亚洲棉短纤维发育相关长链非编码RNA的鉴定及表达

doi:10.3864/j.issn.0578-1752.2023.23.002

中国农业科学 ›› 2023, Vol. 56 ›› Issue (23): 4565-4584.doi: 10.3864/j.issn.0578-1752.2023.23.002

亚洲棉短纤维发育相关长链非编码RNA的鉴定及表达

王晓阳¹(), 彭振¹^,², 邢爱双¹, 赵盈睿¹, 马欣丽¹, 刘方¹^,²(), 杜雄明¹^,²(), 何守朴¹^,²()

¹ 中国农业科学院棉花研究所/棉花生物育种与综合利用全国重点实验室，河南安阳 455000
² 郑州大学农学院/棉花生物育种与综合利用全国重点实验室郑州基地，郑州 450001

收稿日期:2022-12-30 接受日期:2023-03-16 出版日期:2023-12-04 发布日期:2023-12-04
通信作者:
何守朴，E-mail：heshoupu@caas.cn。
何守朴，E-mail：heshoupu@caas.cn。
杜雄明，E-mail：dxm630723@163.com。
刘方，E-mail：liufcri@163.com
联系方式: 王晓阳，E-mail：wangxiaoyang198806@126.com。
基金资助:
国家自然科学基金(32201875)

Identification and Expression Analysis of Fuzz Fiber Development Related Long Noncoding RNAs in Gossypium arboreum

WANG XiaoYang¹(), PENG Zhen¹^,², XING AiShuang¹, ZHAO YingRui¹, MA XinLi¹, LIU Fang¹^,²(), DU XiongMing¹^,²(), HE ShouPu¹^,²()

¹ Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Biological Breeding and Comprehensive Utilization, Anyang 455000, Henan
² School of Agricultural Sciences, Zhengzhou University/Zhengzhou Research Base, National Key Laboratory of Cotton Biological Breeding and Comprehensive Utilization, Zhengzhou 450001

Received:2022-12-30 Accepted:2023-03-16 Published:2023-12-04 Online:2023-12-04

摘要/Abstract

摘要：

【目的】长链非编码RNA（long non-coding RNAs，lncRNAs）是一类无蛋白质编码能力，但参与许多重要生命活动调控过程的长度大于200 nt的RNA。通过对亚洲棉无短纤维突变体（GA0149）和野生型（GA0146）纤维发育早期的转录组数据进行分析，挖掘调控短纤维发育的lncRNA，并明确其调控网络，为进一步解析棉花纤维发育机制奠定基础。【方法】选择GA0146和GA0149 2个材料在开花后当天（0 DPA）及花后3 d（3 DPA）、5 d（5 DPA）和8 d（8 DPA）的胚珠和纤维为材料进行转录组测序。鉴定lncRNA并预测其调控的靶基因；通过mRNA和lncRNA的差异表达分析，比较2个材料在不同纤维发育时期的差异。进一步利用KOBAS软件预测对差异lncRNA的靶基因进行富集分析并预测其参与的生物过程；最后通过实时荧光定量（RT-qPCR）技术对25个差异表达的lncRNA转录组数据进行验证。【结果】共鉴定获得15 339个lncRNA，其中11 595个lncRNA位于基因间区，包括2 428个反义lncRNA、350个内含子lncRNA及966个正义lncRNA。共有1 932个差异表达lncRNA（DE-lncRNA），它们所对应的8 134个靶基因中，有788个为差异表达基因（DE-mRNA）。KEGG代谢通路富集分析表明，DE-mRNA主要参与植物激素信号转导（plant hormone signal transduction）和内质网中蛋白质加工过程（protein processing in endoplasmic reticulum）。共表达调控网络分析显示，表达量差异比较显著的lncRNA（MSTRG.454250.3）和其所调控的靶基因表达趋势一致，仅在野生型（GA0146）短纤维发育早期胚珠中特异表达；而lncRNA（MSTRG.454261.4）与其调控的靶基因表达趋势相反，在突变体（GA0149）中的表达量显著高于野生型。RT-qPCR结果证实了转录组数据的真实性。【结论】鉴定了26个与亚洲棉短纤维发育相关的lncRNA，其通过调控植物激素信号转导途径相关的吲哚乙酸合成酶基因（Ga03G2421）和生长素响应蛋白基因（Ga05G1344）的表达而影响短纤维的发育。

关键词: 亚洲棉, 短纤维突变体, 长链非编码RNA, 调控网络, 荧光定量PCR

Abstract:

【Objective】Long non-coding RNAs(lncRNAs) are a group of RNA molecules longer than 200 bp with no protein coding capacity, which are involved in various biological regulatory processes. In this study, we aim to analyze the RNA-sequencing data of two Gossypium arboreum isogenic lines, a fuzzless mutant (GA0149) and its wildtype (GA0146), to identify the lncRNA involved in early fuzz fiber development, providing a foundation for investigation the mechanism of fiber development. 【Method】We collected 0 DPA, 3 DPA and 5 DPA ovule and 8 DPA ovule and fiber from the G. arboreum fuzzless mutant GA0149 and its isogenic line GA0146 with normal fuzz and lint fibers, were used for RNA-seq to identify lncRNA and predict their target genes. Differentially expressed mRNA (DE-mRNA) and lncRNA(DE-lncRNAs) between the samples were identified. The KOBAS software was used to predict the KEGG enrichment pathways which DE-lncRNAs targets were involved in. To ensure the quality of high-through sequencing, 25 DE-lncRNAs were selected for RT-qPCR detection. 【Result】We identified 15 339 lncRNA-encoding transcripts that 11 595 lncRNAs were located to intergenic regions, 2 428 lncRNAs were classified as antisense lncRNAs, 350 were categorized as intronic lncRNAs and 966 belonged to sense lncRNAs. Compared to mRNAs, lncRNAs in Asian cotton showed shorter exons and lower GC content. Most of lncRNAs had cis-regulatory effects on their neighboring mRNAs. We identified 1 932 differentially expressed (DE) lncRNAs, with 8 134 predicted DE-lncRNA target genes. Further analysis showed that 788 genes (mRNA) were differentially expressed (DE-genes) during four fiber development stages. KEGG enrichment pathways analysis showed that DE-target-mRNAs were mainly enriched in plant hormone signal transduction and protein processing in endoplasmic reticulum. Co-expression network analysis revealed that lncRNA (MSTRG.454250.3) and its associated target genes showed identical expression trends during four fuzz fiber development stages, while lncRNAs (MSTRG.454261.4) and its associated target genes showed contrary expression tendency, exhibiting dramatic higher expression in fuzzless GA0149 compared to wildtype GA0146. The results of RT-qPCR analysis confirmed the authenticity of our RNA-seq data.【Conclusion】A total of 26 specifically expressed lncRNAs were identified which related to cotton fuzz fiber development process. We further confirmed that these lncRNAs affected the fuzz fiber development by regulating the expression of indole-3-acetic acid-amido synthetase (Ga03G2421) and Auxin-responsive protein (Ga05G1344) in the plant hormone signal transduction pathway.

Key words: Gossypium arboreum, fuzzless mutant, long non-coding RNAs, regulation network, RT-qPCR

王晓阳, 彭振, 邢爱双, 赵盈睿, 马欣丽, 刘方, 杜雄明, 何守朴. 亚洲棉短纤维发育相关长链非编码RNA的鉴定及表达[J]. 中国农业科学, 2023, 56(23): 4565-4584.

WANG XiaoYang, PENG Zhen, XING AiShuang, ZHAO YingRui, MA XinLi, LIU Fang, DU XiongMing, HE ShouPu. Identification and Expression Analysis of Fuzz Fiber Development Related Long Noncoding RNAs in Gossypium arboreum[J]. Scientia Agricultura Sinica, 2023, 56(23): 4565-4584.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2023.23.002

https://www.chinaagrisci.com/CN/Y2023/V56/I23/4565

图/表 11

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表1

亚洲棉短纤维突变体（GA0149）和其野生型（GA0146）短纤维发育早期共有差异lncRNA及其表达量变化倍数"

lncRNA编号 lncRNA ID	0 DPA		3 DPA		5 DPA		8 DPA
lncRNA编号 lncRNA ID	log₂ (FC)	P	log₂ (FC)	P	log₂ (FC)	P	log₂ (FC)	P
MSTRG.218820.2	-11.47940	2.03E-09	-10.81080	2.43E-10	-10.95160	6.06E-12	-8.78711	0.001646
MSTRG.488434.1	-10.29570	0.001787	-10.80150	1.25E-07	-7.09785	0.029641	-9.14006	2.37E-10
MSTRG.418233.2	-10.05510	2.04E-07	-9.27025	8.9E-06	-8.75282	1.12E-05	-8.39458	8.77E-08
MSTRG.198809.4	-9.38133	4.29E-09	-9.26064	2.59E-11	-8.07549	6.41E-09	-7.21244	7.73E-06
MSTRG.16035.84	-9.31822	2.15E-10	-8.88159	5.08E-09	-7.31218	0.02019	-6.81111	0.021079
MSTRG.198809.3	-9.22472	4.5E-10	-9.210450	1.32E-11	-7.00735	2.36E-07	-7.83885	5.28E-07
MSTRG.285152.1	-9.21331	7.85E-12	-8.53242	2.5E-08	-7.79328	0.012844	-7.51993	7.56E-06
MSTRG.638435.2	-8.85124	3.69E-10	-9.54015	4.02E-11	-8.56096	4.4E-11	-7.08650	0.002833
MSTRG.295723.2	-8.52846	2.94E-10	-7.02797	0.024719	-6.23242	0.004987	-5.08612	0.029263
MSTRG.286961.2	-8.38087	2.18E-24	-8.53432	3.72E-16	-10.82810	1.07E-17	-7.77000	1.26E-06
MSTRG.454250.3	-8.10113	5.84E-06	-8.32650	8.26E-06	-8.38398	1.85E-09	-7.84265	2.73E-07
MSTRG.199201.1	-7.24116	3.73E-25	-8.99919	7.61E-16	-8.42043	8.79E-29	-8.60699	4.38E-12
MSTRG.454285.1	-7.23820	0.020715	-8.42005	0.006549	-8.41553	4.01E-11	-7.62117	9.89E-07
MSTRG.130836.1	-7.05155	0.002377	-5.18296	0.002243	-5.08014	0.000387	-6.37689	0.000862
MSTRG.295242.1	-7.03069	5.27E-08	-9.25794	3.11E-27	-8.35346	4.59E-24	-8.79585	1.68E-11
MSTRG.35965.5	-6.93155	6.82E-07	-6.56034	4.3E-06	-5.69637	0.000228	-5.22843	0.0079
MSTRG.638435.6	-6.85069	3.17E-05	-6.83353	9.67E-07	-7.21599	2.51E-07	-5.31159	0.005991
MSTRG.59999.2	-6.73057	3.36E-07	-7.29751	3.21E-05	-2.08447	0.00763	-6.51848	0.000256
MSTRG.286961.1	-6.69270	1.49E-45	-12.0248	1.42E-19	-11.82020	7.21E-22	-10.08520	1.62E-12
MSTRG.307567.4	-6.58285	2.63E-05	-3.82355	0.006515	-5.79779	0.009506	-5.85988	0.001595
MSTRG.295242.2	-6.51823	1.18E-07	-11.3313	6.44E-18	-10.83570	1.47E-17	-9.11979	3.32E-10
MSTRG.307567.7	-6.50366	0.003217	-5.55940	5.5E-05	-5.60794	0.001071	-5.06204	0.011061
MSTRG.638435.5	-6.43214	0.047701	-6.53292	0.041702	-7.32729	2.53E-05	-7.07537	0.000546
MSTRG.45779.2	-6.40744	1.35E-06	-7.32454	5.04E-06	-8.15858	2.7E-12	-9.53754	4.03E-11
MSTRG.437516.1	-6.27021	0.00106	-7.00719	1.43E-06	-3.65675	0.01951	-5.36611	0.011425
MSTRG.286961.3	-6.17207	1.08E-08	-10.49060	2.46E-15	-9.76975	1.43E-13	-7.22905	2.95E-05
MSTRG.307567.6	-6.11269	0.004939	-5.41955	0.000106	-4.61031	0.021236	-6.49860	7.95E-05
MSTRG.638435.1	-5.92618	3.08E-05	-10.27230	2.06E-15	-10.22560	5.46E-16	-10.40250	1.2E-13
MSTRG.488434.2	-5.66044	1.13E-06	-11.30660	1.98E-16	-10.63200	3.73E-06	-7.50133	1.21E-08
MSTRG.59999.3	-5.21799	0.000117	-8.14519	2.93E-10	-4.18506	0.020905	-5.03482	0.026929
MSTRG.454260.3	-4.22593	0.035659	-9.16324	4.04E-12	-9.68765	3.53E-12	-8.38584	7.65E-09
MSTRG.198938.1	-4.14982	0.048026	-4.50917	0.00658	-7.85626	0.010503	-7.97808	5.08E-07
MSTRG.32986.1	-4.03325	6.41E-10	-3.45234	0.001688	-3.50965	2.98E-05	-5.08295	0.01343
MSTRG.313969.1	-3.76582	0.005792	-2.32801	1.36E-10	-5.48056	0.000928	-3.64159	0.005345
MSTRG.313969.7	-3.72767	1.74E-09	-3.68611	1.11E-10	-6.04251	2.29E-08	-7.78886	4.99E-06
MSTRG.454260.46	-3.22958	6.5E-06	-1.58662	0.02249	-3.18568	0.00035	-4.42366	1.21E-05
MSTRG.441122.1	-2.82027	4.08E-12	-1.46639	0.005114	-2.79128	1.46E-09	-1.73590	0.036909
MSTRG.454261.4	1.20530	0.009535	1.36848	0.005267	1.25717	0.000401	2.28680	0.00043
MSTRG.439082.1	2.30096	6E-05	3.29579	0.002213	2.70368	6.84E-05	3.54630	0.005178
MSTRG.454256.1	2.34120	8.32E-10	2.45648	3.23E-10	1.78629	4.21E-05	2.13974	0.008473
MSTRG.283424.1	2.71551	1.59E-07	3.25732	1.26E-08	3.11617	9.7E-11	5.59313	0.000127
MSTRG.291781.2	3.85334	2.18E-19	4.13617	9.92E-15	4.37252	2.1E-25	2.40298	0.023372
MSTRG.620320.1	4.21095	0.00561	7.71574	3.77E-09	7.47394	3.76E-08	5.36623	0.007933
MSTRG.638095.1	4.34353	0.003476	4.77389	2.41E-06	4.21478	0.043987	5.81799	0.003952
MSTRG.577666.1	4.71471	2.92E-05	8.04445	2.98E-10	6.67361	7.94E-09	6.61542	1.09E-06
MSTRG.568994.33	5.33652	0.043708	6.71026	4.36E-05	6.73925	3.59E-06	7.12512	1.56E-05
MSTRG.454255.7	5.77743	2.29E-11	5.51520	5.15E-07	5.70722	3.82E-08	2.37151	0.042941
MSTRG.660507.1	5.95775	5.36E-05	6.33436	4.82E-05	5.28420	0.002924	5.26719	0.000406
MSTRG.283950.1	6.85484	5.52E-05	7.60915	8.14E-11	8.14048	1.62E-18	8.86202	2.19E-09
MSTRG.568994.15	7.00698	2.39E-07	7.28587	4.12E-08	7.55757	2.49E-08	6.03203	0.008367
MSTRG.568994.34	7.26201	4.32E-08	7.32716	3.98E-08	8.14198	1.25E-08	6.18129	0.013416
MSTRG.568994.17	7.34288	2.17E-08	7.70496	3.65E-09	7.52666	3.09E-08	6.38978	0.008836
MSTRG.621281.3	7.36016	4.83E-06	6.35723	0.000365	7.16863	1.65E-07	6.05174	0.000871
MSTRG.389122.7	7.39607	1.14E-07	7.27098	1.36E-06	7.48976	6.06E-07	6.82192	4.59E-06
MSTRG.163561.1	7.51752	0.019476	7.53834	7.59E-09	6.35119	0.010928	6.90695	0.018056
MSTRG.496256.3	7.56010	6.72E-07	7.21337	3.29E-07	6.89023	5.83E-06	4.28799	0.001424
MSTRG.306464.2	7.56122	2.97E-07	6.98605	8.63E-06	8.41529	6.49E-10	5.52123	0.005686
MSTRG.283950.2	8.42677	1.12E-09	8.25116	2.97E-08	8.26440	1.52E-10	7.63528	7.04E-07
MSTRG.585009.3	8.94799	4.09E-10	8.79452	2.74E-12	8.71795	7.13E-11	6.67564	0.00045
MSTRG.585009.2	9.30100	9.97E-14	7.95255	1.95E-08	8.70137	1.59E-11	7.51810	6.76E-06
MSTRG.621281.1	9.57909	1.07E-14	9.05022	1.53E-09	9.48013	1.24E-13	8.99004	1.65E-07
MSTRG.638094.1	9.96140	1.4E-15	9.03040	2.28E-11	8.75902	4.75E-11	7.99949	1.07E-07
MSTRG.454315.2	10.09066	2.07E-15	9.64703	2.42E-14	9.54303	2.13E-13	10.26427	2.8E-12
MSTRG.585009.1	10.94786	7.38E-19	11.23440	1.11E-19	8.90520	4.13E-21	11.11503	1.35E-15
MSTRG.198471.1	13.50563	3.23E-28	11.17626	2.17E-34	7.30601	3.33E-50	8.24918	1.16E-13

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基因ID Gene ID	基因注释 Gene annotation	基因 Gene	激素 Hormone	0 DPA	3 DPA	5 DPA	8 DPA
Ga01G2735	转录因子MYC4 Transcription factor MYC4	MYC4	JA	1.66929	1.35158	4.08489	0.49324
Ga02G1269	水杨酸相关蛋白Salicylic acid-related protein	PRP1	SA	0.83454	0.87131	0.41650	0.53005
Ga03G2608	生长素诱导蛋白X10A Auxin-induced protein X10A	AIP10A	IAA	2.23652	0.81687	1.29341	0.96182
Ga03G2421	吲哚乙酸合成酶 GH3.1 Probable indole-3-acetic acid-amido synthetase GH3.1	GH3.1	IAA	1.87383	1.10787	2.11783	0.99925
Ga05G0157	生长素响应蛋白IAA29 Auxin-responsive protein IAA29	IAA29	IAA	1.26487	0.82160	0.51501	0.49518
Ga05G0163	EIN3结合F盒蛋白1 EIN3-binding F-box protein 1	EBF1	ETH	0.93660	1.16611	3.60043	0.40549
Ga05G1344	生长素响应蛋白IAA16 Auxin-responsive protein IAA16	IAA16	IAA	1.49560	1.03839	2.27272	0.57805
Ga05G1988	生长素响应蛋白SAUR50 Auxin-responsive protein SAUR50	SAUR50	IAA	1.06233	0.76972	2.93240	0.34698
Ga07G1535	茉莉酸甲酯合成酶JAR1 Jasmonic acid-amido synthetase JAR1	GH3.5	JA	0.78397	1.26241	1.49571	0.36714
Ga07G0455	生长素响应蛋白IAA9 Auxin-responsive protein IAA9	IAA9	IAA	1.58434	0.75494	2.64841	0.31957
Ga08G2885	蛋白磷酸酶2C 77 Protein phosphatase 2C 77	ABI2	ABA	1.39957	1.33425	3.93469	0.43093
Ga09G2536	生长素诱导蛋白22D Auxin-induced protein 22D	AUX22D	IAA	1.55776	1.02316	2.61126	1.57910
Ga09G2537	生长素响应蛋白IAA14 Auxin-responsive protein IAA14	IAA14	IAA	1.04958	0.48203	0.43195	1.23456
Ga12G2846	赤霉素受体GID1B Gibberellin receptor GID1B	GID1B	GA	1.16381	1.79652	2.13160	0.42108

亚洲棉短纤维发育相关长链非编码RNA的鉴定及表达

Identification and Expression Analysis of Fuzz Fiber Development Related Long Noncoding RNAs in Gossypium arboreum

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