ABSTRACT
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
ABSTRACT
PURPOSE: Low- and middle-income countries (LMICs) are underrepresented in ophthalmic research, despite carrying the highest burden of visual impairment. To assess the representation of local authors in global ophthalmic research, this cross-sectional, bibliometric analysis measured the proportion of LMIC-affiliated authorship in LMIC-based ophthalmic research. METHODS: We sampled original, primary research conducted in LMICs and published in 1 of 7 high-impact ophthalmic journals between 2017 and 2021. For each article, we extracted the number and name of country study site(s), country affiliation(s) of first and last author, proportion of LMIC-affiliated authors, funding sources, and study design. RESULTS: Of the 1,333 studies exclusively conducted in LMICs, 89.4% of first authors and 80.6% of last authors were exclusively LMIC-affiliated. Representation of LMIC-affiliated first authors were lower in studies based in low-income countries (25.0%) or in sub-Saharan Africa (26.5%), published in journals with higher impact factors (68.0% in Ophthalmology), funded by high-income countries (HICs) (41.4%), or conducted in both LMICs and HICs (27.1%). The United States, United Kingdom, and Australia had the 3rd, 6th, and 8th largest shares of last authors. There were only 12 single-country studies conducted in low-income countries, namely Ethiopia, the Gambia, Guinea, Liberia, the Niger, and Sierra Leone. Of these countries, only three held first authorship and one held last authorship. CONCLUSIONS: Although LMIC-based ophthalmic research has demonstrated higher local authorship representation compared to other fields, underrepresentation can be exacerbated by country income level, journal "prestige," and degree of HIC involvement. These discrepancies highlight the need for more equitable data ownership in global ophthalmic research.
ABSTRACT
Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView ( https://PhaeoEpiView.univ-nantes.fr ) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.
