4.6 Article

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum

期刊

PEERJ
卷 10, 期 -, 页码 -

出版社

PEERJ INC
DOI: 10.7717/peerj.13607

关键词

Phaeodactylum tricornutum; Genome assembly; Nanopore sequencing; Telomere-to-telomere; High-molecular weight DNA; Methylation; Transposons

资金

  1. Ontario Graduate Scholarship
  2. Mitacs [IT8360]
  3. Natural Sciences and Engineering Research Council of Canada [RGPIN-03878-2015, RGPIN-201806172, RPGIN-2015-04800]

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Phaeodactylum tricornutum, a marine diatom, has a new telomere-to-telomere genome assembly generated using Oxford Nanopore long reads. The study identified 25 nuclear chromosomes and corrected assembly errors, providing new insights for genetic engineering and synthetic biology applications.
Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.

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