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 u...

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Autores principales:	Achal Rastogi, Uma Maheswari, Richard G. Dorrell, Fabio Rocha Jimenez Vieira, Florian Maumus, Adam Kustka, James McCarthy, Andy E. Allen, Paul Kersey, Chris Bowler, Leila Tirichine
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ae73ac7d9a9049ecb9f15bbfa637e359
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spelling	oai:doaj.org-article:ae73ac7d9a9049ecb9f15bbfa637e3592021-12-02T15:08:11ZIntegrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms10.1038/s41598-018-23106-x2045-2322https://doaj.org/article/ae73ac7d9a9049ecb9f15bbfa637e3592018-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-23106-xhttps://doaj.org/toc/2045-2322Abstract 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.Achal RastogiUma MaheswariRichard G. DorrellFabio Rocha Jimenez VieiraFlorian MaumusAdam KustkaJames McCarthyAndy E. AllenPaul KerseyChris BowlerLeila TirichineNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-14 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Achal Rastogi Uma Maheswari Richard G. Dorrell Fabio Rocha Jimenez Vieira Florian Maumus Adam Kustka James McCarthy Andy E. Allen Paul Kersey Chris Bowler Leila Tirichine Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
description	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.
format	article
author	Achal Rastogi Uma Maheswari Richard G. Dorrell Fabio Rocha Jimenez Vieira Florian Maumus Adam Kustka James McCarthy Andy E. Allen Paul Kersey Chris Bowler Leila Tirichine
author_facet	Achal Rastogi Uma Maheswari Richard G. Dorrell Fabio Rocha Jimenez Vieira Florian Maumus Adam Kustka James McCarthy Andy E. Allen Paul Kersey Chris Bowler Leila Tirichine
author_sort	Achal Rastogi
title	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
title_short	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
title_full	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
title_fullStr	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
title_full_unstemmed	Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
title_sort	integrative analysis of large scale transcriptome data draws a comprehensive landscape of phaeodactylum tricornutum genome and evolutionary origin of diatoms
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/ae73ac7d9a9049ecb9f15bbfa637e359
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Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

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