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 makes 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 genome-wide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.自交不亲和物种球茎拟南芥（Arabidopsis halleri）是自交亲和模式植物拟南芥（Arabidopsis thaliana）的近缘物种。该物种广泛分布于欧亚大陆，且具备重金属超富集能力，使其成为生态基因组学研究的优质模型。我们利用长插入片段mate-pair文库（long-insert mate-pair library），对采集自日本某重金属高污染矿区的球茎拟南芥gemmifera亚种Tada矿株系（W302）的基因组组装进行优化。经5轮强制自交后，该株系的杂合率降至0.04%，为后续基因组组装提供了有利条件。本次组装最终覆盖196 Mb，约占预估基因组大小的78%，并获得712 kb的支架N50（scaffold N50）。为验证组装与注释结果的可靠性，我们通过比对球茎拟南芥Tada矿株系与已发表的近缘物种 lyrata拟南芥（Arabidopsis lyrata）的高质量参考基因组的共线性特征完成了验证。进一步的组装质量验证，则通过调取欧洲球茎拟南芥的已发表序列，对重金属ATP酶4（HEAVY METAL ATPASE4, HMA4）与金属耐受蛋白1（METAL TOLERANCE PROTEIN1, MTP1）区域开展共线性分析与系统发育分析得以实现。我们在单个支架上组装得到3个串联重复的HMA4拷贝——该基因是镉与锌超富集过程中的关键功能基因。本基因组组装将助力球茎拟南芥，以及由 lyrata拟南芥与球茎拟南芥杂交形成的异源多倍体堪察加拟南芥（Arabidopsis kamchatica）的全基因组相关研究。