Identification and Analysis of Tuber-specific Expression Genes in Cyperus esculentus

doi:10.11983/CBB24097

Abstract

Abstract: Tuber is a unique and extremely important organ of Cyperus esculentus, which is rich in oil and has the reproduction ability similar to seed. It is of great significance to study the specific expression genes in the tubers of C. esculentus for analyzing the regulation mechanism of tuber-specific growth and development (especially oil accumulation). Through transcriptome sequencing of the main organs (root, leaf, tillering node, stolon and tuber) of C. esculentus, the genes specifically expressed in tubers were comprehensively screened and the functions of related genes were analyzed. The results showed that a total of 155 tuber-specific expression genes were identified after multiple sets of comparative analysis by taking root, leaf, tillering node and stolon as reference, respectively. GO enrichment analysis showed that 7 GO terms including seed development, seed oilbody biogenesis, oil storage, abscisic acid response, response to abiotic stimulus and protein folding were significantly enriched, and some of the genes involved in these GO terms just reflected the unique development characteristics similar to seed of C. esculentus tubers. Among them, CESC_00080 and CESC_16572 encode caleosin, and meanwhile, CESC_08636, CESC_12549 and CESC_17828 encode oleosin, all of which are involved in the formation of plant oil bodies. Since oil body formation is a key step for plants to complete oil storage, it is indicated that the specific expression of these oil body formation-related genes in tubers may be the key to the storage of large amounts of oil in the tubers of C. esculentus. In addition, this study also screened eight tuber-specific expression transcription factor genes, such as CESC_00448 (abscisic acid insensitive 5-like protein ABI5) and CESC_03736 (heat stress transcription factor C), some of whose potential target genes were found in identified tuber-specific expression genes, indicating that these transcription factor genes may regulate the specific expression of their respective target genes. In summary, the results of this study can provide an important reference for the construction of gene regulatory networks related to tuber development of C. esculentus and the molecular mechanism analysis of tuber-specific gene expression.

Key words: Cyperus esculentus, tuber, transcriptome sequencing, specific expression

Xiangge Zhang, Chen Chen, Shan Cheng, Chunxin Li, Yajing Zhu, Xinran Xu, Huiwei Wang. Identification and Analysis of Tuber-specific Expression Genes in Cyperus esculentus[J]. Chinese Bulletin of Botany, 2025, 60(1): 33-48.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24097

https://www.chinbullbotany.com/EN/Y2025/V60/I1/33

Figures/Tables 9

References 57

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Gene	Forward primer (5′-3′)	Reverse primer (5′-3′)
CESC_13967	ACTCTGGTGATGGTGTGAGC	CCCTCTCTCCGTCAGGATCT
CESC_00080	CTACCACCTCTCCGTGCTTC	CTACCACCTCTCCGTGCTTC
CESC_17828	GCACCAGAGAGAAGGACAGC	GCACCAGAGAGAAGGACAGC
CESC_00330	GACAAACCATCACCACAGCG	ATCACCAGCATCTTCCCGTC
CESC_18197	GCCACTCCATTCCGATTTGC	GCGTGAAGTTGCCGATGATG
CESC_16081	CGGGTCAACAGAAGAAGGAGC	CGTCGACAGTCTTGTTCTCC
CESC_03736	GGATTCGGTGATCTCGTGGG	CAGCTCTATCAGCCTCGCTT

Gene	Forward primer (5′-3′)	Reverse primer (5′-3′)
CESC_13967	ACTCTGGTGATGGTGTGAGC	CCCTCTCTCCGTCAGGATCT
CESC_00080	CTACCACCTCTCCGTGCTTC	CTACCACCTCTCCGTGCTTC
CESC_17828	GCACCAGAGAGAAGGACAGC	GCACCAGAGAGAAGGACAGC
CESC_00330	GACAAACCATCACCACAGCG	ATCACCAGCATCTTCCCGTC
CESC_18197	GCCACTCCATTCCGATTTGC	GCGTGAAGTTGCCGATGATG
CESC_16081	CGGGTCAACAGAAGAAGGAGC	CGTCGACAGTCTTGTTCTCC
CESC_03736	GGATTCGGTGATCTCGTGGG	CAGCTCTATCAGCCTCGCTT

Samples	Clean reads	Clean bases	Q20 (%)	Q30 (%)	Mapped reads	Mapped ratio (%)
Root	57066812	8330335323	97.86	93.98	51517757	90.26
Leaf	54318808	7949486769	97.59	93.40	48848097	89.92
Tillering node	57497577	8370290261	97.26	93.71	51548858	89.66
Stolon	58790213	8560106850	97.72	93.68	52822328	89.85
Tuber	58869179	8582198623	97.65	94.56	52938611	89.93

Samples	Clean reads	Clean bases	Q20 (%)	Q30 (%)	Mapped reads	Mapped ratio (%)
Root	57066812	8330335323	97.86	93.98	51517757	90.26
Leaf	54318808	7949486769	97.59	93.40	48848097	89.92
Tillering node	57497577	8370290261	97.26	93.71	51548858	89.66
Stolon	58790213	8560106850	97.72	93.68	52822328	89.85
Tuber	58869179	8582198623	97.65	94.56	52938611	89.93

Gene	Expression level (FPKM)					Gene	Expression level (FPKM)
Gene	Tuber	Root	Leaf	Stolon	Tillering node	Gene	Tuber	Root	Leaf	Stolon	Tillering node
CESC_17828	34980.30	0.19	0.51	9.23	6.20	CESC_06642	449.61	0.00	3.36	0.08	0.04
CESC_14076	24917.54	0.36	0.42	1.24	0.54	CESC_11684	424.54	2.11	0.12	2.17	0.94
CESC_08636	23808.18	0.00	2.95	1.11	1.38	CESC_00836	424.00	1.18	5.61	0.00	0.57
CESC_16708	20282.53	1.29	4.99	9.63	2.02	CESC_04812	394.97	0.00	0.51	0.02	0.52
CESC_14073	15607.24	0.13	0.50	1.73	7.62	CESC_19053	392.95	0.00	0.00	0.00	0.00
CESC_10265	8803.59	0.59	4.34	0.64	4.16	CESC_13856	384.53	4.48	1.53	3.09	2.19
CESC_13913	6560.83	0.09	0.02	0.06	0.13	CESC_05739	373.39	0.11	0.00	0.00	0.00
CESC_13892	6062.31	0.21	0.18	0.49	0.27	CESC_15162	373.06	2.23	1.79	1.55	1.20
CESC_14077	5890.09	1.05	0.06	0.51	0.77	CESC_21269	357.90	0.00	0.00	0.13	0.03
CESC_00080	4834.92	0.91	0.00	0.03	0.37	CESC_12660	335.49	4.32	2.69	4.42	1.52
CESC_12549	4632.55	0.00	0.03	0.00	0.00	CESC_15141	309.91	0.34	0.04	0.38	0.06
CESC_00832	3760.05	0.05	0.03	0.00	0.20	CESC_15826	293.80	0.44	3.71	1.88	1.94
CESC_15373	3721.68	6.39	6.24	4.11	6.27	CESC_15198	269.77	2.29	2.45	5.19	1.98
CESC_10351	3695.94	0.05	0.00	0.60	0.19	CESC_03736	268.07	0.77	7.39	3.50	8.35
CESC_18271	3694.18	1.46	1.25	3.06	1.59	CESC_21099	239.33	0.00	0.71	0.66	3.22
CESC_21136	3589.62	0.09	0.03	0.00	0.29	CESC_15700	239.04	0.00	2.84	0.90	0.37
CESC_07796	3057.85	0.02	0.06	0.19	0.09	CESC_05388	226.51	1.01	5.53	6.37	2.14
CESC_15694	2900.48	0.27	0.62	0.61	1.47	CESC_16081	208.50	0.00	0.00	0.22	0.38
CESC_03859	1780.16	0.06	0.00	0.26	0.92	CESC_21299	202.95	9.12	0.16	9.83	9.53
CESC_15801	1779.19	0.00	0.00	0.00	0.04	CESC_06038	197.18	0.08	0.24	0.56	1.48
CESC_19612	1385.35	0.00	0.04	0.17	0.02	CESC_13442	192.86	0.00	0.10	0.07	0.02
CESC_08819	1367.03	0.02	0.11	4.98	3.09	CESC_13439	187.91	0.00	0.00	0.13	0.25
CESC_18197	1341.87	3.87	0.03	0.28	0.14	CESC_16862	182.94	3.01	1.50	3.14	3.01
CESC_08728	1103.89	0.00	0.30	0.05	0.04	CESC_16946	174.53	0.28	1.54	4.13	6.34
CESC_17427	906.81	0.49	0.48	0.55	0.98	CESC_12770	173.37	0.06	0.04	0.00	0.00
CESC_17492	882.14	0.26	1.39	0.89	1.05	CESC_01552	165.58	0.86	0.35	0.29	1.30
CESC_17960	855.95	0.00	0.00	0.13	0.02	CESC_22280	164.99	0.01	1.64	3.39	1.20
CESC_08729	799.26	0.00	0.07	0.00	0.01	CESC_19187	163.80	0.79	0.54	0.61	0.23
CESC_12402	780.10	0.00	0.15	2.10	0.99	CESC_06173	160.18	0.00	0.16	0.03	0.00
CESC_14954	746.41	0.64	0.42	0.10	5.62	CESC_06081	156.16	0.12	0.22	1.02	0.41
CESC_08129	744.59	0.06	0.02	0.56	0.14	CESC_06747	155.97	0.00	0.00	0.00	0.00
CESC_21264	741.47	0.00	0.08	0.00	0.01	CESC_12819	149.97	0.00	0.00	0.00	0.00
CESC_15594	641.08	1.91	1.19	1.34	3.11	CESC_02836	146.94	0.08	0.15	2.06	0.23
CESC_23526	629.26	0.00	0.04	0.00	0.00	CESC_05881	145.16	0.38	0.79	0.45	0.11
CESC_08481	628.51	0.08	0.00	0.15	0.11	CESC_02522	138.38	0.08	0.04	0.04	0.04
CESC_10473	599.12	3.10	0.03	5.20	1.41	CESC_18879	122.55	0.02	0.09	2.88	1.18
CESC_00650	581.33	0.21	1.43	0.48	0.66	CESC_19366	117.03	2.24	0.67	4.73	3.77
CESC_19809	503.39	3.58	0.51	2.10	3.52	CESC_09038	116.42	1.54	0.23	7.88	2.86
CESC_19929	496.40	0.00	0.00	0.00	0.01	CESC_16522	115.51	5.22	0.32	6.70	7.14
CESC_02314	487.86	0.01	0.00	0.17	0.11	CESC_16067	112.60	0.00	0.01	0.39	0.12
CESC_22878	467.04	0.28	0.21	0.88	3.23	CESC_21164	108.78	1.17	0.10	2.93	5.67
CESC_14581	106.85	0.00	0.08	0.00	0.12	CESC_20039	28.25	0.08	0.01	0.48	0.42
CESC_00606	106.35	0.05	2.56	0.18	0.65	CESC_05180	27.12	0.00	0.52	1.24	0.88
CESC_19685	101.57	0.10	0.08	0.05	0.07	CESC_08911	24.85	0.00	0.29	0.00	0.17
CESC_18501	100.73	0.13	0.00	0.06	0.01	CESC_14442	24.83	0.02	0.23	0.05	0.49
CESC_13203	98.13	0.06	0.00	2.70	3.72	CESC_07266	23.62	0.00	0.00	0.05	0.07
CESC_03998	92.03	1.35	0.80	1.19	0.84	CESC_16550	23.51	0.59	2.35	2.13	0.42
CESC_00033	91.70	0.02	0.06	2.20	0.67	CESC_07944	22.65	0.26	0.11	0.07	0.73
CESC_08253	90.37	0.12	0.00	0.00	0.00	CESC_09860	22.32	0.00	0.00	0.00	0.02
CESC_16780	89.47	3.47	0.56	2.98	2.45	CESC_21859	21.75	0.02	0.00	0.00	0.00
CESC_17762	89.08	4.78	0.16	2.53	3.16	CESC_00937	21.12	0.00	2.02	0.34	0.04
CESC_01315	87.53	2.04	6.90	0.87	0.70	CESC_22858	20.65	0.08	2.06	0.11	0.12
CESC_20841	87.40	1.66	0.24	0.12	3.91	CESC_07385	20.53	0.00	0.00	0.09	0.26
CESC_03712	83.29	0.00	0.07	0.03	0.06	CESC_14874	20.18	0.00	0.22	1.12	0.16
CESC_07763	77.09	2.08	3.42	5.30	2.33	CESC_05835	19.57	0.06	0.00	0.10	0.14
CESC_15211	76.33	0.38	0.03	0.20	0.09	CESC_07703	19.26	0.76	0.09	1.76	1.75
CESC_16572	74.95	0.00	0.00	0.00	0.01	CESC_09861	18.86	0.65	0.48	0.00	0.05
CESC_00448	70.32	5.66	2.95	5.91	2.01	CESC_03897	17.96	0.40	0.61	0.22	0.06
CESC_23041	68.12	0.00	0.02	1.45	1.87	CESC_00298	16.93	0.00	0.06	0.04	0.06
CESC_00990	68.06	0.36	0.42	4.76	6.24	CESC_08232	16.93	1.39	0.30	0.44	1.59
CESC_12231	67.00	0.94	1.19	5.59	2.33	CESC_07388	16.85	0.00	0.07	0.00	0.05
CESC_00330	66.87	0.10	0.03	0.40	0.25	CESC_21561	16.68	0.05	0.28	0.81	0.85
CESC_10266	65.28	0.00	0.00	0.05	0.00	CESC_11936	16.57	0.00	0.74	0.00	0.20
CESC_18500	59.91	0.00	0.00	0.05	0.02	CESC_16352	16.33	0.02	0.21	0.05	0.00
CESC_18904	59.67	0.59	0.05	0.27	0.10	CESC_04055	16.19	0.00	0.00	0.00	0.04
CESC_18474	58.76	0.61	0.15	0.00	0.00	CESC_21332	16.12	0.01	0.00	0.16	0.10
CESC_15687	58.13	0.72	4.91	1.77	0.88	CESC_04595	15.92	0.14	0.00	0.15	1.08
CESC_19611	56.45	0.00	0.05	0.00	0.00	CESC_08350	15.26	1.35	0.05	0.13	0.09
CESC_16328	55.34	1.70	0.71	1.67	0.74	CESC_12816	14.80	0.02	0.79	0.44	0.16
CESC_03405	55.28	0.20	0.03	0.32	0.27	CESC_15370	14.50	0.04	0.93	0.79	1.23
CESC_18761	54.94	0.78	0.12	3.31	1.48	CESC_19797	14.45	0.24	0.09	0.76	0.28
CESC_21600	53.08	0.00	0.08	0.00	0.02	CESC_01169	14.17	0.00	0.04	0.09	0.04
CESC_16965	52.69	0.35	0.65	0.86	2.69	CESC_18475	13.22	0.60	0.11	0.09	0.06
CESC_04051	51.21	0.00	0.04	0.06	0.03	CESC_18599	12.86	0.00	0.00	0.00	0.01
CESC_06673	47.23	0.00	0.51	0.02	0.00	CESC_00742	11.88	0.58	0.33	0.58	0.21
CESC_05193	40.93	0.00	1.38	0.11	0.04	CESC_11046	11.62	0.02	0.34	0.78	0.39
CESC_21100	40.35	0.00	0.00	0.00	0.09	CESC_01166	10.25	0.22	0.22	0.43	0.25
CESC_21308	32.28	1.24	1.62	0.57	2.02