Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.

物种水平的基因组处于动态变化之中，包含所有个体共有的核心基因（core），以及仅存在于部分个体中的附属基因（dispensable），二者共同构成泛基因组（pan-genome）。本研究对503个玉米（Zea mays）自交系的幼苗RNA开展转录组测序，以解析玉米泛基因组（pan-genome），共鉴定得到8681个代表性转录组装序列（representative transcript assemblies，RTAs），其中16.4%在所有自交系中均有表达，82.7%仅在部分自交系中表达。值得注意的是，通过连锁不平衡作图（linkage disequilibrium mapping）分析，76.7%携带至少一个单核苷酸多态性（single nucleotide polymorphism，SNP）的RTAs可被定位至单个遗传位点，且这些位点主要分布于基因组的非着丝粒区域。对RTAs开展逐步迭代聚类分析后发现，基于本研究使用的基因型材料群体，玉米基因组的转录组基因集合已趋于饱和；在此种质资源基础上进一步开展幼苗RNA测序，新发现的转录序列将极为有限。基于SNP与泛基因组中转本丰度的全基因组关联分析（genome-wide association studies），本研究揭示了与幼龄期向成年营养生长期、以及营养生长期向生殖生长期发育转换时间相关的遗传位点，这两类性状对于物种的适合度与适应性均具有重要意义。本研究阐明了玉米泛基因组的动态特性，并证实物种的大量遗传变异可能存在于单一参考基因组之外。