Identification and Expression Analysis of Expansin Genes in Moso Bamboo (Phyllostachys edulis)

doi:10.7525/j.issn.1673-5102.2022.01.004

Abstract

Abstract:

In order to fully understand the molecular characteristics and expression patterns of expansin genes in moso bamboo（Phyllostachys edulis）， bioinformatics methods were used in this study，and a total of 43 members of the expansin gene family was identified from the genome of moso bamboo， and the members were divided into four subfamilies（EXPA， EXPB， EXLA and EXLB）， which contained 18， 17， 7 and 1 members respectively， and distributed on 37 Scaffolds. Except that PeEXPA1 had no introns and PeEXLB1 had 11 introns， other expansin genes have 1 to 5 introns respectively. The amino acid length of the expansin was 91~508 aa respectively， all amino acids had high-frequency codons， and most of the expansins were basic and hydrophilic. Protein structure analysis showed that most of the expansins of moso bamboo accounted for the smallest proportion of β-turns and the largest proportion of β-sheets in the secondary structure. The tertiary structure of most members in each subfamily was similar. The qRT-PCR results of 18 EXPA subfamily members showed that their expression were significantly different in different tissues， and the highest expression values were found in leaves except PeEXPA2 and PeEXPA6， indicating that they might play an important role in the growth of leaves.

Key words: moso bamboo, expansin gene, bioinformatics, expression pattern analysis

CLC Number:

S795.7

Shuang Ma, Boya Wang, Ying Cao, Shanglian Hu, Zhimin Gao. Identification and Expression Analysis of Expansin Genes in Moso Bamboo (Phyllostachys edulis)[J]. Bulletin of Botanical Research, 2022, 42(1): 29-38.

Figures/Tables 7

Table 1

Fig.1

Fig.2

Table 2

Analysis of basic physicochemical properties of expansins in moso bamboo

基因名称 Gene	基因编号 Accession number	编码氨基酸长度 Coding amino acid length （aa）	理论等电点 pI	分子量 Molecular weight /kDa	不稳定系数 Unstability index	脂肪系数 Aliphatic index	总平均亲水性 GRAVY
PeEXPA1	PH01000000G0970	257	8.38	38.65	33.31	80.86	0.02
PeEXPA2	PH01000009G2460	258	8.59	38.50	33.31	80.12	0.02
PeEXPA3	PH01000083G0540	250	5.47	35.86	41.46	59.00	-0.18
PeEXPA4	PH01000094G0210	126	9.41	19.08	32.18	72.40	-0.12
PeEXPA5	PH01000135G1480	247	9.89	37.13	39.13	63.68	-0.21
PeEXPA6	PH01000160G0990	127	10.00	19.73	30.12	77.38	-0.11
PeEXPA7	PH01000519G0080	275	9.26	38.87	39.22	68.07	-0.07
PeEXPA8	PH01000615G0020	259	8.65	38.20	39.58	65.60	-0.05
PeEXPA9	PH01000659G0190	251	7.55	36.06	37.71	59.16	-0.16
PeEXPA10	PH01000705G0150	256	8.62	38.07	31.13	73.52	0.07
PeEXPA11	PH01001348G0370	247	9.89	37.13	39.13	63.68	-0.21
PeEXPA12	PH01001280G0510	250	5.47	35.86	41.46	59.00	-0.18
PeEXPA13	PH01001032G0370	126	10.00	19.73	30.12	77.38	-0.11
PeEXPA14	PH01001528G0240	260	9.28	38.25	40.04	65.38	-0.08
PeEXPA15	PH01001624G0020	248	8.77	35.92	38.40	69.76	-0.01
PeEXPA16	PH01002238G0310	252	8.07	36.17	40.70	58.93	-0.14
PeEXPA17	PH01003318G0170	118	11.20	17.80	18.81	64.49	-0.30
PeEXPA18	PH01003538G0010	125	9.41	19.08	32.18	72.40	-0.12
PeEXPB1	PH01000028G1350	250	6.02	36.11	38.33	62.12	-0.15
PeEXPB2	PH01000069G0690	134	7.52	19.50	21.87	87.29	0.18
PeEXPB3	PH01000104G0690	91	7.50	12.52	9.96	63.00	-0.02
PeEXPB4	PH01000397G0840	264	6.93	39.65	31.45	71.94	-0.21
PeEXPB5	PH01000397G0850	227	8.47	33.94	36.93	72.88	-0.15
PeEXPB6	PH01000397G0880	267	5.07	39.48	28.81	70.83	-0.12
PeEXPB7	PH01000397G0930	279	6.38	42.25	26.25	66.45	-0.27
PeEXPB8	PH01000995G0300	291	9.03	42.40	34.60	69.14	-0.11
PeEXPB9	PH01001155G0250	262	6.07	39.35	35.82	70.76	-0.19
PeEXPB10	PH01001155G0260	273	9.10	41.20	34.06	70.40	-0.19
PeEXPB11	PH01001155G0300	265	5.20	39.27	27.40	68.91	-0.14
PeEXPB12	PH01001155G0360	276	8.12	42.08	21.19	69.28	-0.30
PeEXPB13	PH01001579G0330	265	8.34	39.90	31.37	72.91	-0.18
PeEXPB14	PH01001963G0300	272	8.76	40.71	29.54	77.46	0.01
PeEXPB15	PH01002134G0230	160	8.82	24.35	22.84	78.19	0.02
PeEXPB16	PH01003173G0150	307	4.67	44.32	27.81	81.07	0.23
PeEXPB17	PH01042209G0010	304	5.08	44.48	30.28	62.96	-0.44
PeEXLA1	PH01000059G1970	251	9.62	37.37	40.02	82.03	0.09
PeEXLA2	PH01000233G0920	251	7.55	36.06	37.71	59.16	-0.16
PeEXLA3	PH01000243G0350	276	7.47	41.11	39.03	77.35	-0.05
PeEXLA4	PH01000724G0610	299	6.45	45.37	41.33	77.02	-0.18
PeEXLA5	PH01001177G0450	271	8.84	41.20	33.98	79.23	-0.07
PeEXLA6	PH01001195G0040	278	8.86	42.12	35.93	85.25	-0.07
PeEXLA7	PH01001848G0230	303	7.93	45.99	36.21	77.62	-0.17
PeEXLB1	PH01000553G0340	508	6.41	76.77	38.91	87.20	-0.02

Table 2

Table 3

Fig.3

Fig.4

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基因名称 Gene name	上游引物 Forward primer（5′→3′）	下游引物 Reverse primer（5′→3′）
PeEXPA1	ACAACGAACTTCTGCGCT	AGCGCAATCTTCTCGAA
PeEXPA2	GCCACCGACGTTACTGACT	ACCATTTTCTCCTCCCCAT
PeEXPA3	TTTGCTACCAGGGATCCAAC	TGAAGGAACCCCATCCTATG
PeEXPA4	TAGGCTTGCTAGTTCTTGCC	TCCTCCCATTGTTCCTGAGG
PeEXPA5	TTCAACCTGGTGCTTGTCAC	GCGTTGTTCTGCCAGTTCTG
PeEXPA6	CCGCCCAACCACCATTT	CCGCCTTCACGAAGACACT
PeEXPA7	TCACGGCCACCAACTTCTG	ACAATGCCGGCCTTGTAGAG
PeEXPA8	ATGGGAGGGGCTTGTGGGTA	TTCGGCGGGCAGAGATTGGT
PeEXPA9	CGGTCGGTGTCGATCAA	CGTCCAGGTACGAGTTGCT
PeEXPA10	TGAAGGACTGGCGGAAAGT	TGGGTGAAGGGGACGAA
PeEXPA11	TCAGAACGGCAAGTGGTG	TCCTGTAGGTGATGGGCAC
PeEXPA12	TCTTCACACAGGGAACCCTT	TTCTGCCCGCCCAACTA
PeEXPA13	GAGGGTTCCATGTGTGAGG	ACAAGTACGAGATTGAAGTAGTCG
PeEXPA14	TTGCCATGCCCATGTTCCTC	AAGTACCGGAACCCGTTGATC
PeEXPA15	ACTTGAACCCAAATTAAGGCC	GATGGAGGAAGAGGAGGACG
PeEXPA16	GTGCCGTGCGTGAAGAA	GAAGTAGGAGTGGCCGTTG
PeEXPA17	GTTCAGGTACTTCAACCTGGTGC	GCGTTGGACTGCCAGTTCT
PeEXPA18	CGACCATCGCCATCTACCA	TCCACATCTGCGTCACCAC
PeTIP41	AAAATCATTGTAGGCCATTGTCG	ACTAAATTAAGCCAGCGGGAGTG

氨基酸 Amino acid	密码子 Codon	相对使用频率 RFSC /%	氨基酸 Amino acid	密码子 Codon	相对使用频率 RFSC /%	氨基酸 Amino acid	密码子 Codon	相对使用频率 RFSC /%	氨基酸 Amino acid	密码子 Codon	相对使用频率 RFSC /%
Phe	UUU	11.00	Ser	UCU	8.33	Tyr	UAU	10.50	Cys	UGU	8.00
Phe	UUC	89.00		UCC	36.00	Tyr	UAC	89.50	Cys	UGC	92.00
Leu	UUA	1.67		UCA	4.67	TER	UAA	18.00	TER	UGA	51.33
	UUG	5.33		UCG	19.67	TER	UAG	30.67	Trp	UGG	100.00
	CUU	9.83	Pro	CCU	9.25	His	CAU	14.00	Arg	CGU	6.00
	CUC	48.33		CCC	42.75	His	CAC	86.00		CGC	35.33
	CUA	2.83		CCA	8.50	Gln	CAA	12.50		CGA	4.00
	CUG	32.00		CCG	39.50	Gln	CAG	87.50		CGG	23.00
Ile	AUU	12.33	Thr	ACU	5.50	Asn	AAU	11.50	Ser	AGU	2.00
Ile	AUC	80.33		ACC	50.75	Asn	AAC	88.50	Ser	AGC	29.33
Met	AUA	7.00		ACA	7.75	Lys	AAA	8.50	Arg	AGA	7.67
Met	AUG	100.00		ACG	36.00	Lys	AAG	91.50	Arg	AGG	24.00
Val	GUU	8.00	Ala	GCU	10.00	Asp	GAU	14.00	Gly	GGU	10.25
	GUC	42.00		GCC	54.50	Asp	GAC	86.00		GGC	63.25
	GUA	3.00		GCA	8.00	Glu	GAA	20.00		GGA	6.50
	GUG	47.00		GCG	27.50	Glu	GAG	80.00		GGG	19.75

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