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

Oliver, Aaron; Podell, Sheila; Pinowska, Agnieszka; Traller, Jesse C.; Smith, Sarah R.; McClure, Ryan; Beliaev, Alex; Bohutskyi, Pavlo; Hill, Eric A.; Rabines, Ariel; Zheng, Hong; Allen, Lisa Zeigler; Kuo, Alan; Grigoriev, Igor V.; Allen, Andrew E.; Hazlebeck, David; Allen, Eric E.

doi:10.1038/s41598-021-95106-3

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

Journal Article · 01 August 2021 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-021-95106-3 · OSTI ID:1811581

Oliver, Aaron; Podell, Sheila; Pinowska, Agnieszka; Traller, Jesse C.; Smith, Sarah R.; McClure, Ryan; Beliaev, Alex; Bohutskyi, Pavlo; Hill, Eric A.; Rabines, Ariel; Zheng, Hong; Allen, Lisa Zeigler; Kuo, Alan; Grigoriev, Igor V.; Allen, Andrew E.; Hazlebeck, David; Allen, Eric E.

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.

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Research Organization:: Global Algae Innovations, Lihue, HI (United States); J. Craig Venter Institute, Inc., Rockville, MD (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: Defense Advanced Research Projects Agency (DARPA); USDOE; USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830; EE0008121; EE0008639; SC0008593

OSTI ID:: 1811581

Report Number(s):: PNNL-SA--161367; 15592; PII: 95106

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 11; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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