小桐子XTH基因家族和与之互作的miRNAs的全基因组鉴定及其在低温适应中的作用

doi:10.13560/j.cnki.biotech.bull.1985.2022-0746

摘要/Abstract

摘要：

小桐子（Jatropha curcas L.）是极具开发潜力的多用途能源植物，也是喜温冷敏植物，低温严重影响其生长和开发利用。已知木葡聚糖内转糖苷酶/水解酶（XTH）作为细胞壁的修饰酶参与植物对逆境胁迫的响应与适应。前期研究表明12℃冷锻炼可显著提高小桐子抗冷性，而XTH基因对冷锻炼过程高响应。本文基于小桐子低温锻炼期间的转录组、miRNA组和降解组数据，在全基因组层面上对小桐子XTH基因家族进行了鉴定、生物信息学分析、表达谱分析及互作miRNAs的鉴定和分析。结果表明，小桐子中鉴定到XTH基因家族成员29个，编码269-341个氨基酸，其蛋白主要定位于细胞壁，结构均具有Glyco_hyho_16和XET_C结构域以及保守位点ExDxE。29个家族成员可分为3个组别，定位于9条染色体上，其中存在8对基因重复事件。对小桐子植株不同器官、低温锻炼过程及干旱和盐胁迫下的表达谱及RT-qPCR分析显示，该基因家族在不同情况下各成员存在显著的差异化表达模式，表明该基因家族不同成员的作用不尽相同。对降解组和miRNA组测序数据分析结果表明，68个miRNAs靶向调控JcXTH基因家族中的26个成员；选取低温锻炼下表达显著的miRNAs进行表达谱分析，并与其靶向的JcXTHs的基因表达进行相关性分析，显示二者之间呈现显著的负相关，表明在低温锻炼下miRNAs负调控JcXTHs基因的表达。研究结果有助于解析小桐子JcXTH基因家族的功能，以及靶向该家族基因的miRNAs与JcXTH基因互作如何来参与小桐子对低温胁迫的适应，从而为后续通过分子育种改良小桐子抗冷性提供参考。

关键词: 小桐子, XTH基因家族, miRNAs, 互作, 低温适应

Abstract:

Jatropha curcas L. has been widely considered as a promising and multi-purpose energy plant, also a kind of thermophilic chilling-sensitive plants, and low temperature severely affects their growth, development and utilization. It is known that xyloglucan endotransglucosylase/hydrolases（XTH）act as cell wall modifying enzymes and are involved in response and adaptation of plants to stresses. The previous work showed that chill-hardening at 12℃ significantly enhanced chilling resistance of J. curcas plants, and XTH genes demonstrated high-response to the chill-hardening. In the present study, genome-wide identification, bioinformatics analysis, expression profile analysis of XTH gene family, and identification and analysis of their interacting miRNAs were performed based on the obtained data of transcriptome, miRNAome and degradome of J. curcas during the chill-hardening. The results showed that 29 members of the XTH gene family were identified in J. curcas, encoding 269 to 341 amino acids, their proteins were mainly located to cell walls, and contained Glyco_hyho_16 and XET_C domains and the conserved site ExDxE. The 29 members of JcXTH family could be divided into three groups, located on nine chromosomes, and there were 8 pairs of gene duplication events. Expression profiling and RT-qPCR analysis demonstrated there were significantly differential expression patterns in different organs of J. curcas plants and under chilling-hardening, drought and salt stresses, implying that there were differential roles in various members of the XTH gene family. Analysis of sequencing data of miRNAome and degradome revealed that 68 miRNAs were found to target 26 members of JcXTH family, and analysis of expression profile and their correlation of these miRNAs and the targeting JcXTH genes highly responsive to the chill-hardening demonstrated a totally negatively regulated relationship, indicating these miRNAs were involved in a negative regulation of JcXTH gene expression. These results will be conducive to elucidating the functions of JcXTH gene family and how the interaction between the miRNAs and the JcXTH genes targeted to was involved in adaptation of J. curcas to low temperature stress, which will provide useful reference for further molecular breeding to improve chilling resistance in J. curcas.

Key words: Jatropha curcas, XTH gene family, miRNAs, interaction, low temperature adaptation

吕宇婧, 吴丹丹, 孔春艳, 杨宇, 龚明. 小桐子XTH基因家族和与之互作的miRNAs的全基因组鉴定及其在低温适应中的作用[J]. 生物技术通报, 2023, 39(2): 147-160.

LV Yu-jing, WU Dan-dan, KONG Chun-yan, YANG Yu, GONG Ming. Genome-wide Identification of XTH Gene Family and Their Interacting miRNAs and Possible Roles in Low Temperature Adaptation in Jatropha curcas L.[J]. Biotechnology Bulletin, 2023, 39(2): 147-160.

图/表 12

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引物名称Primer name	引物序列Primer sequence（5'-3'）
JcXTH2-F	GAGAGCAACAATTCCACCTTTG
JcXTH2-R	GGGTAAGGAACACCGTTTGA
JcXTH3-F	CTCCCTTCACTGCTTCTTACAG
JcXTH3-R	CACCCATTTGAGCCTCTCTT
JcXTH18-F	CTACCAGGGAATACCACACTTAC
JcXTH18-R	CGTTCCACAGGCTTGAGTATAA
JcXTH19-F	GTGCACAAGAACAATGGAGAAC
JcXTH19-R	TGACAACCATCGACGCTAAA
JcXTH23-F	GCAACAAGAGGTGGACTAGAA
JcXTH23-R	CATGGCACTTAGGGCTTGATA
JcXTH27-F	TACTGTTGGGCGCGATAATG
JcXTH27-R	CCAGACCCAGAAACCCTATCTA
GAPDH-F	TGAAGGACTGGAGAGGTGGAAGAGC
GAPDH-R	ATCAACAGTTGGAACACGGAAAGCC

引物名称Primer name	引物序列Primer sequence（5'-3'）
JcXTH2-F	GAGAGCAACAATTCCACCTTTG
JcXTH2-R	GGGTAAGGAACACCGTTTGA
JcXTH3-F	CTCCCTTCACTGCTTCTTACAG
JcXTH3-R	CACCCATTTGAGCCTCTCTT
JcXTH18-F	CTACCAGGGAATACCACACTTAC
JcXTH18-R	CGTTCCACAGGCTTGAGTATAA
JcXTH19-F	GTGCACAAGAACAATGGAGAAC
JcXTH19-R	TGACAACCATCGACGCTAAA
JcXTH23-F	GCAACAAGAGGTGGACTAGAA
JcXTH23-R	CATGGCACTTAGGGCTTGATA
JcXTH27-F	TACTGTTGGGCGCGATAATG
JcXTH27-R	CCAGACCCAGAAACCCTATCTA
GAPDH-F	TGAAGGACTGGAGAGGTGGAAGAGC
GAPDH-R	ATCAACAGTTGGAACACGGAAAGCC

基因名称Gene name	基因ID Gene ID	氨基酸数目 Number of amino acids/aa	等电点Isoelectric point	分子量 Molecular weight/kD	亲水性平均值 GRAVY	亚细胞定位 Subcellular localization
JcXTH1	XM_012218696.1	285	6.42	32.36735	-0.394	细胞壁, 细胞质
JcXTH2	XM_012218694.1	269	9.04	30.94703	-0.438	细胞壁, 细胞质
JcXTH3	XM_012218698.1	286	6.14	32.08499	-0.319	细胞壁, 细胞质
JcXTH4	XM_012218697.1	286	5.47	32.20504	-0.353	细胞壁, 细胞质
JcXTH5	XM_012218699.1	283	5.21	31.86363	-0.405	细胞壁, 细胞质
JcXTH6	XM_012218701.1	283	5.1	31.8406	-0.353	细胞壁, 细胞质
JcXTH7	XM_012218700.1	283	5.18	31.72839	-0.367	细胞壁, 细胞质
JcXTH8	XM_012210833.1	283	5.79	31.90475	-0.296	细胞壁, 细胞质
JcXTH9	XM_012218702.1	299	5.43	34.08454	-0.219	细胞壁, 细胞质
JcXTH10	XM_012210835.1	279	7.61	31.34916	-0.36	细胞壁, 细胞质
JcXTH11	XM_012222502.1	288	8.78	32.76008	-0.301	细胞壁, 细胞质
JcXTH12	XM_012227056.1	294	9.05	33.9776	-0.386	细胞壁
JcXTH13	XM_012209320.1	293	6.64	32.91467	-0.514	细胞壁
JcXTH14	XM_012216981.1	323	6.76	36.95264	-0.393	细胞壁
JcXTH15	XM_012225387.1	341	8.73	39.63884	-0.51	细胞壁
JcXTH16	XM_012229959.1	311	6.41	34.99533	-0.326	细胞壁
JcXTH17	XM_012233283.1	293	8.45	34.01056	-0.452	细胞壁, 细胞质
JcXTH18	XM_012212020.1	293	6.99	34.10647	-0.439	细胞壁, 细胞质
JcXTH19	XM_012236012.1	299	5	34.8449	-0.6	细胞壁
JcXTH20	XM_012218715.1	269	6.31	30.87093	-0.361	细胞壁
JcXTH21	XM_012230444.1	284	6.44	32.68983	-0.361	细胞壁
JcXTH22	XM_012215879.1	293	4.88	32.97573	-0.353	细胞壁
JcXTH23	XM_012224087.1	292	6.7	33.62413	-0.298	细胞壁
JcXTH24	XM_012223597.1	288	5.37	32.77481	-0.297	细胞壁
JcXTH25	XM_012217377.1	294	8.89	34.70349	-0.382	细胞壁
JcXTH26	XM_012221356.1	291	8.51	33.28685	-0.225	细胞壁
JcXTH27	XM_012223052.1	277	8.82	31.58769	-0.288	细胞壁, 细胞质
JcXTH28	XM_012219356.1	291	8.57	33.20157	-0.282	细胞壁, 细胞质
JcXTH29	XM_012237054.1	288	9.03	32.9001	-0.427	细胞壁

基因名称Gene name	基因ID Gene ID	氨基酸数目 Number of amino acids/aa	等电点Isoelectric point	分子量 Molecular weight/kD	亲水性平均值 GRAVY	亚细胞定位 Subcellular localization
JcXTH1	XM_012218696.1	285	6.42	32.36735	-0.394	细胞壁, 细胞质
JcXTH2	XM_012218694.1	269	9.04	30.94703	-0.438	细胞壁, 细胞质
JcXTH3	XM_012218698.1	286	6.14	32.08499	-0.319	细胞壁, 细胞质
JcXTH4	XM_012218697.1	286	5.47	32.20504	-0.353	细胞壁, 细胞质
JcXTH5	XM_012218699.1	283	5.21	31.86363	-0.405	细胞壁, 细胞质
JcXTH6	XM_012218701.1	283	5.1	31.8406	-0.353	细胞壁, 细胞质
JcXTH7	XM_012218700.1	283	5.18	31.72839	-0.367	细胞壁, 细胞质
JcXTH8	XM_012210833.1	283	5.79	31.90475	-0.296	细胞壁, 细胞质
JcXTH9	XM_012218702.1	299	5.43	34.08454	-0.219	细胞壁, 细胞质
JcXTH10	XM_012210835.1	279	7.61	31.34916	-0.36	细胞壁, 细胞质
JcXTH11	XM_012222502.1	288	8.78	32.76008	-0.301	细胞壁, 细胞质
JcXTH12	XM_012227056.1	294	9.05	33.9776	-0.386	细胞壁
JcXTH13	XM_012209320.1	293	6.64	32.91467	-0.514	细胞壁
JcXTH14	XM_012216981.1	323	6.76	36.95264	-0.393	细胞壁
JcXTH15	XM_012225387.1	341	8.73	39.63884	-0.51	细胞壁
JcXTH16	XM_012229959.1	311	6.41	34.99533	-0.326	细胞壁
JcXTH17	XM_012233283.1	293	8.45	34.01056	-0.452	细胞壁, 细胞质
JcXTH18	XM_012212020.1	293	6.99	34.10647	-0.439	细胞壁, 细胞质
JcXTH19	XM_012236012.1	299	5	34.8449	-0.6	细胞壁
JcXTH20	XM_012218715.1	269	6.31	30.87093	-0.361	细胞壁
JcXTH21	XM_012230444.1	284	6.44	32.68983	-0.361	细胞壁
JcXTH22	XM_012215879.1	293	4.88	32.97573	-0.353	细胞壁
JcXTH23	XM_012224087.1	292	6.7	33.62413	-0.298	细胞壁
JcXTH24	XM_012223597.1	288	5.37	32.77481	-0.297	细胞壁
JcXTH25	XM_012217377.1	294	8.89	34.70349	-0.382	细胞壁
JcXTH26	XM_012221356.1	291	8.51	33.28685	-0.225	细胞壁
JcXTH27	XM_012223052.1	277	8.82	31.58769	-0.288	细胞壁, 细胞质
JcXTH28	XM_012219356.1	291	8.57	33.20157	-0.282	细胞壁, 细胞质
JcXTH29	XM_012237054.1	288	9.03	32.9001	-0.427	细胞壁