# Comparative Genomics Insights Into the Evolutionary Disparities Between Nitroplast‐Evolved Ecotype UCYN‐A2 and Its Closest Relative UCYN‐A1

## TL;DR

This study compares two ecotypes of UCYN-A cyanobacteria to uncover evolutionary differences, including unique genetic markers and metabolic traits linked to the emergence of a novel N2-fixing organelle.

## Contribution

The study introduces codon aversion motifs as a novel method for strain-level identification in bacteria and reveals genomic heterogeneity between UCYN-A1 and UCYN-A2.

## Key findings

- UCYN-A2 has 577 unique INDELs in single-copy orthologous genes compared to UCYN-A1.
- Codon usage signatures serve as lineage-specific molecular markers for UCYN-A strains.
- Genomic and metabolic pathway differences suggest UCYN-A2 has evolved toward organellogenesis.

## Abstract

UCYN‐A is a phenomenal diazotrophic cyanobacterium with significant ecological importance. UCYN‐A1 and UCYN‐A2 are the two most abundant ecotypes. Recently, the striking discovery of nitroplast, a novel N2‐fixing organelle in cultured B. bigelowii/UCYN‐A2 endosymbiont, indicated the possibility that UCYN‐A2 has evolved beyond endosymbiosis to an early phase of organellogenesis. This study addresses the following critical question: What evolutionary heterogeneity has emerged between UCYN‐A1 and UCYN‐A2? To investigate this issue, we comprehensively compared a total of seven genomes from UCYN‐A2 and UCYN‐A1. Under similar genome organizations, GC content, and gene composition, we still detected abundant genetic differences, including group–unique orthogroups, ANI below 85%, and 577 UCYN‐A2‐unique INDELs in single‐copy orthologous genes (SCOGs). Moreover, we also focused on the orthologous genes of 40 metabolic‐pathway genes in nitroplast. In addition to high‐informative SNPs and INDELs possessing distinct interlineage differences, we traced abundant codon usage “signatures” that serve as lineage‐unique molecular markers. Most notably, we successfully established a strain‐level identification map for UCYN‐A strains using codon aversion motifs, which represents the first case study of this approach in bacteria. In summary, all the comparative results reported here collectively indicate that UCYN‐A1 and UCYN‐A2 have evolved remarkable genomic heterogeneities. Furthermore, the findings of this work will definitely promote our current understanding of codon aversion and the evolution of UCYN‐A.

This paper conducted comparative genomic analyses among seven UCYN‐A strains in genome content, gene structure, and key metabolic protein genes. In general, our results demonstrated considerable disparities between UCYN‐A1 and UCYN‐A2, providing insights into the evolution of UCYN‐A and nitroplast.