The evolution of interdependence in a four-way mealybug symbiosis

Abstract

Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrientpoor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provide these nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in the cytoplasm of Tremblaya. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared to their closest non-endosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved co-dependencies with each other, Tremblaya, and their insect host.SignificanceMealybugs are sap-feeding insects that house between one and three bacterial endosymbionts to supplement their nutritionally poor diets. Many mealybug-bacteria relationships were established tens or hundreds of millions of years ago, and these ancient examples show high levels host-endosymbiont genomic and metabolic integration. Here, we describe the complete genomes and cellular locations for two bacterial endosymbiont which have recently transitioned from a free-living to an intracellular state. Our work reveals the rapid emergence of metabolic interdependence between these two nascent endosymbionts, their partner bacterial co-symbiont in whose cytoplasm they reside, and their insect host cell. Our work confirms that intracellular bacteria rapidly adapt to a host-restricted lifestyle through breakage or loss of redundant genes.

Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis

“…Although we do not know how long each of our study participants was infected by their respective P. aeruginosa lineage, it is clear that the evolutionary timescale of our study is very short compared with the timescales described in previous studies of genome degradation (Parkhill et al, 2003;Wei et al, 2003). There is a rich body of literature on highly degraded genomes of hostrestricted bacteria (Oakeson et al, 2014;Garber et al, 2021b). Although fewer studies have examined the forces shaping genome evolution earlier along the route from initial host colonization toward host restriction (Burke and Moran, 2011;Renoz et al, 2021), it has been proposed that ancient host-beneficial endo-symbionts likely evolved from opportunistically pathogenic relationships (McCutcheon et al, 2019).…”

“…Pseudogenes commonly form when bacteria undergo an ecological shift that relaxes selection on genes that are no longer required for survival in their new environment (Lerat and Ochman, 2005). Inactivated genes are removed relatively quickly from the genomes of free-living bacteria but are abundant in recently host-restricted bacteria (Kuo and Ochman, 2010;Burke and Moran, 2011;Oakeson et al, 2014;Garber et al, 2021b;Renoz et al, 2021). Consistent with our hypothesis, we found that isolates from patient 33's lineage (all mutators) had the lowest coding density and highest number of predicted pseudogenes, which included genes missing start codons, fragmented genes, and run-on open reading frames (Figures 5A and 5B; Table 2).…”

The B chromosome of Pseudococcus viburni: a selfish chromosome that exploits whole-genome meiotic drive

“…Our genome assembly shows high completeness, as revealed by the presence of >90% single copy orthologs from the insect and hemipteran BUSCO gene sets. Half of the genome (216.2Mb) consists of repetitive sequences, higher than the 38-45% range estimated in Phenacoccus solenopsis (Li et al, 2020) and Pseudococcus longispinus (Garber et al 2021 publicly available at https://ensembl.mealybug.org/Pseudococcus_longispinus_v1) ) and hemipterans such as Acyrthosiphon pisum or Bemisia tabaci (International Aphid Genomics Consortium, 2010;Chen et al, 2016). The vast majority of repeats (96.6%) are unclassified.…”

“…longispinus (Garber et al 2021) . Of all 486 B-linked genes we identified 56 that carry a paralog in the core genome (Supplementary Table S6).…”