甘蔗割手密种LRRII-RLK基因家族演化和表达分析

doi:10.3724/SP.J.1006.2023.24180

作物学报 ›› 2023, Vol. 49 ›› Issue (7): 1769-1784.doi: 10.3724/SP.J.1006.2023.24180

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

甘蔗割手密种LRRII-RLK基因家族演化和表达分析

丁洪艳¹^,²(), 冯晓溪³, 汪柏宇², 张积森¹^,²^,^*()

¹广西大学农学院, 广西南宁 530004
²广西大学亚热带农业生物资源保护与利用国家重点实验室, 广西南宁 530004
³福建农林大学农学院, 福建福州 350002

收稿日期:2022-08-03 接受日期:2022-11-25 出版日期:2023-07-12 网络出版日期:2022-12-14
通讯作者: *张积森, E-mail: zjisen@126.com
作者简介:E-mail: hyding2020@163.com
基金资助:
本研究由国家重点研发计划项目(2021YFF1000100);广东省重点领域研发计划项目(2019B020238001)

Evolution and relative expression pattern of LRRII-RLK gene family in sugarcane Saccharum spontaneum

DING Hong-Yan¹^,²(), FENG Xiao-Xi³, WANG Bai-Yu², ZHANG Ji-Sen¹^,²^,^*()

¹College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
²State Key Laboratory of Conservation and Utilization of Agric-Biological Resources, Guangxi University, Nanning 530004, Guangxi, China
³College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China

Received:2022-08-03 Accepted:2022-11-25 Published:2023-07-12 Published online:2022-12-14
Contact: *E-mail: zjisen@126.com
Supported by:
The National Key Research and Development Program of China(2021YFF1000100);The Science and Technology Planting Project of Guangdong Province(2019B020238001)

摘要/Abstract

摘要：

LRRII-RLK是一种类受体激酶(receptor-like kinase, RLK), 该基因家族在植物中广泛存在, 在植物的生长发育和生物胁迫中发挥着重要的作用, 但目前在甘蔗中未见对该基因家族的系统鉴定和分析。本研究对甘蔗的LRRII-RLK基因进行分类, 并研究了其结构和功能。结合割手密种基因组和发育组织、叶片发育梯度、昼夜节律和生物胁迫反应转录组数据, 在甘蔗割手密种中共鉴定到27个LRRII-RLK基因, 分布在17条染色体上。系统进化分析发现, 它们分别属NIK、SERK和LRRII-C分支, 其中处于LRRII-C分支的SsLRRII-RLK基因出现了显著扩增。顺式元件分析显示, 它们的启动子共包含32类顺式元件, 其主要参与植物光反应、响应胁迫反应、调控植物激素和植物生长发育。这些基因共有35对共线性基因对, 具有多个保守基序, 主要通过片段复制的方式进行扩增, 且根据Ka/Ks比率发现, 它们在演化过程中经历了严格的纯化选择作用。此外, SsLRRII-RLK基因表达分析显示, 它们在甘蔗不同组织中表达量不同, 其中部分基因在昼夜不同时期表达量呈现差异, 这表明它们参与了植物生长和光合作用的调节。值得注意的是, SsLRRII-RLK基因的表达模式在不同病害(甘蔗梢腐病和花叶病)胁迫下呈现差异, 因此, 我们认为这些基因在病毒复制和发病机制过程中发挥作用。本研究结果有助于深入了解甘蔗LRRII-RLK基因的演化过程, 且为LRRII-RLK基因在甘蔗生长发育、光合作用以及在病害胁迫中的功能研究提供初步的理论基础。

关键词: 割手密种, LRRII-RLK基因, 转录组学, 基因表达分析, 演化分析

Abstract:

It is well-known that LRRII-RLK gene family widely exists in plants. These genes are receptor like kinase (RLK), which play a significant role in plant development and biological stress. Up till now, there is no systematic identification and analysis of the LRRII-RLK gene family in sugarcane. Here, we identified 27 LRRII-RLK genes in Saccharum spontaneum, which were distributed on 17 chromosomes. Phylogenetic tree showed the classification of these genes into three different branches including NIK, SERK, and LRRII-C. Furthermore, we observed the significant amplification in the LRRII-C branch. Next, we characterized the cis-regulatory elements, which identified 32 different types of cis elements in the gene promoters, primarily involved in light response, stress response, regulation of hormone mechanism, and plant growth. Interestingly, SsLRRII-RLK genes were detected to be conserved with 35 collinear gene pairs and multiple conserved motifs. These genes were mainly amplified by segmental replication and had undergone strict purification selection during the evolution, according to their K_a/K_s ratios. Furthermore, the relative expression level of SsLRRII-RLK genes varied in different tissues of sugarcane. Additionally, some genes expressed differently during distinct periods of day and night, suggesting that they were associated with plant growth regulation and photosynthesis. Noticeably, the relative expression pattern of SsLRRII-RLK genes varied significantly under different disease conditions (sugarcane pokkah boeng disease and mosaic disease). In conclusion, these genes might play a role in pathogenesis and viral replication. The results of this study are helpful to further understand the evolutionary process of LRRII-RLK gene in sugarcane. This data provides a preliminary theoretical basis for the functional study of LRRII-RLK gene during photosynthesis, growth and development, and disease conditions in sugarcane.

Key words: Saccharum spontaneum, LRRII-RLK genes, transcriptomics, gene expression analysis, phylogenetic analysis

丁洪艳, 冯晓溪, 汪柏宇, 张积森. 甘蔗割手密种LRRII-RLK基因家族演化和表达分析[J]. 作物学报, 2023, 49(7): 1769-1784.

DING Hong-Yan, FENG Xiao-Xi, WANG Bai-Yu, ZHANG Ji-Sen. Evolution and relative expression pattern of LRRII-RLK gene family in sugarcane Saccharum spontaneum[J]. Acta Agronomica Sinica, 2023, 49(7): 1769-1784.

图/表 13

表1

表2

甘蔗割手密种LRRII-RLK家族基因和编码蛋白基本信息"

基因编号 No. of genes	基因 Gene name	染色体 Chr.	氨基酸数 NA	分子量 MW (kD)	等电点 pI	不稳定系数 Instability index	平均疏水性 Grand average of hydropathicity	复制类型 Replication type
Sspon.01G0025910-4D	SsLRRII-RLK-1	1D	629	69.86	5.31	31.89	-0.130	4
Sspon.01G0025910-2B	SsLRRII-RLK-1-2	1B	384	41.90	6.83	30.59	0.105	4
Sspon.03G0036270-1B	SsLRRII-RLK-2	3B	417	45.56	8.85	35.51	-0.022	4
Sspon.03G0036270-2C	SsLRRII-RLK-2-2	3C	417	45.51	8.85	35.15	-0.021	4
Sspon.03G0036270-3D	SsLRRII-RLK-2-3	3D	410	44.65	7.10	26.89	-0.053	4
Sspon.04G0004390-1A	SsLRRII-RLK-3	4A	661	72.62	7.87	38.30	-0.010	4
Sspon.04G0004390-2D	SsLRRII-RLK-3-2	4D	626	68.61	7.25	39.69	-0.037	4
Sspon.04G0009850-1A	SsLRRII-RLK-4	4A	578	63.63	5.57	44.60	-0.181	4
Sspon.04G0009850-3D	SsLRRII-RLK-4-2	4D	625	68.62	5.57	44.03	-0.147	4
Sspon.04G0013270-1A	SsLRRII-RLK-5	4A	606	67.54	5.13	35.40	-0.184	4
Sspon.04G0014480-3D	SsLRRII-RLK-6	4D	715	79.13	5.68	38.88	-0.107	4
Sspon.05G0010060-2C	SsLRRII-RLK-7	5C	458	50.37	5.98	46.82	-0.237	4
Sspon.05G0010060-1A	SsLRRII-RLK-7-2	5A	543	60.94	7.06	45.11	-0.243	4
Sspon.06G0005550-1A	SsLRRII-RLK-8	6A	982	105.55	10.63	46.16	-0.211	4
Sspon.06G0010230-1A	SsLRRII-RLK-9	6A	580	64.21	5.84	43.90	-0.243	4
Sspon.06G0010230-2B	SsLRRII-RLK-9-2	6B	586	64.37	5.66	44.92	-0.166	4
Sspon.06G0010230-3C	SsLRRII-RLK-9-3	6C	584	64.62	5.77	43.86	-0.221	3
Sspon.06G0016870-1A	SsLRRII-RLK-10	6A	581	65.10	5.89	38.07	-0.211	4
Sspon.06G0016880-1A	SsLRRII-RLK-11	6A	925	102.95	8.20	45.98	-0.382	4
Sspon.06G0016880-2B	SsLRRII-RLK-11-2	6B	619	69.48	5.57	38.08	-0.120	2
Sspon.06G0016880-1P	SsLRRII-RLK-12	6B	624	70.00	5.64	38.47	-0.107	4
Sspon.06G0005060-3C	SsLRRII-RLK-13	6C	591	66.41	6.35	34.31	-0.092	4
Sspon.06G0035390-1D	SsLRRII-RLK-14	6D	473	52.30	8.63	32.14	-0.084	4
Sspon.07G0011930-3D	SsLRRII-RLK-15	7D	497	54.79	5.45	39.04	-0.049	4
Sspon.08G0009990-1A	SsLRRII-RLK-16	8A	336	37.00	8.70	33.67	-0.025	4
Sspon.08G0009990-2C	SsLRRII-RLK-16-2	8C	581	63.95	6.89	39.18	-0.130	1
Sspon.08G0009990-3D	SsLRRII-RLK-16-3	8D	551	60.66	7.95	39.71	-0.132	4

表2

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表3

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基因名称 Gene name	正向引物 Forward sequence (5'-3')	反向引物 Reverse sequence (5'-3')
GAPDH	CACGGCCACTGGAAGCA	TCCTCAGGGTTCCTGATGCC
SsLRRII-RLK1	AGAGCGCCTACTTGTTTATCC	GCTTCCTTGCAGACCAATCTA
SsLRRII-RLK4-2	GGATCATGCTTCTGGAGCTTATTA	CTTCTCCTTCAGCAGTCCTTTC
SsLRRII-RLK 5	GGCTATGGGATCATGCTTCTT	CCCTTCTCTCTGTAGCTTCTTTAC
SsLRRII-RLK 9-3	GCCTTCGTGGATTCTGTATGA	GCCAATCTAGTGGAGGTTCAG
SsLRRII-RLK 14	CTACTTCAGGCGGCTCATTAC	GCACCAACAATGCTTCCAATAA
SsLRRII-RLK 16-2	CCAGTGTCCTACAACCTCAATAG	GCCTCCACCAGAACAGAAAT

基因编号 Number of genes	基因名 Gene name	同义突变频率Ks Synonymous	分歧时间 Divergence time (Mya)
Sspon.03G0036270-1B-Sobic.003G051100	SsLRRII-RLK-2-SbLRRII-RLK1	0.1065600	4.512
Sspon.03G0036270-2C-Sobic.003G051100	SsLRRII-RLK-2-2-SbLRRII-RLK1	0.1075050	8.270
Sspon.04G0004390-2D-Sobic.004G252200	SsLRRII-RLK-3-2-SbLRRII-RLK5	0.0616391	4.741
Sspon.04G0009850-3D-Sobic.004G189900	SsLRRII-RLK-4-2-SbLRRII-RLK4	0.0675914	5.199
Sspon.04G0013270-1A-Sobic.004G128200	SsLRRII-RLK-5-SbLRRII-RLK3	0.0586529	4.512
Sspon.04G0014480-3D-Sobic.004G104800	SsLRRII-RLK-6-SbLRRII-RLK2	0.0743093	5.716
Sspon.06G0005550-1A-Sobic.007G142900	SsLRRII-RLK-8-SbLRRII-RLK12	0.2812260	21.633
Sspon.06G0010230-1A-Sobic.007G059600	SsLRRII-RLK-9-SbLRRII-RLK9	0.0693491	5.335
Sspon.06G0010230-2B-Sobic.007G059600	SsLRRII-RLK-9-2-SbLRRII-RLK9	0.1305250	10.040
Sspon.06G0016880-1A-Sobic.005G182400	SsLRRII-RLK-11-SbLRRII-RLK7	0.0387034	2.977
Sspon.06G0016880-2B-Sobic.005G182400	SsLRRII-RLK-11-2-SbLRRII-RLK7	0.0373593	2.874
Sspon.08G0009990-2C-Sobic.010G115300	SsLRRII-RLK-16-2-SbLRRII-RLK15	0.0964024	7.416
Sspon.08G0009990-3D-Sobic.010G115300	SsLRRII-RLK-16-3-SbLRRII-RLK15	0.0919244	7.071
Sspon.06G0035390-1D-Sobic.005G182400	SsLRRII-RLK-14-SbLRRII-RLK7	0.1044750	8.037

甘蔗割手密种LRRII-RLK基因家族演化和表达分析

Evolution and relative expression pattern of LRRII-RLK gene family in sugarcane Saccharum spontaneum

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