Data Sheet 1_Transcriptome analysis reveals DNA repair–related clues associated with divergent leaf nuclear DNA diversity in Leymus chinensis.pdf

Intraorganismal genetic heterogeneity (IGH) arises from the accumulation of somatic mutations during plant growth. Although leaves of Leymus chinensis exhibit pronounced IGH, its molecular basis remains unclear. Under strictly controlled growth conditions, this study compared a wild population (LC-W) with the cultivated cultivar Zhongke No. 2 (LC-ZK2) to search for DNA repair–related clues associated with leaf nuclear DNA diversity. Genomic DNA amplification and Sanger sequencing of three nuclear loci (MCM7, PsaE, and PsaL) showed that, compared with LC-W, LC-ZK2 exhibited fewer polymorphic sites and lower haplotype diversity, indicating a more restricted leaf-scale sequence heterogeneity. De novo leaf transcriptome analysis identified 3,833 differentially expressed genes (DEGs; |log2FC| ≥ 1, FDR < 0.05; log2FC = log2[LC-W/LC-ZK2]). GO and KEGG analyses indicated that DEGs were significantly enriched in DNA damage response and DNA repair pathways, with particularly prominent enrichment of base excision repair (BER) and homologous recombination (HR). The BER scaffold gene XRCC1 plays an important role in these pathways and was significantly upregulated in LC-ZK2 (~2.6-fold), suggesting transcriptional differences in repair-related genes between the two materials. Further Sanger sequencing of the XRCC1 BRCT domain indicated that LC-ZK2 possessed a more concentrated haplotype spectrum and exhibited distinct amino acid substitution combinations, providing candidate sites for subsequent functional validation. Overall, this study links differences in nuclear DNA diversity with repair-associated transcriptomic signatures and provides an interpretive framework for understanding leaf-scale heterogeneity divergence in L. chinensis.

个体内遗传异质性（IGH）源于植物生长过程中体细胞突变的累积。尽管羊草（Leymus chinensis）的叶片存在显著的IGH现象，但其分子机制仍未明确。本研究在严格可控的生长条件下，将野生种群（LC-W）与栽培品种中科2号（LC-ZK2）进行对比，以探寻与叶片细胞核DNA多样性相关的DNA修复相关线索。对3个核基因座（MCM7、PsaE及PsaL）的基因组DNA扩增与桑格测序（Sanger sequencing）结果显示，相较于LC-W，LC-ZK2的多态性位点更少、单倍型多样性更低，表明其叶片尺度的序列异质性更为受限。叶片从头转录组分析共鉴定出3833个差异表达基因（DEGs；|log₂FC| ≥ 1，错误发现率（FDR）< 0.05；log₂FC = log₂[LC-W/LC-ZK2]）。基因本体（GO）与京都基因与基因组百科全书（KEGG）富集分析结果显示，DEGs显著富集于DNA损伤应答与DNA修复通路，其中碱基切除修复（BER）与同源重组（HR）的富集程度尤为显著。碱基切除修复通路的支架基因XRCC1在上述通路中发挥重要作用，且在LC-ZK2中显著上调（约2.6倍），表明两个材料间修复相关基因存在转录水平差异。对XRCC1的BRCT结构域的进一步桑格测序结果显示，LC-ZK2的单倍型谱更为集中，且存在独特的氨基酸替换组合，为后续的功能验证提供了候选位点。综上，本研究将细胞核DNA多样性差异与修复相关的转录组特征建立关联，为理解羊草（L. chinensis）叶片尺度异质性分化提供了阐释框架。