Abstract：
Watermelon, Citrullus lanatus, is the world\'s third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.
摘要：
西瓜,柠檬草，是世界第三大水果作物。具有缺口的参考基因组和狭窄的遗传基础阻碍了西瓜的功能基因组学和遗传改良。这里,我们通过结合高覆盖率和准确的长读数测序数据和多种组装策略,报告了优质西瓜自交系G42的端粒至端粒缺口无基因组的组装.所有11条染色体都组装成单重叠群假分子，没有间隙，代表迄今为止最高的完整性和装配质量。G42参考基因组长度为369.321.829bp，包含24.205个预测的蛋白质编码基因，具有所有22个端粒和11个着丝粒的特征。此外，我们建立了花粉-EMS诱变方案，并从G42中获得了200,000多个M1种子。在采样池中，48个单基因表型突变，从具有形态变化的223个M1和78个M2突变体中选择，得到确认。平均突变密度为每株M1植物1个SNP/1.69Mb和1个indel/4.55Mb，每株M2植物1个SNP/1.08Mb和1个indel/6.25Mb。利用无缺口的G42基因组，来自M1和M2家族的32个植物的8039个突变被鉴定为100%的准确性，而使用97103v2参考基因组鉴定的随机选择的突变中只有25％可以得到证实。利用这个文库和无缺口基因组，确定了两个负责延长果实形状和雄性不育（ClMS1）的基因，两者都是由从G到A的单个碱基变化引起的。经过验证的无缺口基因组及其EMS突变文库为西瓜的功能基因组学和遗传改良提供了宝贵的资源。
