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.自交不亲和物种盐芥（Arabidopsis halleri）是自交亲和模式植物拟南芥（Arabidopsis thaliana）的近缘物种。该物种兼具广泛的欧亚分布范围与重金属超富集特性，使其成为生态基因组学研究的理想模型。本研究采用长插入片段Mate-Pair文库，对采集自日本某重金属高污染矿区的盐芥gemmifera亚种Tada矿源基因型（W302）进行基因组组装优化。经5轮强制自交后，该材料的基因组杂合度降至0.04%，为后续组装工作提供了便利条件。本次组装最终覆盖预估基因组大小的196 Mb（约78%），Scaffold N50长度达到712 kb。为验证组装与注释结果的准确性，本研究将盐芥Tada矿源基因型的基因组与近缘物种拟南芥（Arabidopsis lyrata）已发表的高质量参考基因组进行共线性比对分析。为进一步验证组装质量，本研究还利用已发表的欧洲盐芥序列作为参照，对重金属ATP酶4（HEAVY METAL ATPASE4, HMA4）与金属耐受蛋白1（METAL TOLERANCE PROTEIN1, MTP1）区域开展共线性与系统发育分析。本研究在单个Scaffold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的关键功能基因。本次基因组组装将为盐芥以及由拟南芥（A. lyrata）与盐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提供重要支撑。