Giguere, D. J. | Search bioRxiv

bioRxiv2021

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum

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.

genomics↗

bioRxiv2020

Complete and validated genomes from a metagenome

0.1The assembly and binning of metagenomically-assembled genomes (MAGs) using Illumina sequencing has improved the genomic characterization of unculturable communities. However, short-read-only metagenomic assemblies rarely result in completed genomes because of the difficulty assembling repetitive regions. Here, we present a strategy to complete and validate multiple MAGs from a bacterial community using a combination of short and ultra long reads (N50 > 25 kb). Our strategy is to perform an initial long read-only metagenomic assembly using metaFlye, followed by multiple rounds of polishing using both long and short reads. To validate the genomes, we verified that longs reads spanned the regions that were not supported by uniquely mapped paired-end Illumina sequences. We obtained multiple complete genomes from a naphthenic acid-degrading community, including one from the recently proposed Candidate Phyla Radiation. The majority of the population is represented by the assembled genomes; recruiting 63.77 % of Nanopore reads, and 64.38 % of Illumina reads. The pipeline we developed will enable researchers to validate genomes from metagenomic assemblies, increasing the quality of metagenomically assembled genomes through additional scrutiny.

bioinformatics↗