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

Abstract

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

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.

Figures/Tables 13

Table 1

Table 2

Information of LRRII-RLK gene family in Saccharum spontaneum"

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

Table 2

Fig. 1

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Table 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

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

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