‘脆红李’及其早熟芽变全基因组重测序分析

doi:10.16420/j.issn.0513-353x.2023-0799

摘要/Abstract

摘要：

为揭示‘脆红李’早熟芽变形成的分子基础，采用高通量重测序技术对‘脆红李’及其早熟芽变材料进行了全基因组重测序，测序深度分别为19.40× 和22.82×，基因组覆盖度85%以上。与参考基因组相比，‘脆红李’及其早熟芽变分别检测到1 860 745和1 931 603个单核苷酸多态性点（SNP），419 134和444 892个小片段插入/缺失位点（InDel），其中发生在编码区的非同义突变位点分别为61 997个和63 498个。分析两者间的差异非同义突变，共引起2 391个基因变异。KEGG代谢通路富集分析发现，基因变异主要富集在真核生物核糖体生物发生、RNA运输、苯丙类生物合成、植物—病原体互作等途径上，此外在植物激素转导通路上共注释到12个变异基因。这些基因和其他相关基因变异后能影响其相应蛋白或酶的活性或特异性，从而导致生长发育过程发生变化，使‘脆红李’早熟芽变单株果实成熟期提前。

关键词: 李, 芽变, 早熟, 全基因组重测序

Abstract:

In order to reveal the molecular basis of formation of‘Cuihongli’plum’s early-ripening bud sport mutation，this study used high-throughput re-sequencing technology to resequence the whole genomes of‘Cuihongli’and its early-ripening bud sport mutation，with an average sequencing depth of 19.40× and 22.82×，with a genome coverage of over 85%. The results showed compared with the reference genome，1 860 745 and 1 931 603 single nucleotide polymorphisms（SNPs），419 134 and 444 892 small fragment insertion/deletion sites（InDels）were detected in‘Cuihongli’and its early-ripening bud sport mutation. There are 61 997 and 63 498 nonsynonymous mutations in the coding region，causing a total of 2 391 gene mutations. Metabolic pathway analysis（KEGG）indicated that these genetic variations were mainly involved in the pathways of Ribosome biogenesis in eukaryotes，RNA transport，phenylpropanoid biosynthesis and plant-pathogen interaction. In addition，12 variant genes were annotated with functions in the plant hormone signal transduction pathway. These genes and other related genes variations can affect the activity or specificity of their corresponding proteins or enzymes，leading to changes in the growth and development process，and advancing the mature period of‘Cuihongli’plum’s early-ripening single plant.

Key words: plum, bud sport mutation, early-ripening, whole genome re-sequencing

姚远, 邓利君, 胡娟, 唐晓雨, 王铁, 李航, 孙国超, 熊博, 廖玲, 汪志辉. ‘脆红李’及其早熟芽变全基因组重测序分析[J]. 园艺学报, 2024, 51(10): 2255-2266.

YAO Yuan, DENG Lijun, HU Juan, TANG Xiaoyu, WANG Tie, LI Hang, SUN Guochao, XIONG Bo, LIAO Ling, WANG Zhihui. Whole Genome Resequencing Analysis of‘Cuihongli’Plum and Its Early-Ripening Bud Sport Mutation[J]. Acta Horticulturae Sinica, 2024, 51(10): 2255-2266.

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参考文献 32

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样品 Sample	原始测序序列 Raw read	过滤后剩余序列 Clean read	过滤剩余序列/% Clean reads rate	含N > 5%的Reads/% Ns reads rate	Q30/%	GC含量/% GC content
脆红李 Cuihongli	40 671 358	39 919 834	98.15	0.23	87.48	38.26
早熟芽变 Early-ripening mutant	47 401 654	46 638 688	98.39	0.22	88.45	38.31

样品 Sample	原始测序序列 Raw read	过滤后剩余序列 Clean read	过滤剩余序列/% Clean reads rate	含N > 5%的Reads/% Ns reads rate	Q30/%	GC含量/% GC content
脆红李 Cuihongli	40 671 358	39 919 834	98.15	0.23	87.48	38.26
早熟芽变 Early-ripening mutant	47 401 654	46 638 688	98.39	0.22	88.45	38.31

样品 Sample	Clean bases	Mapped bases	Mapped rate/%	Mean depth/×	Coverage 1×/%	Coverage 4×/%
脆红李 Cuihongli	5 987 975 100	5 513 839 633	92.08	19.40	92.03	85.67
早熟芽变 Early-ripening mutant	6 995 803 200	6 489 148 161	92.76	22.82	92.30	86.83

样品 Sample	Clean bases	Mapped bases	Mapped rate/%	Mean depth/×	Coverage 1×/%	Coverage 4×/%
脆红李 Cuihongli	5 987 975 100	5 513 839 633	92.08	19.40	92.03	85.67
早熟芽变 Early-ripening mutant	6 995 803 200	6 489 148 161	92.76	22.82	92.30	86.83

类别 Category	脆红李 Cuihongli	早熟芽变 Early-ripening mutant	差异数 Difference
总数 Total	1 860 745	1 931 603	70 858
基因间区 Intergenic	1 045 098（56.17%）	1 093 864（56.63%）	48 766
基因上游 Gene upstream	167 118（8.98%）	172 580（8.93%）	5 462
基因下游 Gene downstream	129 169（6.94%）	132 864（6.88%）	3 695
外显子 Exon	118 505（6.37%）	121 031（6.27%）	2 526
内含子 Intron	296 906（15.96%）	304 915（15.79%）	8 009
UTR5′	24 210（1.30%）	24 746（1.28%）	536
UTR3′	45 125（2.43%）	45 988（2.38%）	863
剪切区域 Splicing	434（0.02%）	464（0.02%）	30
其他 Others	34 180（1.83%）	35 151（1.82%）	971