Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

The self-incompatible species Arabidopsis halleri is a close relative of
the self-compatible model plant Arabidopsis thaliana. The broad European
and Asian distribution and heavy metal hyperaccumulation ability make A.
halleri a useful model for ecological genomics studies. We used
long-insert mate-pair libraries to improve the genome assembly of the A.
halleri ssp. gemmifera Tada mine genotype (W302) collected from a site
with high contamination by heavy metals in Japan. After five rounds of
forced selfing, heterozygosity was reduced to 0.04%, which facilitated
subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the
estimated genome size and achieved scaffold N50 length of 712 kb. To
validate assembly and annotation, we used synteny of A. halleri Tada mine
with a previously published high-quality reference assembly of a closely
related species, Arabidopsis lyrata. Further validation of the assembly
quality comes from synteny and phylogenetic analysis of the HEAVY METAL
ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published
sequences from European A. halleri for comparison. Three tandemly
duplicated copies of HMA4, key gene involved in cadmium and zinc
hyperaccumulation, were assembled on a single scaffold. The assembly will
enhance the genomewide studies of A. halleri as well as the allopolyploid
Arabidopsis kamchatica derived from A. lyrata and A. halleri.