RT Journal Article SR Electronic T1 Integrative analysis of large scale transcriptome data draws a comprehensive functional landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms JF bioRxiv FD Cold Spring Harbor Laboratory SP 176024 DO 10.1101/176024 A1 Achal Rastogi A1 Uma Maheswari A1 Richard G. Dorrell A1 Florian Maumus A1 Fabio Rocha Jimenez Vieira A1 Adam Kustka A1 James McCarthy A1 Andy E. Allen A1 Paul Kersey A1 Chris Bowler A1 Leila Tirichine YR 2017 UL http://biorxiv.org/content/early/2017/08/18/176024.abstract AB 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 for the first time of extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping which increases the diversity of transcripts to regulate gene expression in response to nutrient limitations. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete 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 TEs such as SINE, MITE, LINE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.