Evolution of conserved noncoding sequences in Arabidopsis thaliana

Recent pangenome studies have revealed that a large fraction (>20%)
of the gene content within a species exhibits presence-absence variation
(PAV). However, coding regions alone provide an incomplete assessment of
functional genomic sequence variation at the species level. Little to no
attention has been paid to noncoding regulatory regions in pangenome
studies, though these sequences directly modulate gene expression and
phenotype. To uncover regulatory genetic variation, we generated
chromosome-scale genome assemblies for thirty Arabidopsis thaliana
accessions from multiple distinct habitats and characterized species level
variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered
not only evidence for PAV and Positional Variation (PosV) but that
diversity in CNS is non-random, with variants shared across different
accessions. Using evolutionary analyses and chromatin accessibility data,
we provide further evidence supporting conserved and variable CNS roles in
gene regulation. Characterizing species-level diversity in all functional
genomic sequences may later uncover previously unknown mechanistic links
between genotype and phenotype.