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First regional reference database of northern Adriatic diatom transcriptomes.

Mia Knjaz1, Ana Baricevic2, Mirta Smodlaka Tankovic3

  • 1Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia.

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This study provides a new diatom reference database for the northern Adriatic Sea. This resource aids in analyzing marine microbial community functions, especially under nutrient-limited conditions.

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Area of Science:

  • Marine Biology
  • Microbial Ecology
  • Genomics

Background:

  • Marine microbial communities are crucial for ecosystem function and biodiversity.
  • Metagenomics and metatranscriptomics advance the study of microbial communities.
  • Reliable reference transcriptomes are essential for these molecular techniques.

Purpose of the Study:

  • To create a comprehensive diatom reference transcriptome database for the northern Adriatic Sea.
  • To investigate the impact of nutrient availability on diatom gene expression.
  • To support marine metagenomic and metatranscriptomic analyses.

Main Methods:

  • Generated 12 individual transcriptome assemblies from 6 diatom species.
  • Cultured diatoms under phosphate-replete and phosphate-deprived conditions.
  • Filtered reads, assembled transcripts, and assigned proteins taxonomically and functionally.

Main Results:

  • Obtained an average of 64,932 transcripts per assembly.
  • Assigned an average of 8856 functionally known proteins and 6483 diatom-specific proteins per assembly.
  • Dioms grown in replete media showed higher protein assignments; 50% of proteins were shared between conditions.

Conclusions:

  • The developed diatom reference database is a valuable resource for northern Adriatic marine ecosystem studies.
  • The database is particularly useful for analyzing responses to nutrient limitation.
  • Individual transcriptomes can serve as species-specific references for future gene expression studies.