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

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 up-to-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.

Authors:
 [1];  [2];  [1];  [1];  [3];  [4];  [5]; ORCiD logo [6];  [2];  [1];  [1]
  1. PSL Univ., Paris (France)
  2. Wellcome Trust Genome Campus, Cambridge (United Kingdom)
  3. Univ. Paris-Saclay, Versailles (France)
  4. Rutgers Univ., Newark, NJ (United States)
  5. J. Craig Venter Institute Inc., Rockville, MD (United States)
  6. J. Craig Venter Institute Inc., Rockville, MD (United States); Univ. of California, San Diego, CA (United States)
Publication Date:
Research Org.:
J. Craig Venter Institute Inc., Rockville, MD (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1500040
Grant/Contract Number:  
SC0008593
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Rastogi, Achal, Maheswari, Uma, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Maumus, Florian, Kustka, Adam, McCarthy, James, Allen, Andy E., Kersey, Paul, Bowler, Chris, and Tirichine, Leila. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. United States: N. p., 2018. Web. doi:10.1038/s41598-018-23106-x.
Rastogi, Achal, Maheswari, Uma, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Maumus, Florian, Kustka, Adam, McCarthy, James, Allen, Andy E., Kersey, Paul, Bowler, Chris, & Tirichine, Leila. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. United States. doi:10.1038/s41598-018-23106-x.
Rastogi, Achal, Maheswari, Uma, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Maumus, Florian, Kustka, Adam, McCarthy, James, Allen, Andy E., Kersey, Paul, Bowler, Chris, and Tirichine, Leila. Mon . "Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms". United States. doi:10.1038/s41598-018-23106-x. https://www.osti.gov/servlets/purl/1500040.
@article{osti_1500040,
title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms},
author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila},
abstractNote = {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 up-to-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.},
doi = {10.1038/s41598-018-23106-x},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {3}
}

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Works referenced in this record:

Fast and SNP-tolerant detection of complex variants and splicing in short reads
journal, February 2010