Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

Maize is well known for its exceptional structural diversity, including
copy number variants (CNVs) and presence/absence variants (PAVs), and
there is growing evidence for the role of structural variation in maize
adaptation. While PAVs have been described in this important crop species,
the extent of presence/absence variation and the relative position of
inbred-specific regions remain to be elucidated. De novo genome sequencing
of the F2 maize inbred line which played a key role in European breeding
programs over the past 50 years revealed thousands of novel genomic
regions, making up 88Mb of DNA, that are present in the F2 but not in B73.
Comparison of B73 and F2 PAV localization revealed contrasted chromosomal
distributions between the two inbreds and specific evolutionary dynamics
of PAVs as compared to SNPs. Detailed sequence and functional annotation
of F2 PAV sequences revealed hundreds of new genes with transcriptional
support, but also a large fraction of repetitive sequences. Detailed
analysis of sequence breakpoint highlights the role of double strand break
repair, but also transposon insertion in PAV generation. Typing of the B73
and F2 PAVs in maize temperate inbreds revealed that some PAVs are found
only in European Flint material, thus pinpointing structural features that
may be at the origin of adaptive traits involved in the success of this
material. Linkage disequilibrium (LD) analysis revealed that LD is strong
within PAVs, as expected by the absence of recombination in crosses where
PAV is missing in one of the parents.