JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2020, Vol. 44 ›› Issue (3): 41-48.doi: 10.3969/j.issn.1000-2006.201908020
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SHAN Xuemeng(), YANG Kebin, SHI Jingjing, ZHU Chenglei, GAO Zhimin(
)
Received:
2019-08-14
Revised:
2020-02-27
Online:
2020-05-30
Published:
2020-06-11
Contact:
GAO Zhimin
E-mail:shanxuemeng@icbr.ac.cn;gaozhimin@icbr.ac.cn
CLC Number:
SHAN Xuemeng, YANG Kebin, SHI Jingjing, ZHU Chenglei, GAO Zhimin. Genome‑wide identification and expression analysis of GeBP transcription factor gene family in moso bamboo[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2020, 44(3): 41-48.
Table 1
Primers used in quantitative real?time PCR"
基因名称 | 正向序列(5'→3') | 反向序列(5'→3') | 基因名称 | 正向序列(5'→3') | 反向序列(5'→3') |
---|---|---|---|---|---|
gene name | forward sequence | reverse sequence | gene name | forward sequence | reverse sequence |
PeGeBP1 | GCGGCAGCAGTTGCCAC | GCGGCAAACTCCGTCGTAC | PeGeBP10 | GCCAAGAAGGTTTGGGGAA | CCAAATCCTCATCGCTATCTCC |
PeGeBP2 | GTACCGCGTCTGCGCCAA | GGGGTTGATGTCGTCCTCGTC | PeGeBP11 | TTGCCAAGAAGGTTTGGAGG | TCCACTATCTTGCTCCTCCTCA |
PeGeBP3 | GCCAACTCCAGTATCCCCAAT | GTGAGCCCAAGAAATGGTG | PeGeBP12 | GCGCTCGCCGCGGTGA | GGAGCCCCTGATGGAGTCGAAGA |
PeGeBP4 | TGACTACAATGGGATTAGTTCCTCC | TCGGCTACAAGGACGGCAC | PeGeBP13 | GCGCTTCTGCTGCTCTGC | CCAGAATGCGGACCTCGTC |
PeGeBP5 | GGCGCCGCATCGAGAT | GCCTGACCCTTTTCGACTTG | PeGeBP14 | GCCGGTTCCGGCCTTCAAA | AGCCTCTTCTTCTCCGTCTCG |
PeGeBP6 | CCCAGTAGAGGCTGACGCTTAC | CGCGCATTCCTCCTCCAG | PeGeBP15 | CACGCTGGTGGAGCCCA | GCGTGAAGGAACTTGCTCTTG |
PeGeBP7 | CCCTGTAGAGGATGACGTGGAG | TCACCAAGCACCTCGCTCA | PeGeBP16 | CACGGCGAGCTGCCAAACTC | CCTTCTTGGCGTCGTTGTTGTG |
PeGeBP8 | GAGCCCCGAAGATGAGATCAC | ACTGCCCACGAATCTGACTGT | PeNTB | TCTTGTTTGACACCGAAGAGGAG | AATAGCTGTCCCTGGAGGAGTTT |
PeGeBP9 | CCCAATGGGGAAATCAAGTCAC | GCACTTGCACTGGTTGAGGG |
Table 2
Basic characteristics of the proteins encoded by PeGeBPs and subcellular location"
基因 | 登录号 | 多肽长/aa | 分子质量/ku | 理论等电点 | 亚细胞定位 | 基因 | 登录号 | 多肽长/aa | 分子质量/ku | 理论等电点 | 亚细胞定位 |
---|---|---|---|---|---|---|---|---|---|---|---|
gene | accession ID | peptide length | molecular weight | pI | subcellular location | gene | accession ID | peptide length | molecular weight | pI | subcellular location |
PeGeBP1 | PH01000068G0840 | 382 | 41.43 | 5.61 | 细胞核 nucleus | PeGeBP9 | PH01001059G0320 | 313 | 34.64 | 9.24 | 细胞核、细胞质 nucleus, cytoplasm |
PeGeBP2 | PH01000133G0910 | 370 | 39.07 | 5.02 | 细胞核、细胞质 nucleus, cytoplasm | PeGeBP10 | PH01001072G0510 | 284 | 31.57 | 9.61 | 细胞核 nucleus |
PeGeBP3 | PH01000142G0610 | 277 | 29.81 | 6.01 | 细胞核、细胞质 nucleus, cytoplasm | PeGeBP11 | PH01001127G0440 | 284 | 31.72 | 9.67 | 细胞核 nucleus |
PeGeBP4 | PH01000328G0180 | 308 | 32.95 | 5.58 | 细胞核、细胞质 nucleus, cytoplasm | PeGeBP12 | PH01001308G0200 | 285 | 30.38 | 9.90 | 细胞核 nucleus |
PeGeBP5 | PH01000400G0800 | 567 | 62.17 | 5.97 | 细胞核 nucleus | PeGeBP13 | PH01002051G0290 | 296 | 33.38 | 9.42 | 细胞核 nucleus |
PeGeBP6 | PH01000722G0060 | 219 | 23.37 | 6.54 | 细胞质 cytoplasm | PeGeBP14 | PH01003139G0080 | 547 | 58.77 | 7.08 | 细胞核 nucleus |
PeGeBP7 | PH01000887G0620 | 286 | 30.75 | 10.14 | 细胞核 nucleus | PeGeBP15 | PH01005573G0030 | 286 | 30.48 | 9.90 | 细胞核 nucleus |
PeGeBP8 | PH01000937G0050 | 291 | 31.33 | 8.79 | 细胞核 nucleus | PeGeBP16 | PH01005780G0020 | 275 | 30.82 | 9.26 | 细胞核、细胞质 nucleus, cytoplasm |
1 | BALKUNDE R, PESCH M, HÜLSKAMP M. Trichome patterning in Arabidopsis thaliana from genetic to molecular models[J]. Current Topics Development Biology, 2010, 91(91): 299-321. DOI: 10.1016/S0070-2153(10)91010‑7. |
2 | 高英, 郭建强, 赵金凤. 拟南芥表皮毛发育的分子机制[J]. 植物学报, 2011, 46(1): 119-127. |
GAO Y, GUO J Q, ZHAO J F. Molecular mechanism of epidermal hair development in Arabidopsis thaliana[J]. Chinese Bulletin of Botany, 2011, 46(1): 119-127. DOI: 10.3724/SP.J.1259.2011.00119. | |
3 | 张继伟, 赵杰才, 周琴, 等. 植物表皮毛研究进展[J]. 植物学报, 2018, 53(5): 155-166. |
ZHANG J W, ZHAO J C, ZHOU Q, et al. Progress in research of plant trichome[J]. Chinese Bulletin of Botany, 2018, 53(5): 155-166. DOI: 10.11983/CBB17078. | |
4 | ATALAY Z, CELEP F, BARA F, et al. Systematic significance of anatomy and trichome morphology in Lamium (Lamioideae; Lamiaceae)[J]. Flora, 2016, 225: 60-75. DOI: 10.1016/j.flora.2016.10.006. |
5 | 江泽慧. 世界竹藤[M]. 沈阳:辽宁科学技术出版社, 2002. |
JIANG Z H. Bamboo and rattan in the world[M]. Shenyang: Liaoning Science and Technology Publishing House, 2002. | |
6 | 张文燕, 马乃训. 竹类植物花期生物学特性[J]. 林业科学研究, 1989, 2(6): 596-600. |
ZHANG W Y, MA N X. Biological characteristics of bamboo plants at flowering stage[J]. Forest Research, 1989, 2(6): 596-600. DOI:10.13275/j.cnki.lykxyj.1989.06.019. | |
7 | 朱振贤, 张芬耀, 宋盛, 等. 竹亚科植物分类研究进展[J]. 世界林业研究, 2017, 30(3): 35-40. |
ZHU Z X, ZHANG F Y, SONG S, et al. Research advances in Bambuseae taxonomy[J]. World Forest Research, 2017, 30(3): 35-40. DOI: 10.13348/j.cnki.sjlyyj.2007.0033.y. | |
8 | 王润辉, 夏念和, 林汝顺. 箣竹属和牡竹属(竹亚科)叶表皮微形态特征[J]. 热带亚热带植物学报, 2002, 10(1): 22-26. |
WANG R H, XIA N H, LIN R S. Micromorphological study on leaf epiderm is of Bambusa and Dendrocalamus (Poaceae: Bambusoideae)[J]. Journal of Tropical and Subtropical Botany, 2002, 10(1): 22-26. DOI: 10.3969/j.issn.1005-3395.2002.1.004. | |
9 | 普莉, 索金凤, 薛勇彪. 植物表皮毛发育的分子遗传控制[J]. 遗传学报, 2003, 30(11): 1078-1084. |
PU L, SUO J F, XUE Y B. Molecular control of plant trichome development[J]. Journal of Genetics and Genomics, 2003, 30(11): 1078-1084. | |
10 | CHEVALIER F, PERAZZA D, LAPORTE F, et al. GeBP and GeBP‑like proteins are noncanonical leucine‑zipper transcription factors that regulate cytokinin response in Arabidopsis[J]. Plant Physiology, 2008, 146(3): 1142-1154. DOI: 10.2307/40065924. |
11 | 陈凯, 刘金秋, 宋海慧, 等. 番茄GeBP转录因子家族的鉴定及其进化和表达分析[J]. 分子植物育种, 2017, 15(9): 3438-3445. |
CHEN K, LIU J Q, SONG H H, et al. Identification, evolution and expression analysis of GeBP transcription factors family in tomato[J]. Molecular Plant Breeding, 2017, 15(9): 3438-3445. DOI: 10.13271/j.mpb.015.003438. | |
12 | 石蕾. 水稻GeBP家族基因的功能初探[D]. 武汉:华中农业大学, 2013. |
SHI L. Preliminary functional analysis of the GeBP gene family in rice[D]. Wuhan: Huazhong Agricultural University, 2013. | |
13 | CURABA J, HERZOG M, VACHON G. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA‑binding activity and is regulated by KNAT1[J]. The Plant Journal, 2003, 33(2): 305-317. DOI: 10.1046/j.1365-313X.2003.01622.x. |
14 | PENG Z H, LU Y, LI L B, et al. The draft genome of the fast growing non‑timber forest species moso bamboo (Phyllostachys heterocycla)[J]. Nature Genetics, 2013, 45(4): 456-461. DOI: 10.1038/ng.2569. |
15 | ZHAO H S, PENG Z H, FEI B H, et al. BambooGDB: a bamboo genome database with functional annotation and an analysis platform[J]. Database (Oxford), 2014, 2014: bau006. DOI: 10.1093/database/bau006. |
16 | GAO Z M, LI X P, LI L B, et al. An effective method for total RNA isolation from bamboo[J]. Chinese Forestry Science and Technology, 2006, 5(3): 52-54. |
17 | 郭安源, 朱其慧, 陈新, 等. GSDS: 基因结构显示系统[J]. 遗传, 2007, 29(8): 1023-1026. |
GUO A Y, ZHU Q H, CHEN X, et al. GSDS: a gene structure display server[J]. Hereditas, 2007, 29(8): 1023-1026. DOI: 10.3321/j.issn:0253-9772.2007.08.021. | |
18 | TAMURA K, STECHER G, PETERSON D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Molecular Biology and Evolution, 2013, 30(12): 2725-2719. DOI: 10.1093/molbev/mst197. |
19 | ZHAO H S, GAO Z M, WANG L, et al. Chromosome‑level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. GigaScience, 2018, 7(10): gjy115. DOI: 10.1093/gigascience/giy115. |
20 | FAN C, MA J, GUO Q, et al. Selection of reference genes for quantitative real‑time PCR in bamboo (Phyllostachys edulis)[J]. PLoS One, 2013, 8(2): e56573. DOI: 10.1371/journal.pone.0056573. |
21 | LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real‑time quantitative PCR and the 2‑△△CT method[J]. Methods, 2001, 25(4): 402-408. DOI: 10.1006/meth.200. |
22 | 康桂娟, 黎瑜, 曾日中. 巴西橡胶树HbNAM基因克隆和表达分析[J]. 南京林业大学学报(自然科学版), 2016, 40(1): 59‑64. |
KANG G J, LI Y, ZENG R Z. Clone and expression analysis of HbNAM from Hevea brasiliensis Muell. Arg.[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 2016, 40(1): 59-64. DOI: 10.3969/j.issn.1000-2006.2016.01.010. | |
23 | 董京祥, 任丽, 张园, 等. 白桦BpTCPs基因家族生物信息学及时空表达分析[J]. 南京林业大学学报(自然科学版), 2018, 42(4): 113-118. |
DONG J X, REN L, ZHANG Y, et al. Bioinformatics and expression analysis of BpTCPs in Betula platyphylla Suk[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 2018, 42(4): 113-118. DOI: 10.3969/j.issn.1000-2006.201709001. | |
24 | 田晶, 赵雪媛, 谢隆圣, 等. SPL转录因子调控植物花发育及其分子机制研究进展[J]. 南京林业大学学报(自然科学版), 2018, 42(3): 159-166. |
TIAN J, ZHAO X Y, XIE L S, et al. Research advances and molecular mechanism on SPL transcription factors in regulating plant flower development[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 2018, 42(3): 159‑166. DOI: 10.3969/j.issn.1000-2006.201708015. | |
25 | 赵广枝, 孙化雨, 赵韩生, 等. 毛竹基因组测序及数据应用研究现状[J]. 世界竹藤通讯, 2015, 13(3): 8-12. |
ZHAO G Z, SUN H Y, ZHAO H S, et al. A study of genome sequencing of Phyllostachys edulis and its data applications[J]. World Bamboo and Rattan, 2015, 13(3): 8-12. DOI: 10.13640/j.cnki.wbr.2015.03.002. | |
26 | YANG K B, LI Y, WANG S N, et al. Genome‑wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)[J]. Peer J, 2019, 6: e6242. DOI: 10.7717/peerj.6242. |
27 | ZHAO H S, DONG L L, SUN H Y, et al. Comprehensive analysis of multi‑tissue transcriptome data and the genome‑wide investigation of GRAS family in Phyllostachys edulis[J]. Scientific Reports, 2016, 6: 27640. DOI: 10.1038/srep27640. |
28 | 黎帮勇, 胡尚连, 曹颖, 等. 毛竹NAC转录因子家族生物信息学分析[J]. 基因组学与应用生物学, 2015, 34(8): 1769-1777. |
LI B Y, HU S L, CAO Y, et al. Bioinformatics analysis of NAC gene family in moso bamboo[J]. Genomics and Applied Biology, 2015, 34(8): 1769-1777. DOI: 10.13417/j.gab.034.001769. | |
29 | CURABA J, HERZOG M, VACHON G. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA‑binding activity and is regulated by KNAT1[J]. The Plant Journal, 2003, 33(2): 305-317. DOI: 10.1046/j.1365-313X.2003.01622.x. |
30 | ZHAO M, MOROHASHI K, HATLESTAD G, et al. The TTG1‑bHLH‑MYB complex controls trichome cell fate and patterning through direct targeting of regulatory loci[J]. Development, 2008, 135(11): 1991-1999. DOI: 10.1242/dev.016873. |
31 | DOROSHKOV A V, KONSTANTINOV D K, AFONNIKOV D A, et al. The evolution of gene regulatory networks controlling Arabidopsisthaliana L. trichome development[J]. BMC Plant Biology, 2019, 19(Suppl 1): 53. DOI: 10.1186/s12870⁃019⁃1640‑2. |
32 | ZHOU Z, SUN L, ZHAO Y, et al. Zinc finger protein 6 (ZFP6) regulates trichome initiation by integrating gibberellin and cytokinin signaling in Arabidopsis thaliana[J]. New Phytologist, 2013, 198(3): 699-708. DOI: 10.1111/nph.12211. |
33 | WANG S, KWAK S H, ZENG Q, et al. TRICHOMELESS1 regulates trichome patterning by suppressing GLABRA1 in Arabidopsis[J]. Development, 2007, 134(21): 3873-3882. DOI: 10.1242/dev.009597. |
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