Are any of these condition-specific, particularly with regard to the resting stages?
| Study | Species | Results | Notes |
|---|---|---|---|
| Mock et al., 2017 | Fragilariopsis cylindrus | "approximately 66% (4,030) of diverged alleles showed greater than fourfold significant differential expression relative to optimal nutrient-replete growth and approximately 45% (2,730) of divergent alleles showed greater than fourfold unequal bi-allelic expression between allele 1 and allele 2 in at least one RNA-seq experiment" | |
| Nomaguchi et al., 2018 | Fistulifera solaris | "subgenomic preferences in approximately 61% of homoeologous gene pairs" | Allopolyploid so, may be a different case in S. marinoi |
| Hoguin et al., 2021 | Phaeodactylum tricornutum | "1395 (~ 11%) genes were categorized as ‘BAE’, 2662 (~ 22%) genes were characterized as ‘ASE’, and 129 (~ 1%) genes were denoted ‘MAE’." |
- BAE = biallelic expression (low % expression bias)
- ASE = allele-specific expression (moderate % expression bias)
- MAE = monoallelic expression (high % expression bias)
| Study | Species | Results | Notes |
|---|---|---|---|
| Rastogi et al., 2018 | Phaeodactylum tricornutum | (See below) | |
| Goldman et al., 2019 | Thalassiosira pseudonana | "we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase [...] generating transcript isoforms that would encode proteins with and without an active site." | Focused on a select group of genes |
| Cheng et al., 2021 | Thalassiosira weissflogii | "3113 AS events were detected, with the genes containing two isoforms ranked the highest (1105)" | Used PacBio; no ref. genome |
Points of interest from Rastogi et al. paper:
- "From the 12,177 Phatr3 gene models, 2,924 (~24%) and 2,444 (~20%) genes undergo IR and ES, respectively."
- "A total of 1,335 (~11%) genes are found to undergo both ES and IR, hence can perform alternative splicing."
- "Surprisingly, we found that genes that can undergo intron-retention are more highly expressed than genes that do not show alternative splicing."
- "To further assess the biological role of alternative splicing, we identified 1341 genes showing IR and 1099 genes with ES during an 18-hour time course under nitrogen-free growth conditions"
- "we found a significant increase in the expression levels of genes undergoing intron retention"
- "we observed a significant decrease in the expression of genes undergoing ES across different time-points of nitrogen-free growth"
- "We identified 81 GO categories which were significantly over-represented in either IR or ES across all or dif- ferent time-points and with plausible functions in tolerating nitrogen starvation"