Telomere-to-telomere genome assembly of 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 bui...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2022-07, Vol.10, p.e13607-e13607, Article e13607
Main Authors: Giguere, Daniel J, Bahcheli, Alexander T, Slattery, Samuel S, Patel, Rushali R, Browne, Tyler S, Flatley, Martin, Karas, Bogumil J, Edgell, David R, Gloor, Gregory B
Format: Article
Language:English
Subjects:
Artificial chromosomes
Bioinformatics
Chloroplasts
Chromosome 19
Diatoms - genetics
Ethanol
Ethylenediaminetetraacetic acid
Genetic engineering
Genetically modified organisms
Genome assembly
Genome, Mitochondrial - genetics
Genomes
Genomics
Haplotypes
High-molecular weight DNA
Manufacturers
Marine Biology
Methylation
Mitochondria
Nanopore sequencing
Phaeodactylum tricornutum
Plant Science
Synthetic Biology
Telomere - genetics
Telomere-to-telomere
Telomeres
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Summary: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 . 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.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.13607