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

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

doi:10.1038/s41598-021-95106-3

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.

Highlights

A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua
Isolate GAI-293 is capable of growth using a C O2 supply derived from power plant flue gas and using recycled growth media in large-scale outdoor raceways (Fig. 1A), demonstrating average productivity of 22 g/m2/day on an ash-free dry weight basis over a 2.5 month cultivation period
To understand the molecular basis of this tolerance, we investigated the identities and abundance of several putative components of the biophysical carbon concentrating mechanism (CCM), including bicarbonate transporters and carbonic anhydrases (CAs)

Summary

Introduction

A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. Aside from well-characterized model organisms like Thalassiosira pseudonana[3] and Phaeodactylum tricornutum[4], most currently available diatom genomes contain hundreds to thousands of small contigs that cannot be assigned to individual chromosomes[5,6,7,8,9] These short fragments can be difficult to distinguish from sequencing and assembly errors, requiring extensive transcriptome data for validation[10] and potentially leading to omission of genuine allelic variants. We present the first photosynthetic genome representative from genus Nitzschia This near-complete diploid nuclear genome and accompanying organelle assemblies provide new insights into the genomic capabilities of pennate diatoms in the context of allelic diversity, and robust new references for future functional and transcriptomic studies

Methods

Results

Conclusion