Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

TitleIntegrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
Publication TypeJournal Article
Year of Publication2018
AuthorsRastogi A., Maheswari U., Dorrell R.G, Vieira F.RJ, Maumus F., Kustka A., McCarthy J., Allen A.E, Kersey P., Bowler C., Tirichine L.
JournalScientific Reports
Volume8
Date Published2018/03
Type of ArticleArticle
ISBN Number2045-2322
Accession NumberWOS:000427688100027
KeywordsAlgae; diversity; eukaryotes; gene; intron size; metabolism; plastid endosymbiosis; prediction; protein; Science & Technology - Other Topics; transposable elements
Abstract

Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used upto-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.

DOI10.1038/s41598-018-23106-x
Short TitleSci Rep
Student Publication: 
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