Biology subjects

Ferrari, B.

Publications and source records attributed to Ferrari, B..

3 recordsLinked to original sources

bioRxiv2024

Pushing the limits of single molecule transcript sequencing to uncover the largest disease-associated transcript isoforms in the human neural retina

Sequencing technologies have long limited the comprehensive investigation of large transcripts associated with inherited retinal diseases (IRDs) like Usher syndrome, which involves 11 associated genes with transcripts up to 19.6 kb. To address this, we used PacBio long-read mRNA isoform sequencing (Iso-Seq) following standard library preparation and an optimized workflow to enrich for long transcripts in the human neural retina. While our workflow achieved sequencing of transcripts up to 15 kb, this was insufficient for Usher syndrome-associated genes USH2A and ADGRV1, with transcripts of 18.9 kb and 19.6 kb, respectively. To overcome this, we employed the Samplix Xdrop System for indirect target enrichment of cDNA, a technique typically used for genomic DNA capture. This method facilitated the successful capture and sequencing of ADGRV1 transcripts as well as the full-length 18.9 kb USH2A transcripts. By combining algorithmic analysis with detailed manual curation of sequenced reads, we identified novel isoforms and alternative splicing events across the 11 Usher syndrome-associated genes, with implications for diagnostics and therapy development. Our findings demonstrate the Xdrop systems adaptability for cDNA capture and the advantages of integrating computational and manual transcript analyses. The full neural retina sequencing dataset is available via EGA under identifier EGAD50000000720.

genetics↗

bioRxiv2024

A proteogenomic atlas of the human neural retina

The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/595273v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e0810org.highwire.dtl.DTLVardef@1a382b6org.highwire.dtl.DTLVardef@1da7d9eorg.highwire.dtl.DTLVardef@16d29a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

Spatio-temporal surveys of the brown meagre Sciaena umbra using passive acoustics for management and conservation

Conservation of exploited fish populations is a priority for environmental managers. Spatio-temporal knowledge on reproductive sites is mandatory for species and habitat conservation but is often difficult to assess, particularly over vast geographic areas. Regular and long-term standardized surveys are necessary to identify reproductive sites, assess population trends and their distribution. Here we emphasize the utility of Passive Acoustic Monitoring (PAM) for the survey and management of a depleted vulnerable Mediterranean fish species, the brown meagre, Sciaena umbra. Acoustic surveys of reproductive calls were conducted combining 1) spatial data from standardized surveys within three MPAs and from 49 unprotected sites throughout the Northwestern Mediterranean basin, as well as 2) temporal data from a two-year-long survey at a presumed spawning location. The MPA surveys, which rapidly scanned ~30-50 km of the rocky coastlines per MPA, unveiled maps of distribution and reproductive activity of the brown meagre, including potential spawning sites. They were also effective in emphasizing effects linked to management actions: Full-protection zones had a higher number of vocalizations (70% of the listening sites) compared to less protected zones (30% of the sites) or sites outside MPAs (45% of the sites). This was also reflected in the number of singers that was generally low (< 3 individuals) in less protected zones and outside MPAs, implying lower fish densities. Highest calling aggregations were observed in potential spawning areas that represented only 0.04% of all listening sites, and were almost all in older, fully protected MPAs, which thus play a key role for fish stock recovery. The two-year survey revealed a 5-month reproductive season (from May to October) with a strong positive correlation between calling activity and temperature. Overall this study confirms the role of PAM as an efficient, replicable and standardized non-invasive method for population management that can identify functional sites and key protection zones, provide valuable information on reproduction, spatial and temporal occurrence, but also on population trends and climate-driven changes. HighlightsO_LIMonitoring of threatened species and their key habitats is critical for environmental managers. C_LIO_LIManagement requires methods to assess population trends at large spatial and temporal scales. C_LIO_LIPassive acoustics (PA) is efficient in mapping and monitoring vulnerable fish species. C_LIO_LIDistribution, reproductive sites and population dynamics can be assessed over vast geographical areas. C_LIO_LIWe show the utility of PA to identify key conservation zones and assess effects of management actions. C_LI

ecology↗