Data from: Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis

Many insects rely on obligate microbial symbioses, often involving
multiple partners. Although symbiont replacement is well-documented, how
newly acquired and resident obligate symbionts adapt after such events
remains unclear. Here, we investigate the dual obligate symbiosis of the
aphid Lachnus tropicalis, where an ancestral Serratia lineage was replaced
by a newly acquired another Serratia lineage while the primary symbiont
Buchnera remained. Our metagenomic sequencing yielded complete genomes of
Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic
complementarity. Although the Serratia genome retained abundant gene sets
for amino acid synthesis, it also contained pseudogenes in leucine and
methionine pathways, which would be compensated for by Buchnera or the
host. Comparison with L. roboris, which harbors the ancestral Serratia
lineage, showed that the newly acquired Serratia in L. tropicalis exhibits
identical tissue localization and vertical transmission pattern,
suggesting the smooth succession of the prior’s microniche. Notably,
Buchnera in L. tropicalis exhibited a slightly more degenerated genome
than its counterpart in L. roboris, indicating that symbiont replacement
can accelerate gene loss even in ancient symbionts. Overall, our findings
provide new insights into the dynamics of novel mutualism establishment
and highlight symbiont replacement as a driver of host-symbiont
co-evolution.