‘月月粉’月季NAC家族全基因组鉴定及皮刺发育相关成员的筛选

doi:10.3864/j.issn.0578-1752.2022.24.009

摘要/Abstract

摘要：

【目的】从‘月月粉’月季全基因组中鉴定NAC家族成员，并进行生物信息学和表达模式分析，为研究‘月月粉’NAC的潜在功能提供理论基础，筛选可能参与皮刺发育的候选基因。【方法】以拟南芥NAC氨基酸序列为参考，利用双向Blast及HMM结构域检索筛选RcNAC；对筛选成员进行理化性质、亚细胞定位、序列特征、顺式元件和系统进化分析；基于已释放转录组数据，分析RcNAC在不同组织器官，和不同逆境处理条件下的表达特性；同时通过‘月月粉’不同发育阶段皮刺组织转录组测序，筛选与皮刺发育可能相关的RcNAC。【结果】共鉴定得到116个RcNACs，均含有完整典型的NAM保守结构域，其编码蛋白包含69—713个氨基酸，等电点从4.43—9.54，分子质量从7.87—79.99 kD，81个RcNACs被预测定位于细胞核内；115个RcNACs在7条染色体上不均匀分布，1个RcNAC未明确位置信息；系统进化树分析将AtNACs、OsNACs和RcNACs聚为21类；在不同组织器官中，116个RcNACs表达模式各异，遭受水胁迫和感染灰霉病之后，31个RcNACs表达量发生变化；在衰老的花组织中，6个RcNACs表达量上升；皮刺转录组数据中检测到53个RcNACs，其中26个RcNACs为差异表达基因。【结论】基于已有转录组数据分析，RcNACs协同调控植物组织发育及逆境胁迫响应；结合皮刺转录组数据，部分成员可能参与皮刺细胞增殖、次生细胞壁生物合成及细胞程序性死亡等过程，可作为皮刺发育相关候选基因进行深入研究。

关键词: ‘月月粉’, NAC转录因子, 转录组测序, 皮刺发育

Abstract:

【Objective】This study was designed to identify the NAC gene family in Rosa chinensis Old Blush and to analyze the sequences characteristics and expression pattern of RcNACs to reveal the biological functions of RcNACs, which also provided an important foundation to explore the role of RcNACs in prickles. 【Method】The BLATP and HMMER search were conducted to identify NAC proteins in Rosa chinensis Old Blush using the sequences of NAC proteins of Arabidopsis. Physical and chemical properties, subcellular location, structure and phylogenetic relationship of each gene were further analyzed. Based on the released transcriptome data, the expression characteristics of RcNACs in different tissues and organs under different stress conditions were analyzed. What’s more, the technology of RNA-seq was used to screen RcNAC genes that might be related to the prickle development. 【Result】In this study, 116 NAC genes from Rosa chinensis Old Blush genome were identified and characterized. These RcNACs genes encoded proteins containing 69 to 713 amino acids, with the theoretical isoelectric points ranging from 4.43 to 9.54 and the molecular weight ranging from 7.87 to 79.99 kD. The prediction of subcellular localization showed that 81 RcNACs were located in the nucleus. Moreover, RcNACs were unevenly distributed on 7 chromosomes. According to phylogenetic relationships, AtNACs, OsNACs and RcNACs were clustered into 21 groups. These 116 RcNACs were differentially expressed in various tissues and organs, and the expression levels of 31 members changed in response to abiotic and biotic stresses. Furthermore, in the RNA-seq data of prickles, 53 RcNACs were detected, among which 26 members were differentially expressed genes. 【Conclusion】This study demonstrated that RcNACs were involved in the regulation of plant development and stress responses. Some members might be involved in the processes of prickle cell proliferation, secondary cell wall biosynthesis, and programmed cell death, which could be selected as candidate genes related with prickle development for further study.

Key words: Rosa chinensis ‘Old Blush’, NAC transcription factor, transcriptome sequencing, prickle development

由玉婉,张雨,孙嘉毅,张蔚. ‘月月粉’月季NAC家族全基因组鉴定及皮刺发育相关成员的筛选[J]. 中国农业科学, 2022, 55(24): 4895-4911.

YOU YuWan,ZHANG Yu,SUN JiaYi,ZHANG Wei. Genome-Wide Identification of NAC Family and Screening of Its Members Related to Prickle Development in Rosa chinensis Old Blush[J]. Scientia Agricultura Sinica, 2022, 55(24): 4895-4911.

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基因名称 Gene name	正向引物 Forward primer (5'-3')	反向引物 Reverse primer (5'-3')	基因ID Gene ID	基因注释 Gene annotation
RcNAC001	TGATGAAGGGACAAAGTGGGC	GCTCGATCTATCTTGGCCATT	RchiOBHmChr0c19g0500091	NAC
RcNAC010	TTCGGTGACGGGCAATTCTTA	CTGCTCAACCAGAGGTTCACT	RchiOBHmChr1g0334901	NAC
RcNAC012	CGACAACACCAGCAGCATAAC	CAAAAGCTCCCTCCTGATCGT	RchiOBHmChr1g0360971	NAC
RcNAC057	TGGGAGTAGGACCGATTGGAT	GATGAAGAACAAGGCGCAAGG	RchiOBHmChr4g0429461	NAC
RcNAC063	AATGTGGTATGGGCACTCCAG	TCCCTATTCTGGCCTCCTTGA	RchiOBHmChr5g0009331	NAC
RcNAC098	GCTTCTCCAACCATGAGTCCA	GTTTTCAAGCAAGGCCCTCAG	RchiOBHmChr7g0181751	NAC
RcNAC111	CTGTGTGAGGGTAAGCAGTGG	CGACACAACACGTATCCGCTA	RchiOBHmChr7g0225481	NAC
RcGST	CCTCAGATCCCAAGCCAAGTT	TCGGGCACTCTGGTTCAATAC	RchiOBHmChr5g0027341	谷胱甘肽转移酶Glutathione transferase
RcTGL	CAGGCATCAGGGAAGAACCTT	CCCAAACCATACACACCCGTA	RchiOBHmChr2g0141171	三酰基甘油脂肪酶Triacylglycerol lipase
RcWRKY	CTGAGGTAGCTTTGCCTCACA	GTGTTTCCCCTCGTATGTGGT	RchiOBHmChr2g0166991	WRKY
RcbHLH	GGAAAAACGACCCCGGAAAAG	GAAGACGTTCGGGACTCTTGT	RchiOBHmChr7g0209751	bHLH
RcEXPA	TTAGTGGTGGACACCTTGCTG	CAAAATGTCCTGGCCCAAACC	RchiOBHmChr6g0279781	EXPA
RcNAC032	GTGGTGGCACTGGAATTAGGA	TGTGATATTTGGTGTGGCGGA	RchiOBHmChr1g0383091	NAC
RcNAC035	TGGACCGGAATAAAGTGGCAA	CGGCGAGAATACATGATCCGA	RchiOBHmChr2g0122871	NAC
RcNAC052	GAAAGCTCTGCGACTCCAAAC	TGTTGTTGTCTCCTCCAGCAA	RchiOBHmChr3g0482951	NAC

分组 Group	基因数 Gene	范围 Range			亚细胞定位 Subcellular localization
分组 Group	基因数 Gene	蛋白长度 Length (aa)	等电点 pI	分子质量 Molecular weight (kD)	亚细胞定位 Subcellular localization
A	5	292-494	5.07-9.16	32.8-55.76	细胞核 Nucleus
C	22	75-573	4.87-9.08	8.69-64.42	细胞核 Nucleus:14; 液泡 Cytosol:3; 内质网 Endoplasmic reticulum:3; 叶绿体 Chloroplast:2
D	4	382-617	4.66-6.01	42.85-67.7	细胞核 Nucleus:2; 叶绿体 Chloroplast:2
E	4	268-688	5.04-5.62	30.46-78.38	细胞核 Nucleus:2; 细胞膜 Plasma membrane:1; 过氧化物酶体 Peroxisome:1
F	2	577-713	5-5.05	64.55-79.99	细胞核 Nucleus
G	8	184-474	5.97-9.78	20.48-52.9	细胞核 Nucleus
H	2	287-341	5.67-6.45	33.02-38.55	细胞核 Nucleus:1; 叶绿体 Chloroplast:1
I	8	179-421	5.07-9.35	21.03-47.55	细胞核 Nucleus:5; 过氧化物酶体 Peroxisome:1; 叶绿体 Chloroplast:2
J	2	225-596	4.9-9.12	26.13-67.31	细胞核 Nucleus:1; 叶绿体 Chloroplast:1
L	3	150-379	6.4-8.55	17.19-25.83	细胞核 Nucleus:1; 叶绿体 Chloroplast:1; 液泡 Cytosol:1
M	3	256-291	5.91-6.55	28.94-32.66	细胞核 Nucleus
N	8	166-467	6.18-9.54	19.44-53.02	细胞核 Nucleus:6; 液泡 Cytosol:2
O	2	289-315	6.32-8.13	32.96-36.17	细胞核 Nucleus
P	1	352	8.38	39.75	细胞核 Nucleus
Q	7	162-552	5.68-9.54	18.63-62.59	细胞核 Nucleus:5; 液泡 Cytosol:1; 叶绿体 Chloroplast:1
R	5	197-251	4.73-9.42	22.55-28.29	细胞核 Nucleus:4; 液泡 Cytosol:1
S	5	172-658	5.4-9.47	19.83-76.46	细胞核 Nucleus:2; 液泡 Cytosol:2; 叶绿体 Chloroplast:1
T	25	69-595	4.43-9.41	7.87-66.08	细胞核 Nucleus:17; 液泡 Cytosol:5; 叶绿体 Chloroplast:2; 高尔基体 Golgi apparatus:1