Characterizing lineage-specific genes in testate lobose amoebae (Arcellinida)

Abstract

Arcellinida are an abundant and diverse order of testate (shelled) amoebae that are important bioindicators of changing climates. Despite their ecological importance, the molecular mechanisms that underlie their adaptations, including those involving lineage-specific genes, remain largely unknown. Lineage-specific gene families (LSGFs) are linked to evolutionary innovations, yet the evolution of LSGFs remains underexplored across the tree of life, with most research restricted to model eukaryotes. Here, we assess the evolution of Arcellinida-specific gene families using a set of 197 Arcellinida transcriptomes representing 12 Arcellinida genera. We employ a conservative filtering approach to identify 3424 Arcellinda-specific gene families. Our analyses show that these lineage-specific gene families are shorter and exhibit lower expression compared to more conserved genes, congruent with trends observed in other eukaryotic lineages. Although there are inherent limitations regarding missing data with transcriptomics, we recover substantially more lineage-specific gene family births in the symbiont-bearing species Hyalosphenia papilio compared to Hyalosphenia elegans. Our results demonstrate a method to identify lineage-specific genes in non-model organisms where no reference genome are available, and expand our understanding of the evolution of lineage-specific genes in eukaryotes.