Jing Liu

and 4 more

Transposable elements (TEs), acting as symbiotic entities within host genomes, their landscapes represent a pivotal subject in evolutionary discourse. Previous investigations on the impact of ecological niches on the shaping of TE landscapes have yielded inconsistent conclusions. This study assessed the effect of ecological niches on the dynamics of TEs, employing pollinating fig wasps and non-pollinating fig wasps (NPFWs) residing in the syconia of figs as models. Our findings reveal a significantly positive correlation between TE content and genome size, exhibiting conspicuous phylogenetic signal. Significant differences emerge in the quantity, total length, and family types of TEs between pollinators and NPFWs. Notably, pollinators exhibit ‘dormant’ TE landscapes characterized by inactivity along with rapid decay attributable to smaller effective population sizes. This results in only a few remnants persisting over nearly a million years. Despite the relaxed selection pressure on pollinators in an effort to prolonging TE retention, their abundance remains limited. In contrast, NPFWs exhibit ‘aggressive’ TE landscapes, marked by the continual generation of new insertions. The larger effective population sizes contribute to decelerating the decay of TEs, as demonstrated by the substantial TE accumulation in the last one million years. These observed dynamics are intrinsically linked to the distinctive ecological niche provided by figs. TE remains suggest a functional role in facilitating pollinators’ adaptation to stress induced by their niche. Numerous cis-regulatory modules that originate from TEs and locate near genes involved in processing environmental information, which emphasizes their potential functional significances.

Jing Liu

and 3 more

The co-evolution of fig wasps with fig trees provide an excellent model for studying ecological systems and adaptive evolution. Transposable elements (TEs), as an important component of the genomes, are the powerful driver for environmental adaptation of the organisms. Here, the TEs in the genomes of six pollinator and five non-pollinator species were analyzed in the characteristics of composition, historical burst patterns, and their possible effects on the functions of conjunctive genes. Compared with pollinators, non-pollinators’ TEs showed a significant burst state with more types, longer lengths, and higher contents in the genomes, which might be related to their different evolutionary and life histories, as well as their different sensitivity to environmental changes. However, we identified a common TE burst peak period of 32-34 Mya in both groups, highly consistent with the glacial epoch of Eocene-Oligocene transition in geological history. Further functional enrichment analysis of the genes within 1 Kb near the insertion positions of TEs in the four geological periods representing the major continental ice sheet growth or decay was demonstrated, and the results showed that large amount of TEs were inserted near genes related to the environmental information processing, especially the Circadian entrainment pathway. These TEs might act as cis-regulatory modules to regulate the conjunctive genes in response to geo-climate changes. These results revealed the molecular basis of the fig wasp’s response to changes in the syconia microenvironment and paleoclimate macroenvironment from the perspective of genomic TEs. Keywords: transposable elements, fig wasp, adaptive evolution, geo-climate, cis-regulatory modules

Jing Liu

and 3 more

The mutualistic lifestyle of pollinating fig wasps and fig trees provides an excellent model for studying ecological and adaptive evolution issues. Transposable elements (TEs), as an important component of the genomes, are powerful driver for organisms to adapt to environment. Here, the genomic TEs of six pollinating fig wasps and five non-pollinating fig wasps were analyzed in the characteristics of composition and their effects on genome size, the historical burst patterns and their association with effective population size and paleoclimate changes, to infer the role of TEs in environmental adaptation in fig wasps. Compared with non-pollinators, pollinators’ TEs showed a significantly different burst state with less types and amount, shorter lengths, and lower contents in the genomes. The recent smaller effective population size and contractive demography failed to cause pollinators to accumulate more TEs, while the large number of TEs accumulated in non-pollinators positively correlated with their population expansion. The major TEs burst peaks in the history of pollinators highly overlapped with the warmer times in the Coolhouse in geological history. TEs located in the major peak period were mostly inserted near genes related to environment information processing such as Circadian entrainment pathway, and might act as CRMs (cis-regulatory modules) to regulate the conjunctive genes in response to paleoclimate changes in pollinators. These results revealed the molecular basis of the fig wasp’s response to changes in the syconia microenvironment and paleoclimate macroenvironment from the perspective of genomic TEs.