Two chromosome-level genome assemblies of Sarracenia reveal repeat-driven expansion and gene loss associated with carnivory.

Abstract

Premise of the StudyCarnivory has evolved repeatedly across the plant tree of life despite being a dramatic shift from typical plant nutrient acquisition strategies. It remains largely unclear whether the evolution of carnivory takes a similar genomic trajectory. Here, we explore the genomic consequences of carnivory in the pitcher plant genus Sarracenia. MethodsWe use a combination of Pacbio HiFi long-read sequencing and trio-binning to assemble chromosome-scale genome sequences for S. psittacina and S. rosea. We conduct comparative analyses with other asterid genomes to evaluate patterns of gene family expansion and contraction during the transition to carnivory. ResultsBoth Sarracenia genomes are large ([~]3.5 Gbp) and highly repetitive ([~]87% repeats) yet only contain [~]22,000 genes. This reduced gene content reflects widespread gene family contraction. In total, 3,654 gene families have contracted, including the complete loss of 934 gene families, while only 751 gene families have expanded. The gene losses are enriched for functions related to photosynthesis, including nuclear-encoded subunits of the NADH dehydrogenase (Ndh) complex, as well as immune-related genes. ConclusionsThese results indicate that the evolution of carnivory in Sarracenia is associated with widespread gene loss rather than extensive gene family expansion. The loss of genes involved in photosynthesis and immune response suggest the relaxation of selection on these functions, which may be partially supplanted by prey-derived nutrient acquisition and pitcher-associated microbiome. These chromosome-level assemblies will enable future comparative studies in plant evolution, while also serving as critical resources for the conservation of this ecologically significant lineage.