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.

自交不亲和物种高山拟南芥（Arabidopsis halleri）是自交亲和模式植物拟南芥（Arabidopsis thaliana）的近缘物种。其广泛分布于欧亚大陆且具备重金属超富集能力，使得高山拟南芥（以下简称A. halleri）成为生态基因组学研究的优质模式物种。我们使用长插入片段配对末端文库（long-insert mate-pair libraries）对采自日本某高重金属污染场地的A. halleri ssp. gemmifera田边矿（Tada mine）基因型W302的基因组组装进行了优化。经5轮强制自交后，该材料的杂合度降至0.04%，为后续基因组组装提供了便利。本次组装的基因组序列总长达到196 Mb，覆盖预估基因组大小的78%，同时获得的支架N50（scaffold N50）长度为712 kb。为验证基因组组装与注释的准确性，我们将A. halleri田边矿基因型的基因组与近缘物种 lyrata拟南芥（Arabidopsis lyrata）已发表的高质量参考基因组组装结果进行共线性（synteny）分析。本研究还通过比对欧洲A. halleri的已发表序列，对重金属ATP酶4（HEAVY METAL ATPASE4，HMA4）与金属耐受蛋白1（METAL TOLERANCE PROTEIN1，MTP1）基因区域开展共线性与系统发育分析，进一步验证了基因组组装的质量。参与镉与锌超富集过程的关键基因HMA4存在3个串联重复拷贝，且被组装至同一支架序列中。本次基因组组装将助力A. halleri以及由A. lyrata与A. halleri杂交形成的异源多倍体堪察加拟南芥（Arabidopsis kamchatica）的全基因组研究。