PEG和NaCl胁迫下毛竹萌发种子中环状RNA特征及其表达研究

doi:10.12302/j.issn.1000-2006.202204063

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南京林业大学学报（自然科学版） ›› 2023, Vol. 47 ›› Issue (6): 17-24.doi: 10.12302/j.issn.1000-2006.202204063

所属专题： “攥紧中国种子”视域下的中国林草种业研究专题Ⅱ

• 专题报道Ⅰ：“攥紧中国种子”视域下的中国林草种业研究专题Ⅱ（执行主编施季森李维林） • 上一篇下一篇

PEG和NaCl胁迫下毛竹萌发种子中环状RNA特征及其表达研究

王晓静¹^,²(), 王涛³, 杨凯⁴, 李潞滨¹^,^*()

1.中国林业科学研究院林业研究所,林木遗传育种国家重点实验室,国家林业和草原局林木培育重点实验室, 北京 100091
2.运城学院,山西运城 044011
3.北京植物园,北京市花卉园艺工程技术研究中心/城乡生态环境北京实验室,北京 100093
4.北京农学院植物科学与技术学院,北京 100096

收稿日期:2022-04-27 修回日期:2022-06-27 出版日期:2023-11-30 发布日期:2023-11-23
通讯作者: *李潞滨(lilubin@126.com),研究员。
基金资助:
中国林业科学研究院中央级公益性科研院所基本科研业务费专项资金(CAFYBB2017ZY005);优秀博士来晋科研专项(QZX2023001)

Expressional profiling of circRNAs under PEG and NaCl stresses in germinated moso bamboo seeds

WANG Xiaojing¹^,²(), WANG Tao³, YANG Kai⁴, LI Lubin¹^,^*()

1. State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2. Yuncheng University, Yuncheng 044011, China
3. Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing 100093, China
4. College of Plant Science and Technology, Beijing Agriculture University, Beijing 100096, China

Received:2022-04-27 Revised:2022-06-27 Online:2023-11-30 Published:2023-11-23

摘要/Abstract

摘要：

【目的】环状RNA(circRNAs)是一类由转录本反向可变剪接产生的内源非编码RNA,在植物生长发育过程中具有重要作用。通过鉴定毛竹(Phyllostachys edulis)萌发期种子中的circRNAs,探究其在干旱和盐胁迫条件下的表达,为深入开展非生物胁迫条件下竹类植物种子萌发的分子调控机制提供基础。【方法】分别使用聚乙二醇(PEG)和NaCl模拟干旱和盐胁迫,构建H₂O、10%(质量分数,下同)PEG、15% PEG、50 mmol/L NaCl和100 mmol/L NaCl处理下毛竹种皮破裂阶段种子的链特异性文库,通过高通量测序和生物信息学分析揭示样本中的circRNAs及其表达谱。【结果】所有样本中共鉴定了1 446个circRNAs,76.34%的circRNAs来源于外显子区;不同处理下毛竹萌发种子中表达量最高的circRNA分别为plant_circ_0001703、plant_circ_0001728、plant_circ_0000358、plant_circ_0001236和plant_circ_0001728;与对照相比,524、505、467和474个circRNAs在4个胁迫处理下萌发的种子中显著差异表达;差异表达circRNAs的源基因显著富集在不同的GO条目和KEGG途径中。【结论】1 446个circRNAs能够在毛竹萌发期种子中表达,其中有1 056个circRNAs在种子萌发阶段响应了PEG或NaCl胁迫;作用于酸酐的水解酶活性和鞘脂代谢途径的基因可能对circRNAs调控PEG或NaCl胁迫下的毛竹种子萌发有重要意义。

关键词: 毛竹, 种子萌发, 聚乙二醇(PEG), NaCl, circRNAs

Abstract:

【Objective】 Circular RNAs (circRNAs) are a class of endogenous non-coding RNA produced by reverse alternative splicing of transcripts, which play crucial roles in plant growth and development. This study aimed to identify circRNAs in germinated seeds of moso bamboo (Phyllostachys edulis), and investigate their expression under drought and salt stress conditions, providing a foundation for exploring the molecular regulation mechanism of bamboo seed germination under abiotic stress resistance. 【Method】 polyethylene glycol (PEG) 6000 and NaCl were used to simulate drought and salt stress, respectively. The strand specific libraries were constructed for moso bamboo seeds samples at the seed coat rupture stage under treatments of H₂O, 10% (mass fraction) PEG, 15% PEG, 50 and 100 mol/L NaCl. High throughout sequencing and biological information analysis were used to identify and analysis the expressional pattern of circRNAs. 【Result】 A total of 1 446 circRNAs were identified in all samples, with 76.34% of circRNAs originating from exon region; The circRNAs with the highest expression levels in bamboo germinating seeds under different treatments were identified as plant_ circ_ 0001703, plant_ circ_ 0001728, plant_ circ_ 0000358, plant_ circ_ 0001236 and plant_ circ_ 0001728;Compared with control, 524, 505, 467 and 474 circRNAs were significantly differentially expressed in germinating seeds under the four stress treatments. The original genes of differentially expressed circRNAs were significantly enriched in various GO and KEGG pathways. 【Conclusion】 A total of 1 446 circRNAs were found to be expressed in moso bamboo germinating seeds, with 1 056 circRNAs responding to drought or salinity stresses during seed germination. Genes involved in acylhydrolase enzyme activity and sphingolipid metabolism pathways may play a crucial role in regulating bamboo seed germination under PEG or NaCl stress conditions.

Key words: moso bamboo, germination, polyethylese glycol (PEG), NaCl, circRNAs

中图分类号:

S795

王晓静,王涛,杨凯,等. PEG和NaCl胁迫下毛竹萌发种子中环状RNA特征及其表达研究[J]. 南京林业大学学报（自然科学版）, 2023, 47(6): 17-24.

WANG Xiaojing, WANG Tao, YANG Kai, LI Lubin. Expressional profiling of circRNAs under PEG and NaCl stresses in germinated moso bamboo seeds[J].Journal of Nanjing Forestry University (Natural Science Edition), 2023, 47(6): 17-24.DOI: 10.12302/j.issn.1000-2006.202204063.

图/表 7

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样品 sample	原始读序对数 raw reads pairs	过滤后读序对数 clean reads pairs	Q20/%	Q30/%	GC含量/% GC content	clean reads比对率/% mapping rate of clean reads
A1	53 299 336	53 115 622	98.9;98.4	96.6;95.3	52.5;53.4	82.16
B1	59 263 271	58 962 390	98.5;98.1	95.8;94.5	53.1;53.7	83.56
C1	51 634 439	51 456 574	98.8;98.4	96.5;95.3	52.4;53.2	84.98
D1	51 121 342	50 943 632	98.8;98.4	96.6;95.2	52.6;53.4	77.70
E1	51 241 315	51 068 350	98.8;98.5	96.5;95.4	53.0;53.7	81.93

PEG和NaCl胁迫下毛竹萌发种子中环状RNA特征及其表达研究

Expressional profiling of circRNAs under PEG and NaCl stresses in germinated moso bamboo seeds

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