstract
BackgroundThe marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds.ResultsWe have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes.ConclusionDespite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is ‘better’ than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.
Highlights
The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group
It is worth noting that further analysis of the Canu contigs representing alternative haplotypes indicated that most CoDi insertions were located in only a single haplotype, which is consistent with the observations of Maumus et al [15]
Like most genomes sequenced in the 2000s, the T. pseudonana and P. tricornutum reference genomes were generated by paired-end Sanger sequencing of small, medium and large insert libraries followed by extensive manual finishing to resolve low-quality, ambiguous and gap regions
Summary
The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. The haploid 27.4 Mbp P. tricornutum genome assembly was comprised of 179 contigs assembled into 33 chromosome-sized scaffolds [11] Both genome projects predicted protein-coding genes based in part on expressed sequence tag (EST) data, identifying speciesspecific genes as well as genes shared between the two species and among all stramenopiles [3, 11]. Despite the relatively recent divergence of the Mediophyceae and Bacillariophyceae (~ 172 Mya), the gene contents of these two diatom species are very different: only ~ 57% of P. tricornutum genes were found to be shared with T. pseudonana, suggesting that diatoms and their genomes have diversified at an unusually rapid rate [11]
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