Architectural Groups of a Subtelomeric Gene Family Evolve Along Distinct Paths in Candida albicans

Abstract

Subtelomeres are dynamic genomic regions shaped by elevated rates of recombination, mutation, and gene birth/death. These processes contribute to formation of lineage-specific gene family expansions that commonly occupy subtelomeres across eukaryotes. Investigating the evolution of subtelomeric gene families is complicated by the presence of repetitive DNA and high sequence similarity among gene family members that prevents accurate assembly from whole genome sequences. Here we investigated the evolution of the telomere-associated (TLO) gene family in Candida albicans using 189 complete coding sequences retrieved from 23 genetically diverse strains across the species. TLO genes conformed to the three major structural groups ( /{beta} /{gamma}) previously defined in the genome reference strain but significantly differed in the degree of within-group diversity and positional conservation. One group, TLO{beta}, was always found at the same chromosome arm with strong sequence similarity among all strains. In contrast, diverse Tlo sequences have proliferated among chromosome arms. Tlo{gamma} genes formed seven primary clades that included each of the previously identified Tlo{gamma} genes from the genome reference strain with limited mobility among chromosome arms. Structural groups displayed regions of high conservation that resolved newly identified functional motifs, providing insight into potential regulatory mechanisms that distinguish groups. Thus, by resolving intra-species subtelomeric gene variation, it is possible to identify previously unknown gene family complexity that may underpin adaptive functional variation.