Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus

Abstract

The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.

Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to salinity and temperature shifts in the sea-ice diatom Fragilariopsis cylindrus

“…The polar diatom F. cylindrus should be physiologically adapted to the control conditions tested in this study, which are close to the polar oceanic conditions in terms of temperature and salinity. Our observations are consistent with previous experiments which showed no alteration of the F.cylindrus growth in those conditions which are used as stock conditions (Krell et al 2008;Bayer-Giraldi et al 2011;Lyon et al 2016;Paajanen et al 2017). The growth rate at S34 and 4°C in this study is similar to Lyon et al (2016) (0.22 doubling day -1 in our 9-day study versus 0.25 doubling day -1 over 7 days, data not shown).…”

Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy

“…Another obstacle to algal phenomics is the limited capacity to manipulate the genetics of many non-model microalgal species. Many microalgae have complex life cycles (Graham et al, 2009) and their genomes are often large and highly repetitive, defying typical shot-gun sequencing techniques for genome sequencing and assembly (Paajanen et al, 2017). However, 3rd generation methods that allow long-read sequencing -such as Nanopore and PacBio sequencing -are breaking the log-jam.…”

Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness

“…We also added the protein IDs of 53 allelic variants corresponding to protein IDs that were already included in the model (see supplementary excel Table Supp3 for a list of the 53 protein IDs and their associated 111 enzyme names; i.e., some protein IDs are annotated with more than 1 enzyme name). The divergent allelic variants were resolved and validated using independent sequencing approaches and genome assembly approaches [25].…”

“…A special feature of the 61.1 megabase's draft genome of F. cylindrus is that it contains 6071 highly divergent alleles (sequence divergence of up to 6%) out of a total of 21,066 predicted genes [23]. Interestingly, the highly divergent alleles were differentially expressed across environmental conditions and suggested to be involved in the adaptation to strong environmental fluctuations in the Southern Ocean [23,25]. Reconstruction of a genome-scale model from these genomic data will help to estimate to what extent the metabolism and growth of a common polar diatom [23,26] is robust to cellular perturbations, a feature that likely helps diatoms to thrive under extreme and variable polar conditions.…”