Biology subjects

Ferrante, M. I.

Publications and source records attributed to Ferrante, M. I..

4 recordsLinked to original sources

bioRxiv2026

Multi-modal single-cell profiling reveals transcriptional states and commitment dynamics during sexual reproduction in the diatom Pseudo-nitzschia multistriata

Diatoms, single-celled photosynthetic eukaryotes, traditionally considered primarily influenced by resource availability, are now recognized to exhibit complex developmental processes reminiscent of those in multicellular organisms. Sexual reproduction is an obligate choice in many species, albeit with variable frequency and efficiency. In order to explore decision making mechanisms and cellular heterogeneity inherent to this specific phase of the diatom life cycle, we applied a multi-modal strategy to follow sexual reproduction events in the model diatom Pseudo-nitzschia multistriata: i) we employed image-enabled cell sorting to link sexual stages morphology with gene expression ii) we developed a single-nucleus RNA sequencing assay, and iii) conducted proteomic profiling. Combining phenotypes with single-cell profiling allowed us to identify sexual state-specific transcription programs and different states within morphologically identical parental cells, revealing a widespread commitment of the majority of the population to sexual reproduction. This implies that the bottleneck to successful sexual reproduction in this species can be placed downstream of the signalling phase between mating cells, with additional, yet unidentified, factors influencing mating success at sea.

microbiology↗

bioRxiv2023

DNA methylation is linked to the monoallelic expression of MRP3, a diatom mating type determining gene

Diatoms are unicellular microalgae widely distributed in aquatic ecosystems. In diatoms, sexual reproduction is needed to counteract cell miniaturization imposed by the rigid silica shell, and only small cells, below a species-specific size threshold, are competent for sex. We performed a genome-wide Enzymatic Methyl-seq analysis in the heterothallic diatom Pseudo-nitzschia multistriata comparing cells of different size and opposite mating type (MT) to investigate potential epigenetic controls in life cycle transitions. We found an imprinting-like pattern of methylation at the sex locus: alleles of the gene responsible for the specification of the MT+, MRP3, are hypermethylated in MT- and differentially methylated in MT+, with transcription occurring only on the MT+ hypomethylated variant. The methylation pattern is overall stable over the P. multistriata life cycle. Absence of methylation in MRP3 is necessary for its expression but not sufficient, since large non-sexual cells have the same methylation profile of small sexual cells but do not express MRP3, suggesting that additional controls are involved in the mechanism of sex determination. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/561864v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@ea2482org.highwire.dtl.DTLVardef@2d553org.highwire.dtl.DTLVardef@350aaorg.highwire.dtl.DTLVardef@1a4f2f6_HPS_FORMAT_FIGEXP M_FIG C_FIG The methylation profile of the mating type determining gene MRP3 of the diatom Pseudo-nitzschia multistriata is different between opposite mating types. Lack of methylation is necessary but not sufficient for MRP3 expression in the sexually competent MT+ strains. HighlightsO_LI- The mating type locus is differentially methylated in MT+ and MT- C_LIO_LI- DNA methylation is linked to MRP3 expression C_LIO_LI- DNA methylation does not play a role in the acquisition of sexual competence C_LI

genetics↗

bioRxiv2021

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

BackgroundTransposable elements (TEs) widely contributed to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However a specific search for the existence of full-length transpositionally competent TEs has not been performed in this genus. ResultsHere we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be active driving germline polymorphisms among individuals and somatic polymorphisms in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. ConclusionsThe neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full lenght LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.

genomics↗

bioRxiv2020

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

bioinformatics↗