First regional reference database of northern Adriatic diatom transcriptomes

Knjaz, Mia; Baričević, Ana; Smodlaka Tanković, Mirta; Kužat, Nataša; Vlašiček, Ivan; Grižančić, Lana; Podolšak, Ivan; Pfannkuchen, Martin; Kogovšek, Tjaša; Marić Pfannkuchen, Daniela (2024) First regional reference database of northern Adriatic diatom transcriptomes. Scientific Reports, 14 (1). ISSN 2045-2322

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Abstract

Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.

Item Type:	Article
Uncontrolled Keywords:	northern Adriatic sea; diatom; transcriptomes; reference database
Subjects:	NATURAL SCIENCES NATURAL SCIENCES > Interdisciplinary Natural Sciences NATURAL SCIENCES > Interdisciplinary Natural Sciences > Marine Science
Divisions:	Center for Marine Research
Projects:	Project title Project leader Project code Project type Molekularne životne strategije fitoplanktona u Jadranu-Adri LIFE Daniela Marić Pfannkuchen UIP-2020-02-7868 HRZZ Životne strategije fitoplanktona u sjevernom Jadranu-P-limit Martin Pfannkuchen UIP-2014-09-6563 HRZZ Joint European Research Infrastructure of Coastal Observatories: Science, Service, Sustainability-JERICO-S3 Martin Pfannkuchen 871153 EK
Depositing User:	Virna Brumnić
Date Deposited:	27 Feb 2026 08:55
URI:	http://fulir.irb.hr/id/eprint/11283
DOI:	10.1038/s41598-024-67043-4

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