Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

Abstract

Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of H. defensa from the pea aphid Acyrthosiphon pisum. Chosen strains also spanned the breadth of the H. defensa phylogeny and differed in strength of protection conferred against parasitoids. Results indicated that strains shared most genes with roles in nutrient acquisition, metabolism, and essential housekeeping functions. In contrast, the inventory of mobile genetic elements varied substantially, which generated strain specific differences in gene content and genome architecture. In some cases, specific traits correlated with differences in protection against parasitoids, but in others high variation between strains obscured identification of traits with likely roles in defense. Transcriptome data generated continuous distributions to genome assemblies with some genes that were highly expressed and others that were not. Single molecule real-time sequencing further identified differences in DNA methylation patterns and restriction modification systems that provide defense against phage infection.

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

“…This toxin cassette encodes for a single putative virulence-associated protein with no recognisable signal peptide. Previous studies have classified the APSE-2 variant found in Hamiltonella strain ZA17 as APSE-8 (Brandt et al, 2017;Chevignon et al, 2018;Doremus and Oliver, 2017;Patel et al, 2019). However, we found that the only difference in its toxin cassette was the pseudogenisation of the first putative toxin gene within this region when compared to APSE-2 5AT and NY26.…”

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

“…Search for genomic variants was restricted to SNPs and short insertions and deletions. The analysis of large genomic rearrangements may bring additional information on the symbiotic genomic diversity [ 67 ]. Short variant information seems to be sufficient to reconstruct symbiotic phylogenetic trees, since most phylogenetic studies rely on gene sequences analyses, and generally do not integrate rearrangements, but this structural variation should not be neglected in order to reconstruct full genomes for the main microbial genotypes existing in pea aphid holobionts.…”

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems

“…Bayesian inference was performed in MrBayes v3.2.5 (Ronquist et al, 2012) using the GTR+I+G AASM running two independent analyses with four chains each for 3,000,000 generations and checked for convergence. For phylogenetic inference of the Hamiltonella symbionts, we followed Chevignon et al (2018) and used the genes accD, dnaA, gyrB, hrpA, murE, ptsI, and recJ. The original authors of the aforementioned study kindly provided the alignment files, we then followed to add the newly acquired sequences and re-aligned using MUSCLE v3.8.31 (Edgar, 2004) and then removed divergent and ambiguously aligned blocks using Gblocks v0.91b.…”

“…These Hamiltonella strains show highly syntenic reduced genomes of around 1.4 Mbp, contrasting the 2.2 Mbp genomes of the Hamiltonella defensa facultative symbionts of Ac. pisum (Chevignon et al, 2018). Based on 16S, their closes relatives are H. defensa strains ZA17, AS3, and A2C (99% identity, 2737 bit-score).…”

“…Based on 16S, their closes relatives are H. defensa strains ZA17, AS3, and A2C (99% identity, 2737 bit-score). Additionally, a multi-gene phylogenetic reconstruction following Chevignon et al (2018) shows that these Hamiltonella symbionts are nested within H. defensa symbionts (supplementary fig. S4, Supplementary Material online), confidently assigning these newly sequenced symbionts within the taxon.…”