全基因组分析杨树WOX基因家族在茎部发育中的作用
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摘要
WUSCHEL-related homeobox (WOX)家族是植物特有的转录因子家族,参与分生组织细胞分裂分化、初生和次生物质代谢及植物激素信号转导等多个发育过程,目前尚未有从全基因组分析该基因家族参与杨树茎部发育的相关研究。本项研究旨在对杨树WOX基因家族进行鉴定,在杨树基因中发现18个WOX候选基因,将这些候选基因分为三组,同一分组的大多数WOX家族成员具有相似的基因结构和保守的基序。根据不同发育阶段茎部转录组数据,系统分析了WOX家族成员在茎部不同发育阶段的特异表达情况,并采用qRT-PCR对上述结果进行了验证。结果表明,杨树WOX基因家族在茎部不同发育阶段表现出不同的表达模式,为毛果杨WOX家族的功能研究与利用奠定基础。
The WUSCHEL-related homeobox( WOX) family is a plant-specific transcription factor family involved in multiple developmental processes including meristematic cell division and differentiation,primary and secondary biomass metabolism,and plant hormone signaling. At present,there is no relevant research on genome-wide analysis of the gene family involved in stem development of poplar. We identified the poplar WOX gene family,and found 18 WOX candidate genes in the poplar gene. These candidate genes were divided into three groups. Most of the WOX family members in the same group had similar gene structure and conservation motif. According to the transcriptome data of stems at different developmental stages,the specific expression of WOX family members in different developmental stages of stems was systematically analyzed,and the above results were verified by qRT-PCR. The poplar WOX gene family showed different expression patterns at different developmental stages of the stem,which laid a foundation for the functional research and utilization of the WOX family.
The WUSCHEL-related homeobox( WOX) family is a plant-specific transcription factor family involved in multiple developmental processes including meristematic cell division and differentiation,primary and secondary biomass metabolism,and plant hormone signaling. At present,there is no relevant research on genome-wide analysis of the gene family involved in stem development of poplar. We identified the poplar WOX gene family,and found 18 WOX candidate genes in the poplar gene. These candidate genes were divided into three groups. Most of the WOX family members in the same group had similar gene structure and conservation motif. According to the transcriptome data of stems at different developmental stages,the specific expression of WOX family members in different developmental stages of stems was systematically analyzed,and the above results were verified by qRT-PCR. The poplar WOX gene family showed different expression patterns at different developmental stages of the stem,which laid a foundation for the functional research and utilization of the WOX family.
引文
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2 . Tuskan G A,Difazio S,Jansson S,et al. The genome of black cottonwood,Populus trichocarpa(Torr.&Gray)[J].Science,2006,313(5793):1596-1604.
3 . Zhang X,Zong J,Liu J H,et al. Genome-wide analysis of WOX gene family in rice,sorghum,maize,Arabidopsis and poplar[J]. Journal of Integrative Plant Biology,2010,52(11):1016-1026.
4 . Schoof H,Lenhard M,Haecker A,et al. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes[J]. Cell,2000,100(6):635-644.
5 . Sarkar A K,Luijten M,Miyashima S,et al. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers[J]. Nature,2007,446(7137):811-814.
6 . Haecker A,Groβ-Hardt R,Geiges B,et al. Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana[J]. Development,2004,131(3):657-668.
7 . Hirakawa Y,Kondo Y,Fukuda H. TDIF peptide signaling regulates vascular stem cell proliferation via the WOX4 homeobox gene in Arabidopsis[J]. The Plant Cell,2010,22(8):2618-2629.
8 . Park S O,Zheng Z G,Oppenheimer D G,et al. The PRETTY FEW SEEDS2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development[J]. Development,2005,132(4):841-849.
9 . Zhu J H,Shi H Z,Lee B H,et al. An Arabidopsis homeodomain transcription factor gene,HOS9,mediates cold tolerance through a CBF-independent pathway[J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(26):9873-9878.
10 . Liu J C,Sheng L H,Xu Y Q,et al. WOX11 and 12 are involved in the first-step cell fate transition during de novo root organogenesis in Arabidopsis[J]. The Plant Cell,2014,26(3):1081-1093.
11 . Romera-Branchat M,Ripoll J J,Yanofsky M F,et al. The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit[J]. The Plant Journal,2013,73(1):37-49.
12 . Tang F,Chen N Z,Zhao M L,et al. Identification and functional divergence analysis of WOX gene family in paper mulberry[J]. International Journal of Molecular Sciences,2017,18(8):1782.
13 . Yang Z E,Gong Q,Qin W Q,et al. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses[J]. BMC Plant Biology,2017,17(1):113.
14 .唐跃辉,包欣欣,王健,等.小桐子WOX基因家族全基因组鉴定与表达分析[J].分子植物育种,2019,17(4):1154-1162.Tang Y H,Bao X X,Wang J,et al. Genome-wide identification and expression analysis of the WOX gene family in physic nut[J]. Molecular Plant Breeding,2019,17(4):1154-1162.
15 . Liu J W,Hai G H,Wang C,et al. Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth[J]. Journal of Proteomics,2015,126:94-108.
16 . Wang Z C,Liu Q G,Wang H Z,et al. Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa[J]. Scientific Reports,2016,6(1):36274.
17 . Li D D,Xu X M,Hu X Q,et al. Genome-wide analysis and heavy metal-induced expression profiling of the HMA gene family in Populus trichocarpa[J]. Frontiers in Plant Science,2015,6:1149.
18 . Zhang J,Li Y,Jia H X,et al. The heat shock factor gene family in Salix suchowensis:a genome-wide survey and expression profiling during development and abiotic stresses[J]. Frontiers in Plant Science,2015,6:748.
19 . Zang L N,Zheng T C,Chu Y G,et al. Genome-wide analysis of the fasciclin-like arabinogalactan protein gene family reveals differential expression patterns,localization,and salt stress response in Populus[J]. Frontiers in Plant Science,2015,6:1140.
20 . Han H B,Zhang G H,Wu M Y,et al. Identification and characterization of the Populus trichocarpa CLE family[J].BMC Genomics,2016,17:174.
21 . Zhang C X,Meng S,Li M J,et al. Genomic identification and expression analysis of the phosphate transporter gene family in poplar[J]. Frontiers in Plant Science,2016,7:1398.
22 .芦强,邵芬娟,邱德有.毛果杨LBD基因家族的全基因组分析[J].基因组学与应用生物学,2018,37(1):313-325.Lu Q,Shao F J,Qin D Y. Genome-wide analysis of gene family of lateral organ boundaries domain in Populus trichocarpa[J]. Genomics and Applied Biology,2018,37(1):313-325.
23 . Zhong R Q,Mccarthy R L,Lee C,et al. Dissection of the transcriptional program regulating secondary wall biosynthesis during wood formation in poplar[J]. Plant Physiology,2011,157(3):1452-1468.
2 . Tuskan G A,Difazio S,Jansson S,et al. The genome of black cottonwood,Populus trichocarpa(Torr.&Gray)[J].Science,2006,313(5793):1596-1604.
3 . Zhang X,Zong J,Liu J H,et al. Genome-wide analysis of WOX gene family in rice,sorghum,maize,Arabidopsis and poplar[J]. Journal of Integrative Plant Biology,2010,52(11):1016-1026.
4 . Schoof H,Lenhard M,Haecker A,et al. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes[J]. Cell,2000,100(6):635-644.
5 . Sarkar A K,Luijten M,Miyashima S,et al. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers[J]. Nature,2007,446(7137):811-814.
6 . Haecker A,Groβ-Hardt R,Geiges B,et al. Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana[J]. Development,2004,131(3):657-668.
7 . Hirakawa Y,Kondo Y,Fukuda H. TDIF peptide signaling regulates vascular stem cell proliferation via the WOX4 homeobox gene in Arabidopsis[J]. The Plant Cell,2010,22(8):2618-2629.
8 . Park S O,Zheng Z G,Oppenheimer D G,et al. The PRETTY FEW SEEDS2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development[J]. Development,2005,132(4):841-849.
9 . Zhu J H,Shi H Z,Lee B H,et al. An Arabidopsis homeodomain transcription factor gene,HOS9,mediates cold tolerance through a CBF-independent pathway[J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(26):9873-9878.
10 . Liu J C,Sheng L H,Xu Y Q,et al. WOX11 and 12 are involved in the first-step cell fate transition during de novo root organogenesis in Arabidopsis[J]. The Plant Cell,2014,26(3):1081-1093.
11 . Romera-Branchat M,Ripoll J J,Yanofsky M F,et al. The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit[J]. The Plant Journal,2013,73(1):37-49.
12 . Tang F,Chen N Z,Zhao M L,et al. Identification and functional divergence analysis of WOX gene family in paper mulberry[J]. International Journal of Molecular Sciences,2017,18(8):1782.
13 . Yang Z E,Gong Q,Qin W Q,et al. Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses[J]. BMC Plant Biology,2017,17(1):113.
14 .唐跃辉,包欣欣,王健,等.小桐子WOX基因家族全基因组鉴定与表达分析[J].分子植物育种,2019,17(4):1154-1162.Tang Y H,Bao X X,Wang J,et al. Genome-wide identification and expression analysis of the WOX gene family in physic nut[J]. Molecular Plant Breeding,2019,17(4):1154-1162.
15 . Liu J W,Hai G H,Wang C,et al. Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth[J]. Journal of Proteomics,2015,126:94-108.
16 . Wang Z C,Liu Q G,Wang H Z,et al. Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa[J]. Scientific Reports,2016,6(1):36274.
17 . Li D D,Xu X M,Hu X Q,et al. Genome-wide analysis and heavy metal-induced expression profiling of the HMA gene family in Populus trichocarpa[J]. Frontiers in Plant Science,2015,6:1149.
18 . Zhang J,Li Y,Jia H X,et al. The heat shock factor gene family in Salix suchowensis:a genome-wide survey and expression profiling during development and abiotic stresses[J]. Frontiers in Plant Science,2015,6:748.
19 . Zang L N,Zheng T C,Chu Y G,et al. Genome-wide analysis of the fasciclin-like arabinogalactan protein gene family reveals differential expression patterns,localization,and salt stress response in Populus[J]. Frontiers in Plant Science,2015,6:1140.
20 . Han H B,Zhang G H,Wu M Y,et al. Identification and characterization of the Populus trichocarpa CLE family[J].BMC Genomics,2016,17:174.
21 . Zhang C X,Meng S,Li M J,et al. Genomic identification and expression analysis of the phosphate transporter gene family in poplar[J]. Frontiers in Plant Science,2016,7:1398.
22 .芦强,邵芬娟,邱德有.毛果杨LBD基因家族的全基因组分析[J].基因组学与应用生物学,2018,37(1):313-325.Lu Q,Shao F J,Qin D Y. Genome-wide analysis of gene family of lateral organ boundaries domain in Populus trichocarpa[J]. Genomics and Applied Biology,2018,37(1):313-325.
23 . Zhong R Q,Mccarthy R L,Lee C,et al. Dissection of the transcriptional program regulating secondary wall biosynthesis during wood formation in poplar[J]. Plant Physiology,2011,157(3):1452-1468.