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为探索适应不同生境基质植物基因组特征变异规律，本研究以生长在喀斯特石灰岩上特有种广西天葵(Semiaquilegia guangxiensis)和与之近缘且主要生长在泥土上的广布种天葵(Semiaquilegia adoxoides)为研究对象，利用流式细胞术和基于二代测序的基因组Survey分析，评估基因组大小、杂合率、重复序列、 GC含量和倍性，比较和分析基因组特征差异。流式细胞术预估广西天葵和天葵的基因组大小分别为392.12 Mb、 337.68 Mb。K-mer分析预估两者基因组大小分别为390.68 Mb、341.12 Mb,杂合率分别为0.54%、 0.08%,重复序列分别为52.40%、 47.70%,预测两者均为二倍体。基因组初步组装得到两者基因组大小分别为311.62 Mb、 264.24 Mb, GC含量分别为36.47%、 36.34%,经BUSCO评估组装完整性相对较好。以上结果表明，专性生长在喀斯特石灰岩的广西天葵的基因组大小、杂合度、重复序列均高于分布广泛的天葵。对基因组进行重复序列注释和功能分析显示，广西天葵的重复序列和转座子比例均比天葵高，广西天葵重复序列功能注释到了氧化还原、能量代谢、次生代谢物合成、调控Ca2+、细胞壁合成等条目，这可能与其适应喀斯特生境有关。本研究为天葵属植物的全基因组测序、组装和精细图谱绘制进而解析适应不同生境的分子机理奠定基础，也为资源保护和开发利用提供参考。
Abstract：To explore the rule of genome characteristic variations of plants adapted to different habitats, in this study, we used flow cytometry and genome survey analyses based on second-generation sequencing to assess the genome sizes, heterozygosities, repetitive sequences, GC contents, and genome ploidies of the limestone Karst endemic species Semiaquilegia guangxiensis and its cogeneric and loam soil colonizer S. adoxoides and compared and analyzed differences in genomic features. The results showed that the genome sizes of S. guangxiensis and S. adoxoides predicted by flow cytometry were 392.12 Mb and 337.68 Mb, respectively. The K-mer analyses predicted that the genome sizes were 390.68 Mb and 341.12 Mb, respectively, with heterozygosity ratios of 0.54% and 0.08%, and repetitive sequences ratios of 52.40% and 47.70%, respectively, and both species were diploid. The preliminary assembly yielded 311.62 Mb and 264.24 Mb genomes for S. guangxiensis and S. adoxoides, with GC contents of 36.47% and 36.34%, respectively, and the assembly integrity assessed by BUSCO was relatively high. Semiaquilegia guangxiensis endemic in limestone habitats had larger genome size, higher heterozygosity and more repetitive sequences than the widespread S. adoxoides. Repetitive sequence annotation and functional analysis showed that the proportions of repeat sequences and transposons were higher in S. guangxiensis than in S. adoxoides, and the repetitive sequence function of S. guangxiensis was annotated to the entries of redox, energy metabolism, synthesis of secondary metabolites, regulation of Ca2+, and cell wall synthesis, which may be related to its adaptation to Karst habitats. The results of this study lay a foundation for whole genome sequencing, assembly and fine mapping of Semiaquilegia and also provide a reference for the conservation and development or application of the resources.
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基本信息:
DOI：10.13417/j.gab.044.000355
中图分类号:Q943.2
引用信息:
[1]莫晓芫,张强,黄夕洋,等.适应喀斯特与非喀斯特生境的两种天葵属植物的基因组特征研究[J].基因组学与应用生物学,2025,44(04):355-369.DOI:10.13417/j.gab.044.000355.
基金信息:
国家自然科学基金项目(32260045); 广西自然科学基金项目(2022GXNSFBA035450); 广西喀斯特植物保育与恢复生态学重点实验室项目(22-035-26)共同资助
2025-04-25
2025-04-25