Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase

Abstract

Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.

Keywords: Blasia; Nostoc; hornworts; liverworts; nanopore; phylogenomics.

Fig. 1.

—Comparative analyses of cyanobacteria genomes. (A) Considerable differences in genome organization were found among the four cyanobiont genomes sequenced in this study. Ribbons connect the syntenic blocks, with red ribbons marking the location of the vnf gene cluster. Note the contig lengths are not to scale. (B) The four cyanobiont strains show very little 16S sequence divergence. (C) Although the majority of the orthogroups are shared among the four genomes, gains and losses appear to be common. “Leio.”: strain isolated from Leiosporoceros dussii; “Phaeo.”: from Phaeoceros carolinianus; “Blasia”: from Blasia pusilla. “o” indicates circular chromosomes or plasmids. (D) A conserved vnf-associated gene cluster was found in cyanobacteria. Genes shared among at least three genomes are labeled in red. Green ribbons connect genes that have been functionally characterized in Anabaena variabilis ATCC 29413. Blue and orange gene blocks distinguish the transcription directions. “†” indicates a truncated gene in Anabaena variabilis.