Identification of the Cysteine Protease Family and Corresponding miRNAs in Jatropha curcas and Their Response to Chill-hardening

doi:10.11983/CBB21014

Abstract

Abstract: Jatropha curcas is a kind of promising energy plants, but also a chilling-sensitive plant, which can be chill- hardening at 12°C with significant improvement of its chilling tolerance. In this study, the cysteine protease gene family of J. curcas and their corresponding miRNAs were identified at the genome-wide level. The results showed that a total of 39 cysteine protease genes were identified in J. curcas genome, which were located on 11 chromosomes and could be divided into six subfamilies (C1A, C2, C12, C13, C14 and C15); all encoding 181-2 158 amino acids with Cys and His active sites. Based on the sequencing results of miRNAome and degradome, 283 miRNAs were found to be targeted to 14 members of cysteine protease gene family. In addition, the co-expression analysis of those miRNAs targeting to JcDEK1, JcRD21B and JcXBCP3L during chill-hardening demonstrated significantly negative correlation during the chill-hardening at 12°C, suggesting that these miRNAs are involved in the regulation of the cysteine protease genes, and this regulation should be related to the enhancement of chilling tolerance induced by the chill-hardening. This study will be helpful for better understanding the function of cysteine protease gene family in J. curcas and the interaction of the family genes with their corresponding miRNAs, and how this interaction regulates the response of J. curcas to low temperature.

Key words: Jatropha curcas, cysteine protease, gene family, microRNAs, low temperature response

Dandan Wu, Yongkun Chen, Yu Yang, Chunyan Kong, Ming Gong. Identification of the Cysteine Protease Family and Corresponding miRNAs in Jatropha curcas and Their Response to Chill-hardening[J]. Chinese Bulletin of Botany, 2021, 56(5): 544-558.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB21014

https://www.chinbullbotany.com/EN/Y2021/V56/I5/544

Figures/Tables 11

References 44

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Primer name	Sequence (5′→ 3′)
miR1314-y-F	GCCGGTCTCCAATGTTAGG
miR1151-y-F	ATCTGGTTGTGGGACCCG
miR5156-x-F	GCGAGACTGTGAAACTGCAAA
miR6483-y-F	GCGTTGTAGAAATTTTCAGGATCA
JcXBCP3L-F	TCTGTGGGTATGGATGGTTCTGC
JcXBCP3L-R	ACCCCAGTCAGTACCCCACGA
JcRD21B-F	CAACGCTTTAGGAGAGAAGGAA
JcRD21B-R	ACGCAACTTGTTCCTCCTGAC
JcDEK1-F	TGCTGGGAAATTCTGGTG
JcDEK1-R	AGCCGTCAAACCCACCA
Reverse primer	GCTGTCAACGATACGCTACGTAACG
U6-F	GGAACGATACAGAGAAGATT
GAPDH-F	TGAAGGACTGGAGAGGTGGAAGAGC
GAPDH-R	ATCAACAGTTGGAACACGGAAAGCC

Primer name	Sequence (5′→ 3′)
miR1314-y-F	GCCGGTCTCCAATGTTAGG
miR1151-y-F	ATCTGGTTGTGGGACCCG
miR5156-x-F	GCGAGACTGTGAAACTGCAAA
miR6483-y-F	GCGTTGTAGAAATTTTCAGGATCA
JcXBCP3L-F	TCTGTGGGTATGGATGGTTCTGC
JcXBCP3L-R	ACCCCAGTCAGTACCCCACGA
JcRD21B-F	CAACGCTTTAGGAGAGAAGGAA
JcRD21B-R	ACGCAACTTGTTCCTCCTGAC
JcDEK1-F	TGCTGGGAAATTCTGGTG
JcDEK1-R	AGCCGTCAAACCCACCA
Reverse primer	GCTGTCAACGATACGCTACGTAACG
U6-F	GGAACGATACAGAGAAGATT
GAPDH-F	TGAAGGACTGGAGAGGTGGAAGAGC
GAPDH-R	ATCAACAGTTGGAACACGGAAAGCC

Locus ID	Gene name	Subgroup	Chr.	Size (aa)	Mw (Da)	pI
XM_012209792.1	JcRD21A	C1A	Chr. 10	475	52682.16	5.39
XM_012221410.1	JcSAG12H4	C1A	Chr. 4	340	37417.89	5.13
XM_012226309.1	JcSAG12H1	C1A	Chr. 3	311	34256.46	6.89
XM_012216029.1	JcSAG12H2	C1A	Chr. 7	268	28610.75	4.66
XM_012216557.1	JcXBCP3	C1A	Chr. 4	441	48817.81	6.06
XM_012218796.1	JcRD21A1	C1A	Chr. 10	358	40417.25	5.10
XM_012223641.1	JcALP1	C1A	Chr. 7	347	38935.92	8.43
XM_012225588.1	JcRD19B	C1A	Chr. 10	409	44955.43	6.71
XM_012230158.1	JcCEP2	C1A	Chr. 7	358	39943.84	6.19
XM_012233098.1	JcSAG12H5	C1A	Chr. 9	340	37592.12	5.01
XM_012236390.1	JcXBCP3L	C1A	Chr. 3	524	58042.85	5.24
XM_012219020.1	JcXCP1	C1A	Chr. 5	349	39054.13	5.59
XM_012211812.1	JcRD19A	C1A	Chr. 2	370	40564.71	5.95
XM_012212907.1	JcRD21B	C1A	Chr. 4	466	51785.03	5.28
XM_012213199.1	JcSAG12H3	C1A	Chr. 2	339	37598.38	5.94
XM_012216569.1	JcRD19C	C1A	Chr. 4	368	40923.12	5.81
XM_012218200.1	JcXCP2	C1A	Chr. 4	350	39176.15	5.40
XM_012221663.1	JcTHI1	C1A	Chr. 11	358	39435.49	5.88
XM_012223907.1	JcRD21C	C1A	Chr. 7	366	41119.35	5.40
XM_012224546.1	JcCEP1	C1A	Chr. 5	360	40142.92	5.69
XM_020685390.1	JcSAG12H6	C1A	Chr. 3	181	20779.04	9.49
XM_020685389.1	JcSAG12H7	C1A	Chr. 3	181	20779.04	9.49
XM_012227664.1	JcCTB1	C1A	Chr. 8	358	39709.10	6.07
XM_012225478.1	JcDEK1	C2	Chr. 1	2158	239010.06	6.03
XM_012224060.1	JcUCH2	C12	Chr. 4	337	38597.28	6.43
XM_012214672.1	JcUCH3	C12	Chr. 9	236	26006.51	4.66
XM_012231737.1	JcVPE2	C13	Chr. 9	495	55104.34	5.58
XM_012221936.1	JcVPE1	C13	Chr. 11	493	54253.23	5.93
XM_012232060.1	JcVPE3	C13	Chr. 5	485	54983.84	6.22
XM_012229170.1	JcAMC4G	C14	Chr. 5	418	45953.22	5.18
Locus ID	Gene name	Subgroup	Chr.	Size (aa)	Mw (Da)	pI
XM_012227353.1	JcAMC9A	C14	Chr. 3	317	35221.20	5.84
XM_012213747.1	JcAMC3B	C14	Chr. 2	374	41063.04	5.71
XM_012213748.1	JcAMC1C	C14	Chr. 2	330	37646.13	8.05
XM_012213889.1	JcAMC2D	C14	Chr. 2	406	45165.20	8.65
XM_012213890.1	JcAMC1E	C14	Chr. 2	335	37746.43	8.10
XM_012228350.1	JcAMC1F	C14	Chr. 8	362	39681.00	6.41
XM_012235144.1	JcAMC1H	C14	Chr. 5	370	40503.80	6.34
XM_012230023.1	JcPCP1	C15	Chr. 7	217	23577.96	6.07
XM_012233456.1	JcPCP2	C15	Chr. 6	219	23969.43	6.08

Locus ID	Gene name	Subgroup	Chr.	Size (aa)	Mw (Da)	pI
XM_012209792.1	JcRD21A	C1A	Chr. 10	475	52682.16	5.39
XM_012221410.1	JcSAG12H4	C1A	Chr. 4	340	37417.89	5.13
XM_012226309.1	JcSAG12H1	C1A	Chr. 3	311	34256.46	6.89
XM_012216029.1	JcSAG12H2	C1A	Chr. 7	268	28610.75	4.66
XM_012216557.1	JcXBCP3	C1A	Chr. 4	441	48817.81	6.06
XM_012218796.1	JcRD21A1	C1A	Chr. 10	358	40417.25	5.10
XM_012223641.1	JcALP1	C1A	Chr. 7	347	38935.92	8.43
XM_012225588.1	JcRD19B	C1A	Chr. 10	409	44955.43	6.71
XM_012230158.1	JcCEP2	C1A	Chr. 7	358	39943.84	6.19
XM_012233098.1	JcSAG12H5	C1A	Chr. 9	340	37592.12	5.01
XM_012236390.1	JcXBCP3L	C1A	Chr. 3	524	58042.85	5.24
XM_012219020.1	JcXCP1	C1A	Chr. 5	349	39054.13	5.59
XM_012211812.1	JcRD19A	C1A	Chr. 2	370	40564.71	5.95
XM_012212907.1	JcRD21B	C1A	Chr. 4	466	51785.03	5.28
XM_012213199.1	JcSAG12H3	C1A	Chr. 2	339	37598.38	5.94
XM_012216569.1	JcRD19C	C1A	Chr. 4	368	40923.12	5.81
XM_012218200.1	JcXCP2	C1A	Chr. 4	350	39176.15	5.40
XM_012221663.1	JcTHI1	C1A	Chr. 11	358	39435.49	5.88
XM_012223907.1	JcRD21C	C1A	Chr. 7	366	41119.35	5.40
XM_012224546.1	JcCEP1	C1A	Chr. 5	360	40142.92	5.69
XM_020685390.1	JcSAG12H6	C1A	Chr. 3	181	20779.04	9.49
XM_020685389.1	JcSAG12H7	C1A	Chr. 3	181	20779.04	9.49
XM_012227664.1	JcCTB1	C1A	Chr. 8	358	39709.10	6.07
XM_012225478.1	JcDEK1	C2	Chr. 1	2158	239010.06	6.03
XM_012224060.1	JcUCH2	C12	Chr. 4	337	38597.28	6.43
XM_012214672.1	JcUCH3	C12	Chr. 9	236	26006.51	4.66
XM_012231737.1	JcVPE2	C13	Chr. 9	495	55104.34	5.58
XM_012221936.1	JcVPE1	C13	Chr. 11	493	54253.23	5.93
XM_012232060.1	JcVPE3	C13	Chr. 5	485	54983.84	6.22
XM_012229170.1	JcAMC4G	C14	Chr. 5	418	45953.22	5.18
Locus ID	Gene name	Subgroup	Chr.	Size (aa)	Mw (Da)	pI
XM_012227353.1	JcAMC9A	C14	Chr. 3	317	35221.20	5.84
XM_012213747.1	JcAMC3B	C14	Chr. 2	374	41063.04	5.71
XM_012213748.1	JcAMC1C	C14	Chr. 2	330	37646.13	8.05
XM_012213889.1	JcAMC2D	C14	Chr. 2	406	45165.20	8.65
XM_012213890.1	JcAMC1E	C14	Chr. 2	335	37746.43	8.10
XM_012228350.1	JcAMC1F	C14	Chr. 8	362	39681.00	6.41
XM_012235144.1	JcAMC1H	C14	Chr. 5	370	40503.80	6.34
XM_012230023.1	JcPCP1	C15	Chr. 7	217	23577.96	6.07
XM_012233456.1	JcPCP2	C15	Chr. 6	219	23969.43	6.08