Identification of Cerasus humilisSPL Gene Family and Expression Analysis during Fruit Development

doi:10.13560/j.cnki.biotech.bull.1985.2025-0563

Abstract

Abstract:

Objective To study the structure function and expression of the SPL gene family members in Cerasus humilis, laying a foundation for further research on the function of the SPL gene family in C. humilis. Method Based on the whole genome and transcriptome data of C. humilis, the SPL gene family members were systematically identified, and the ChSPL gene family was subjected to bioinformatics analysis and expression pattern analysis. Result A total of 17 ChSPL gene family members (ChSPL01-ChSPL17) were identified. ChSPLs were unevenly distributed on 7 chromosomes. The gene structures and conserved domains within each subfamily showed high similarity. ChSPL14-ChSPL16 were located in the cytoplasm, while the other family members were located in the nucleus. The cis-acting element analysis indicated that the light-response elements were the most abundant in ChSPLs, followed by anaerobic induction response elements (ARE), abscisic acid response elements (ABRE), and methyl jasmonate response elements (CGTCA-motif). Based on transcriptome and RT-qPCR analysis, most ChSPLs (ChSPL01, ChSPL02, ChSPL06, ChSPL09, and ChSPL11) showed high expressions in the early stage of fruit development, and their expressions gradually decreased as the fruit matured. In contrast, ChSPL12, ChSPL14, and ChSPL16 showed gradually increasing expressions during fruit development, with ChSPL12 having the highest expression at the fruit maturity stage. ChSPLs also had obvious tissue-specific expression. ChSPL02, ChSPL05, ChSPL06, ChSPL10, and ChSPL17 had relatively high expressions in the stems and leaves; ChSPL01, ChSPL04, and ChSPL09 had relatively high expressions in the leaves; while ChSPL14, ChSPL15, and ChSPL16 had relatively high expressions in the flowers and fruits. Conclusion A total of 17 ChSPL genes in C. humilis were identified. It is speculated that the ChSPL gene family plays an important role in fruit development, and ChSPL12, ChSPL14, and ChSPL16 may be key candidate genes promoting fruit ripening, providing a reference for future research on the function of ChSPL genes.

Key words: Cerasus humilis, SPL gene family, bioinformatics analysis, fruit development, analysis of gene expression, cis-acting elements

LI Tian-yuan, QI Xin-liang, LIU Shan, ZHANG Jian-cheng, WANG Peng-fei, ZHANG Shuai, JIA Lu-ting, MU Xiao-peng. Identification of Cerasus humilisSPL Gene Family and Expression Analysis during Fruit Development[J]. Biotechnology Bulletin, 2026, 42(3): 362-373.

Figures/Tables 11

References 30

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基因名称 Gene name	上游引物序列 Forward primer sequence （5′‒3′）	下游引物序列 Reverse primer sequence （5′‒3′）
ChSPL01	AAGAGGAGGAGGAGGAGGAG	TGCTTGACAAGATGGCCTTG
ChSPL02	GCTGTGCTCTCTCTCTTCTGTCAA	TTGAGTCAGTGACTCCTGTGACG
ChSPL03	CCAAGGAAAACGTAGTTGTCGTAGA	TCAAATTCAGGAAGCTGATGAAATC
ChSPL04	TGGTGCTGATTTTGTTGAGGC	CACTTCTCTGCTTGACAACATGGT
ChSPL05	GCCACTGCTCAGTCTAAAGC	TTCAACTTGGCAGTGTGGTG
ChSPL06	CAAGAGAGGCAGAGGAGGAG	ACTCCTTTGCGTTCATCAGC
ChSPL07	ATTCTGGAGCTGGGACTCAC	CGTTGGAGCTGTGAGGAAAG
ChSPL08	GCAAACAGGCAAATGCTTCC	CTGAACTCCTGCTGAATGGC
ChSPL09	GGGTGATAATAGTGGAAGAATTCGG	TGGCCACATACATCCTTCAACTG
ChSPL10	CTTCTGCCTGCCAACAACTT	CTGAGCTGGCCAGATTGAAC
ChSPL11	CATAACCAGCATCTCCAACTGC	AAGACCGGTATCAGCCTCAGC
ChSPL12	CCAAGCAGATGCAGAGGTTC	GAGAGTGAGCCGTGAGGTAA
ChSPL13	GGCCTGTGGAAGCCAAAAAG	TCTGCTTTCTGCAGGTGAGG
ChSPL14	ATGCCAAGGATTACCACCGA	TATTATGGCCAGCCAAACGC
ChSPL15	ATTGTGATGGTGGAGCAGGA	CAGGCACTGAACTGAGGGTA
ChSPL16	GCGTTTGGCTGGCCATAATA	TGGCTAGGCTCCTCAGTAGA
ChSPL17	CCTTCAACAACCTCGTCCCT	TAGATGGAGTGGAGCTGCTG
ChActin	TTCAAAGACCAGCTCATCTGTGG	CAATGCCAGGGAACATAGTGGA

基因名称 Gene name	上游引物序列 Forward primer sequence （5′‒3′）	下游引物序列 Reverse primer sequence （5′‒3′）
ChSPL01	AAGAGGAGGAGGAGGAGGAG	TGCTTGACAAGATGGCCTTG
ChSPL02	GCTGTGCTCTCTCTCTTCTGTCAA	TTGAGTCAGTGACTCCTGTGACG
ChSPL03	CCAAGGAAAACGTAGTTGTCGTAGA	TCAAATTCAGGAAGCTGATGAAATC
ChSPL04	TGGTGCTGATTTTGTTGAGGC	CACTTCTCTGCTTGACAACATGGT
ChSPL05	GCCACTGCTCAGTCTAAAGC	TTCAACTTGGCAGTGTGGTG
ChSPL06	CAAGAGAGGCAGAGGAGGAG	ACTCCTTTGCGTTCATCAGC
ChSPL07	ATTCTGGAGCTGGGACTCAC	CGTTGGAGCTGTGAGGAAAG
ChSPL08	GCAAACAGGCAAATGCTTCC	CTGAACTCCTGCTGAATGGC
ChSPL09	GGGTGATAATAGTGGAAGAATTCGG	TGGCCACATACATCCTTCAACTG
ChSPL10	CTTCTGCCTGCCAACAACTT	CTGAGCTGGCCAGATTGAAC
ChSPL11	CATAACCAGCATCTCCAACTGC	AAGACCGGTATCAGCCTCAGC
ChSPL12	CCAAGCAGATGCAGAGGTTC	GAGAGTGAGCCGTGAGGTAA
ChSPL13	GGCCTGTGGAAGCCAAAAAG	TCTGCTTTCTGCAGGTGAGG
ChSPL14	ATGCCAAGGATTACCACCGA	TATTATGGCCAGCCAAACGC
ChSPL15	ATTGTGATGGTGGAGCAGGA	CAGGCACTGAACTGAGGGTA
ChSPL16	GCGTTTGGCTGGCCATAATA	TGGCTAGGCTCCTCAGTAGA
ChSPL17	CCTTCAACAACCTCGTCCCT	TAGATGGAGTGGAGCTGCTG
ChActin	TTCAAAGACCAGCTCATCTGTGG	CAATGCCAGGGAACATAGTGGA

基因 ID Gene ID	基因 Gene	染色体位置 Chr. No.	编码氨基酸长度 Length （aa）	分子量Molecular weight （kD）	等电点 pI	不稳定系数 Instability index	脂肪族氨基酸指数 Aliphatic index	亲水性 Grand average of hydropathicity	亚细胞定位 Subcellular localization
ouLi_011577-RA	SPL01	Chr3	489	38.03	5.26	28.89	30.88	0.681	Nucleus
ouLi_006828-RA	SPL02	Chr2	1 152	95.94	5.01	58.50	23.96	0.800	Nucleus
ouLi_019229-RA	SPL03	Chr6	1 143	95.19	5.01	58.64	23.80	0.797	Nucleus
ouLi_010488-RA	SPL04	Chr3	489	38.23	5.24	19.82	26.99	0.648	Nucleus
ouLi_002187-RA	SPL05	Chr1	1 446	119.72	4.99	44.37	28.56	0.805	Nucleus
ouLi_017116-RA	SPL06	Chr5	1 230	100.61	5.01	45.43	24.07	0.786	Nucleus
ouLi_024093-RA	SPL07	Chr8	1 656	137.64	4.99	43.99	28.02	0.724	Nucleus
ouLi_002823-RA	SPL08	Chr1	1 497	124.27	5.01	42.47	29.33	0.743	Nucleus
ouLi_013789-RA	SPL09	Chr4	570	44.99	5.22	23.54	30.88	0.724	Nucleus
ouLi_002175-RB	SPL10	Chr1	951	78.33	5.08	38.32	28.08	0.802	Nucleus
ouLi_024712-RA	SPL11	Chr8	1 227	102.04	5.02	52.67	29.01	0.858	Nucleus
ouLi_026147-RA	SPL12	Chr8	3 213	265.03	4.84	42.23	27.23	0.725	Cytoplasm/Nucleus
ouLi_012144-RA	SPL13	Chr4	1 176	97.79	5.02	47.01	26.53	0.799	Nucleus
ouLi_000956-RA	SPL14	Chr1	3 105	255.36	4.86	41.47	28.28	0.716	Cytoplasm
ouLi_001341-RA/RB	SPL15	Chr1	2 451	202.05	4.91	39.97	27.46	0.696	Cytoplasm
ouLi_000956-RD	SPL16	Chr1	3 033	248.56	4.87	40.26	28.39	0.699	Cytoplasm
ouLi_017119-RA	SPL17	Chr5	1 137	97.28	4.94	62.14	21.37	1.115	Nucleus

基因 ID Gene ID	基因 Gene	染色体位置 Chr. No.	编码氨基酸长度 Length （aa）	分子量Molecular weight （kD）	等电点 pI	不稳定系数 Instability index	脂肪族氨基酸指数 Aliphatic index	亲水性 Grand average of hydropathicity	亚细胞定位 Subcellular localization
ouLi_011577-RA	SPL01	Chr3	489	38.03	5.26	28.89	30.88	0.681	Nucleus
ouLi_006828-RA	SPL02	Chr2	1 152	95.94	5.01	58.50	23.96	0.800	Nucleus
ouLi_019229-RA	SPL03	Chr6	1 143	95.19	5.01	58.64	23.80	0.797	Nucleus
ouLi_010488-RA	SPL04	Chr3	489	38.23	5.24	19.82	26.99	0.648	Nucleus
ouLi_002187-RA	SPL05	Chr1	1 446	119.72	4.99	44.37	28.56	0.805	Nucleus
ouLi_017116-RA	SPL06	Chr5	1 230	100.61	5.01	45.43	24.07	0.786	Nucleus
ouLi_024093-RA	SPL07	Chr8	1 656	137.64	4.99	43.99	28.02	0.724	Nucleus
ouLi_002823-RA	SPL08	Chr1	1 497	124.27	5.01	42.47	29.33	0.743	Nucleus
ouLi_013789-RA	SPL09	Chr4	570	44.99	5.22	23.54	30.88	0.724	Nucleus
ouLi_002175-RB	SPL10	Chr1	951	78.33	5.08	38.32	28.08	0.802	Nucleus
ouLi_024712-RA	SPL11	Chr8	1 227	102.04	5.02	52.67	29.01	0.858	Nucleus
ouLi_026147-RA	SPL12	Chr8	3 213	265.03	4.84	42.23	27.23	0.725	Cytoplasm/Nucleus
ouLi_012144-RA	SPL13	Chr4	1 176	97.79	5.02	47.01	26.53	0.799	Nucleus
ouLi_000956-RA	SPL14	Chr1	3 105	255.36	4.86	41.47	28.28	0.716	Cytoplasm
ouLi_001341-RA/RB	SPL15	Chr1	2 451	202.05	4.91	39.97	27.46	0.696	Cytoplasm
ouLi_000956-RD	SPL16	Chr1	3 033	248.56	4.87	40.26	28.39	0.699	Cytoplasm
ouLi_017119-RA	SPL17	Chr5	1 137	97.28	4.94	62.14	21.37	1.115	Nucleus

蛋白 Protein	α-螺旋 Alpha helix （%）	延伸链 Extended strand （%）	无规则卷曲 Random coil （%）
SPL01	31.48	5.56	62.96
SPL02	9.40	4.96	85.64
SPL03	11.05	6.05	82.89
SPL04	31.48	5.56	62.96
SPL05	9.36	4.57	86.07
SPL06	11.98	6.36	81.66
SPL07	12.52	3.63	83.85
SPL08	9.04	4.02	86.95
SPL09	28.57	7.41	64.02
SPL10	10.76	6.96	82.28
SPL11	10.78	6.13	83.09
SPL12	28.04	5.23	66.73
SPL13	9.72	6.14	84.14
SPL14	27.37	7.93	64.70
SPL15	28.80	8.46	62.75
SPL16	25.64	4.95	69.41
SPL17	11.64	6.88	81.48