Untitled ItemA chromosome-scale genome assembly of Malus domestica, a multi-stress resistant and high-quality apple variety

<b>Background: </b>Hanfu apples have the advantages of cold resistance, drought resistance, and high yield, and they have become the main variety grown in the cool areas of Northeast, Northwest, and North China (40–42° N), which have an average temperature of -12 to -10 ℃ in January.<b></b> <b>Results: </b>Here, we proposed a chromosome-level Hanfu genome assembly using PacBio long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data. The total contig length was 628.99 Mb, and the N50 contig length was 1.25 Mb. The total scaffold length was 631.76 Mb, the N50 scaffold length was 36.18 Mb, and the genome mount rate was 99.18%. The Hanfu genome had a total of 39 617 genes, and we predicted the function for 38 816 (98.0%) of these. Repetitive sequences accounted for 54.29% of the genome. Evolutionary analysis showed that the differentiation time of apples and pears was approximately 8.9 Mya. Whole genome duplication (WGD) analysis revealed a γ event in Hanfu, which was a recent whole genome duplication when the 4dTv value was 0.075. By comparing and analyzing the genomic differences between Hanfu and the homozygous line HFTH1, three variation types were determined: single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants (SVs). We identified 605 species-specific gene families. Among these, 122 Hanfu gene families (including 814 genes) significantly expanded, while 421 gene families significantly contracted (including 1528 genes), and there are 61 candidate genes subject to positive selection. A significant expansion of genes involved in the MAPK signal transduction pathway, calcium-mediated signal transduction pathway, plant hormone signal transduction pathway, sugar metabolism pathway, and phloem development were found; this may explain the formation of ‘Hanfu’s’ unique phenotype. <b>Conclusions:</b> This high quality genome will help explain the formation mechanism of the unique phenotype of Hanfu. In addition, it can provide reference for the genetic improvement of apples and for breeding more varieties with high resistance and high quality.

<b>背景：</b>寒富苹果具备抗寒、抗旱与高产的优良特性，现已成为中国东北、西北及华北北纬40°至42°冷凉地区的主栽品种，该区域1月平均气温为-12℃至-10℃。<b>结果：</b>本研究结合PacBio长读长测序（PacBio long reads）、Illumina短读长测序（Illumina short reads）、10× Genomics连锁读长测序（10× Genomics linked reads）及Hi-C技术（Hi-C data），构建了染色体级别的寒富苹果基因组组装序列。该基因组总重叠群（contig）长度为628.99 Mb，重叠群N50长度为1.25 Mb；总支架序列（scaffold）长度为631.76 Mb，支架序列N50长度为36.18 Mb，基因组挂载率达99.18%。寒富苹果基因组共注释得到39617个蛋白编码基因，其中38816个（占比98.0%）完成了功能注释；重复序列占基因组总长度的54.29%。进化分析显示，苹果与梨的分化时间约为8.9百万年前（Mya）。全基因组复制（Whole Genome Duplication, WGD）分析发现，寒富苹果基因组存在一次γ复制事件，结合4倍简并同义替换率（4dTv）值为0.075可知，该事件属于近期全基因组复制事件。通过对比分析寒富苹果与纯合品系HFTH1的基因组差异，本研究鉴定出三类变异类型：单核苷酸多态性（single-nucleotide polymorphisms, SNPs）、插入/缺失（insertions/deletions, indels）及结构变异（structural variants, SVs）。本研究共鉴定得到605个寒富苹果物种特异性基因家族，其中122个基因家族（包含814个基因）发生显著扩张，421个基因家族（包含1528个基因）发生显著收缩，另有61个候选基因受到正向选择作用。研究发现，参与丝裂原活化蛋白激酶（MAPK）信号通路、钙介导信号通路、植物激素信号通路、糖代谢通路以及韧皮部发育的基因发生了显著扩张，这或可解释寒富苹果独特表型的形成机制。<b>结论：</b>本研究获得的高质量寒富苹果基因组，将有助于解析其独特表型的形成机制；同时可为苹果的遗传改良以及培育更多抗逆优质的苹果新品种提供重要参考依据。