Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricor...

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Autores principales:	Aaron Oliver, Sheila Podell, Agnieszka Pinowska, Jesse C. Traller, Sarah R. Smith, Ryan McClure, Alex Beliaev, Pavlo Bohutskyi, Eric A. Hill, Ariel Rabines, Hong Zheng, Lisa Zeigler Allen, Alan Kuo, Igor V. Grigoriev, Andrew E. Allen, David Hazlebeck, Eric E. Allen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3434cbb5361e48b6b1723b84731549bb
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spelling	oai:doaj.org-article:3434cbb5361e48b6b1723b84731549bb2021-12-02T16:36:36ZDiploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom10.1038/s41598-021-95106-32045-2322https://doaj.org/article/3434cbb5361e48b6b1723b84731549bb2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95106-3https://doaj.org/toc/2045-2322Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.Aaron OliverSheila PodellAgnieszka PinowskaJesse C. TrallerSarah R. SmithRyan McClureAlex BeliaevPavlo BohutskyiEric A. HillAriel RabinesHong ZhengLisa Zeigler AllenAlan KuoIgor V. GrigorievAndrew E. AllenDavid HazlebeckEric E. AllenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aaron Oliver Sheila Podell Agnieszka Pinowska Jesse C. Traller Sarah R. Smith Ryan McClure Alex Beliaev Pavlo Bohutskyi Eric A. Hill Ariel Rabines Hong Zheng Lisa Zeigler Allen Alan Kuo Igor V. Grigoriev Andrew E. Allen David Hazlebeck Eric E. Allen Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
description	Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.
format	article
author	Aaron Oliver Sheila Podell Agnieszka Pinowska Jesse C. Traller Sarah R. Smith Ryan McClure Alex Beliaev Pavlo Bohutskyi Eric A. Hill Ariel Rabines Hong Zheng Lisa Zeigler Allen Alan Kuo Igor V. Grigoriev Andrew E. Allen David Hazlebeck Eric E. Allen
author_facet	Aaron Oliver Sheila Podell Agnieszka Pinowska Jesse C. Traller Sarah R. Smith Ryan McClure Alex Beliaev Pavlo Bohutskyi Eric A. Hill Ariel Rabines Hong Zheng Lisa Zeigler Allen Alan Kuo Igor V. Grigoriev Andrew E. Allen David Hazlebeck Eric E. Allen
author_sort	Aaron Oliver
title	Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
title_short	Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
title_full	Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
title_fullStr	Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
title_full_unstemmed	Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
title_sort	diploid genomic architecture of nitzschia inconspicua, an elite biomass production diatom
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3434cbb5361e48b6b1723b84731549bb
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Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

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