日本落叶松木质部发育相关基因筛选及其共表达网络构建

doi:10.11707/j.1001-7488.20210105

摘要/Abstract

摘要：

目的: 鉴定日本落叶松木质部发育相关基因，构建核心基因与木质部发育相关基因的共表达网络，为后期开展日本落叶松木材形成相关研究提供参考。方法: 对日本落叶松木质部、韧皮部和针叶3个组织进行二代和三代转录组测序，利用R软件的DEseq2包筛选木质部相对韧皮部和木质部相对针叶的差异表达基因，通过整合2组差异基因获得木质部特异表达基因，借助GO、KEGG及BLASTN等生物信息学分析手段探索基因功能，利用WGCNA分析构建木质部特异表达基因共表达网络。结果: 共获得2 596个木质部特异的高表达和低表达基因；GO分析结果显示这些基因在代谢过程、细胞过程、定位膜、细胞、细胞组件、催化活性、位点结合和转运活性等分类中显著富集；KEGG分析结果显示这些基因在淀粉和蔗糖代谢、类黄酮生物合成和代谢途径通路中显著富集，在苯丙烷代谢途径及淀粉和蔗糖代谢途径中分别富集到38个和196个基因；鉴定出木材形成相关基因，包括木质素合成相关基因PAL4、CCR1、C4H、HCT、COMT1、PER12、PER52、CYP98A3、LAC12和LAC17等，纤维素和半纤维素合成相关基因DEC、CEL1、Csl、CTL2和SPS3等；2 596个木质部特异的高表达和低表达基因经WGCNA分析后筛选出与木质部发育相关基因关联度较高的17个核心基因。结论: 筛选的日本落叶松木质部发育相关基因参与半乳甘露聚糖合成、木葡聚糖合成、纤维素微纤丝形成、细胞壁纤维素合成、次生细胞壁形成过程、纤维伸长过程、调控合成木质素的碳代谢流、木质素生物合成及降解、木质素单体聚合、木质素单体甲基化和细胞程序化死亡等木材形成相关生物学过程；在共表达网络中筛选出的17个核心基因可作为今后研究的重点来探索其在木材形成过程中的具体功能。

关键词: 日本落叶松, 木质部, 差异表达基因, GO, KEGG, 核心基因

Abstract:

Objective: In this study, we identified xylem development-related genes in differentiating xylem of Larix kaempferi and built a gene co-expression network among hub genes and xylem development-related genes, aiming to provide reference for wood formation-related studies in L. kaempferi in future. Method: Illumia-seq and SMRT-seq were used to sequence xylem, phloem and needles of L. kaempferi; The differential expressed genes(DEGs) between xylem and phloem and between xylem and needles were identified by DEseq2 package in R software. The specifically expressed genes in differentiating xylem were obtained by comparing DEGs in the two parallel groups. The functions of these xylem-specific genes were predicted using GO, KEGG and BLASTN method. WGCNA method was used to build a co-expression network. Result: We obtained 2 596 genes in total that were specifically up or down regulated in the differentiating xylem of L. kaempferi; GO analysis showed that these genes were mainly enriched in metabolic process, cellular process, localization, membrane, cell, cell part, catalytic activity, binding and transporter activity. KEGG analysis showed that these genes were significantly enriched in starch and sucrose metabolism, flavonoid biosynthesis and metabolic pathways. 38 and 196 genes were enriched in phenylpropanoid biosynthesis and starch and sucrose metabolism pathway, respectively; In the differentiating xylem of L. kaempferi, lignin formation-related genes were identified including PAL4, CCR1, C4H, HCT, COMT1, PER12, PER52, CYP98A3, LAC12 and LAC17, and cellulose and hemicellulose formation-related genes were identified including DEC, CEL1, Csl, CTL2 and SPS3. All 2 596 up or down regulated genes were analysed by WGCNA method, 17 hub genes having close relationship with wood formation-related genes were obtained. Conclusion: Xylem development-related genes in Larix kaempferi participate in biological processes of wood formation such as galactomannan biosynthesis, xyloglucan biosynthesis, microfibrils formation, fiber biosynthesis in cell wall, secondary cell wall formation, fiber elongation, carbon flux to lignins, biosynthesis and degradation of lignin, monolignol polymerization, monolignol methylation and programmed cell death; the 17 hub genes in gene co-expression network are candidates for function exploration during wood formation in future.

Key words: Larix kaempferi, xylem, differentially expressed genes, GO, KEGG, hub gene

中图分类号:

S718.46

李慧,代新仁,周再知,李全梓. 日本落叶松木质部发育相关基因筛选及其共表达网络构建[J]. 林业科学, 2021, 57(1): 40-52.

Hui Li,Xinren Dai,Zaizhi Zhou,Quanzi Li. Screening and Co-Expression Network Building of Xylem Development-Related Genes in Larix kaempferi[J]. Scientia Silvae Sinicae, 2021, 57(1): 40-52.

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木材形成相关基因功能注释"

基因 Gene	拟南芥同源基因 Homolog in Arabidopsis	基因名 Gene name	注释 Annotation	参考文献 Reference
Lkgene393, 1210, 546, 10216, 1545, 189	AT3G10340	PAL4	催化L-苯丙氨酸生物合成中的第一反应Catalyze the first reaction in the biosynthesis from L-phenylalanine	杨立，2016
Lkgene3952	AT1G15950	CCR1	参与木质素合成的后期反应Involve in the latter stages of lignin biosynthesis	Wang et al., 2019a; Yan et al., 2019
Lkgene231, 166	AT2G30490	C4H	调控合成木质素的碳代谢流Control carbon flux to lignins	Kajita et al., 1997
Lkgene19432	AT5G05340	PER52	木质素生物合成及降解Biosynthesis and degradation of lignin	Valério et al., 2004
Lkgene4199, 8671	AT1G71695	PER12	木质素生物合成及降解Biosynthesis and degradation of lignin	Valério et al., 2004
Lkgene1394, 2505	AT5G48930	HCT	参与木质素合成Involve in the biosynthesis of lignin	杨立，2016
Lkgene3070, 834, 8363	AT5G54160	COMT1	催化木质素单体甲基化Catalyze the methylation of monolignols	Osakabe et al., 1999
Lkgene5584, 540, 826, 816	AT2G40890	CYP98A3	参与木质素生物合成Essential for the biosynthesis of lignin	Amann et al., 2004
Lkgene26047, 24638, 30550, 18632, 23499, 27977, 20214, 28123, 30125, 27556, 17746, 19212, 18598, 28597, 27567, 20222, 25143, 27539, 27532, 27443, 24826, 27783, 29817, 18090, 20304, 16114, 22264, 29559, 19527, 24209, 24522, 26047, 22691, 19315, 20120, 17571	AT5G05390	LAC12	木质素降解Degradation of lignin	Rigamonte et al., 2011
Lkgene2825, 12019, 19328, 27605, 21583, 13836, 13786, 5005, 16084, 12626, 17261, 16031, 5049, 5610, 15000, 10412, 25453, 30079, 29273, 20576, 10602, 13502, 15304	AT5G60020	LAC17	木质素单体聚合Polymerization of monolignols	Berthet et al., 2011
Lkgene24340, 114, 7969, 13943	AT3G16920	CTL2	纤维素合成及纤维素和半纤维素相互作用Biosynthesis of cellulose and interactions between hemicelluloses and cellulose	Sanchez et al., 2012
Lkgene1782	AT2G19860	HXK2	调控细胞程序化死亡Regulate the execution of programmed cell death	Kim et al., 2006
Lkgene2468, 1670, 3934, 811, 10000, 7280, 1786	AT5G03760	CSLA9	参与半乳甘露聚糖合成Participate in galactomannan biosynthesis	徐宗昌等，2017
Lkgene25783, 11296, 7496	AT5G20950	F22D1.120	参与木葡聚糖代谢Participate in xyloglucan metabolism	Sampedro et al., 2017
Lkgene946, 1213, 1637	AT5G49720	DEC	参与纤维素微纤维和次生细胞壁形成Require for cellulose microfibrils formation and secondary cell wall formation	Nicol et al., 1998
Lkgene5019	AT1G70710	CEL1	参与细胞壁纤维素形成Require for cellulose formation of the cell wall	Nicol et al., 1998
Lkgene1125, 5823, 4380, 6726, 12809, 2982	AT1G04920	SPS3	参与纤维伸长Regulate fiber elongation	Lutfiyya et al., 2007

表3

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组织 Tissue	总读长 Total reads	比对读长 Mapped reads	比对率 Mapping rate	总基因数 Total gene number
木质部Xylem	66 463 409	24 451 888	36.79%	21 535
韧皮部Phloem	77 166 823	31 954 781	41.41%	22 986
针叶Needle	63 449 442	34 865 468	54.95%	23 233

基因号 Gene ID	毛果杨同源基因 Homolog in P.trichocarpa	基因名 Gene name	基因号 Gene ID	毛果杨同源基因 Homolog in P.trichocarpa	基因名 Gene name
Lkgene 10602	Potri.001G054600	LAC17	Lkgene8671	Potri.005G195600	PER12
Lkgene1213	Potri.001G078900	KOR	Lkgene6367	Potri.005G203300	F7D19.4
Lkgene5088	Potri.001G083100	MJC20.20	Lkgene7691	Potri.006G114400	LRR-RLK
Lkgene8137	Potri.001G239300	PLL4	Lkgene11959	Potri.006G136700	SUS2
Lkgene19612	Potri.001G312600	UGT85A2	Lkgene26047	Potri.008G073700	LAC12
Lkgene4380	Potri.001G317600	SPS3	Lkgene13943	Potri.010G141600	HST
Lkgene18758 Lkgene27841	Potri.002G202300	SUS2	Lkgene1394 Lkgene2505	Potri.003G183900	HST
Lkgene560 Lkgene979 Lkgene961	Potri.004G089300	F28G11.11	Lkgene8640 Lkgene6881 Lkgene8812 Lkgene28309 Lkgene19434	Potri.005G145300	SBT1.7
Lkgene540 Lkgene816	Potri.006G033300	CYP98A3	Lkgene166 Lkgene231	Potri.013G157900	CYP73A5
Lkgene416	Potri.003G126800	TUBB6	Lkgene19432	Potri.013G083600	PER52
Lkgene1637	Potri.003G151700	KOR	Lkgene5019	Potri.014G126900	CEL1
Lkgene3952	Potri.003G181400	CCR1	Lkgene1882	Potri.014G197500	—
Lkgene3070	Potri.015G003100	OMTI	Lkgene7135	Potri.017G029000	T28P16.12
Lkgene1125	Potri.017G057800	SPS3	Lkgene15312	Potri.018G096100	AXX17
Lkgene1643	Potri.019G038200	MS1	Lkgene189	Potri.019G049500	4CL2
Lkgene11485	Potri.T070100.1	MS2	Lkgene15627	—	—

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