AUTHOR=Hicks McKenna , Tran-Dao Thuy-Khanh , Mulroney Logan , Bernick David L. 

TITLE=De-novo Assembly of Limnospira fusiformis Using Ultra-Long Reads

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.657995

DOI=10.3389/fmicb.2021.657995

ISSN=1664-302X

ABSTRACT=<p>The <italic>Limnospira</italic> genus is a recently established clade that is economically important due to its worldwide use in biotechnology and agriculture. This genus includes organisms that were reclassified from <italic>Arthrospira</italic>, which are commercially marketed as “<italic>Spirulina</italic>.” <italic>Limnospira</italic> are photoautotrophic organisms that are widely used for research in nutrition, medicine, bioremediation, and biomanufacturing. Despite its widespread use, there is no closed genome for the <italic>Limnospira</italic> genus, and no reference genome for the type strain, <italic>Limnospira fusiformis</italic>. In this work, the <italic>L. fusiformis</italic> genome was sequenced using Oxford Nanopore Technologies MinION and assembled using only ultra-long reads (&gt;35 kb). This assembly was polished with Illumina MiSeq reads sourced from an axenic <italic>L. fusiformis</italic> culture; axenicity was verified via microscopy and rDNA analysis. Ultra-long read sequencing resulted in a 6.42 Mb closed genome assembled as a single contig with no plasmid. Phylogenetic analysis placed <italic>L. fusiformis</italic> in the <italic>Limnospira</italic> clade; some <italic>Arthrospira</italic> were also placed in this clade, suggesting a misclassification of these strains. This work provides a fully closed and accurate reference genome for the economically important type strain, <italic>L. fusiformis</italic>. We also present a rapid axenicity method to isolate <italic>L. fusiformis</italic>. These contributions enable future biotechnological development of <italic>L. fusiformis</italic> by way of genetic engineering.</p>