Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (13): 2602-2612.doi: 10.3864/j.issn.0578-1752.2014.13.012

• HORTICULTURE • Previous Articles     Next Articles

Bioinformatics and Expression Analysis of the LysM Gene Family in Apple

 ZHOU  Zhe, ZHANG  Cai-Xia, ZHANG  Li-Yi, WANG  Qiang, LI  Wu-Xing, TIAN  Yi, CONG  Pei-Hua   

  1. Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture/National Apple Breeding Center, Xingcheng 125100, Liaoning
  • Received:2014-01-13 Online:2014-07-01 Published:2014-03-04

RichHTML

6

PDF

2481

Cited

2

Abstract: 【Objective】 The objective of this study is to lay a basis for the further functional identification and application of LysM genes by bioinformatics and expression analysis. 【Method】 Based on apple genome database GDR and FEM-IASMA, the sequences of LysM family genes were identified and numbered in apple. Basic information of the MdLysM amino acid sequence was predicted by ExPASy Proteomics Server, the prediction of the sublocation was finished by the WoLF PSORT. A phylogenetic tree was constructed using the MEGA5 software. The plaza was used to draw the structure of the genes. Information about the chromosome location was obtained from the GMDO. Finally, the map of the chromosome location of the 39 MdLysM genes was accomplished through MapInspector. In addition, real-time qRT-PCR was used to determine the expression pattern of these genes, and the significance of difference was analyzed by SPSS. 【Result】A sum of 39 LysM genes were identified systematically in apple. The number of amino acid of the 39 MdLysM proteins ranges from 241 to 1 119. The isoelectric point distributed from 4.70 to 9.60. Sublocation results indicated that the LysM proteins in apple exist in the nucleus, cytoplasm, chloroplast, vacuole and extracellular matrix. They were classified into three groups (group A, B and C), of which group A was divided into three subgroups according to the phylogeny relationship and gene structures, this implies that function differentiation may have happened. The predicted results of the protein domains were congruent with the clustering in phylogenetic tree. The results of chromosomes location indicated that among apple’s all 17 chromosomes, 13 chromosomes have LysM genes located on and the distribution of these genes was not homogeneous. Compared to other chromosomes, chromosome No. 4 contains more genes with a number of 9, while none of the identified genes localized on chromosomes No.1, No.5, No.7 and No.8. Ten pairs and 1 group of paralogs were identified in apple LysM gene family. Tandem and segmental duplication exist among them, and they are the main power for the expansion of apple LysM gene family. The expression patterns of the 39 MdLysM genes in roots, stems, leaves, flowers and fruits were determined by quantitative real-time PCR, and the result shows that their expression can be detected in all of the five organs. Their expression patterns are diverse which indicate that they may play different roles in different organs.【Conclusion】Thirty-nine LysM gene family in apple were identified in genome-wide scan. These genes were classified into three groups and distributed on 13 chromosomes with different tissues expression patterns. These results were significant to forecast the functions of LysM gene family in apple.

Key words: apple , LysM gene family , phylogenetic analysis , expression analysis

[1]Zhang X C, Wu X, Findley S, Wan J, Libault M, Nguyen H T, Cannon S B, Stacey G. Molecular evolution of Lysin motif-type receptor-like kinases in plants. Plant Physiology, 2007, 144: 623-636.

[2]Zhang X C, Cannon S B, Stacey G. Evolutionary genomics of LysM genes in land plants. BMC Evolutionary Biology, 2009, http://dx.doi. org/10.1186/1471-2148-9-183.

[3]田义, 康国栋, 张彩霞, 张利义, 郝玉金, 丛佩华. 几丁质触发植物免疫的研究现状与展望. 中国农业科学, 2013, 46(15): 3115-3124.

Tian Y, Kang G D, Zhang C X, Zhang L Y, Hao Y J, Cong P H. Progress and perspectives in research of chitin triggered immunity in plant. Scientia Agricultura Sincia, 2013, 46(15): 3115-3124. (in Chinese)

[4]Brown S. Apple. Fruit Breeding, 2012, 8: 329-367.

[5]程曦, 田彩娟, 李爱宁, 邱金龙. 植物与病原微生物互作分子基础的研究进展. 遗传, 2012, 34(2): 134-144.

Cheng X, Tian C J, Li A N, Qiu J L. Advances on molecular mechanisms of plant-pathogen interactions. Hereditas, 2012, 34(2): 134-144. (in Chinese)

[6]Boller T, He S Y. Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science, 2009, 324: 742-744.

[7]Thomma B P, Nürnberger T, Joosten M H. Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell, 2011, 23(1): 23: 4-15.

[8]Zipfel C. Early molecular events in PAMP-triggered immunity. Current Opinion in Plant Biology, 2009, 12: 414-420.

[9]Liu T, Liu Z, Song C, Hu Y, Han Z, She J, Fan F, Wang J, Jin C, Chang J, Zhou J M, Chai J. Chitin-induced dimerization activates a plant immune receptor. Science, 2012, 336: 1160-1164.

[10]Sun Y, Li L, Macho A P, Han Z, Hu Z, Zipfel C, Zhou J M, Chai J. Structural basis for flg22-induced-activation of the Arabidopsis FLS2-BAK1 immune complex. Science, 2013, 342: 624-628.

[11]阙友雄, 宋弦弦, 许莉萍, 陈如凯. 植物与病原真菌互作机制研究进展. 生物技术通讯, 2009, 20(2): 282-285.

Que Y X, Song X X, Xu L P, Chen R K. Research progress on the interaction mechanism between plant and fungi. Leters in Biotechnology, 2009, 20(2): 282-285. (in Chinese)

[12]Kaku H, Nishizawa Y, Ishii-Minami N, Akimoto-tomiyama C, Dohmae N, Takio K, Minami E, Shibuya N. 2006, plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(29): 11086-11091.

[13]Shimizu T, Nakano T, Takamizawa D, Desaki Y, Ishii-Minami N, Nishizawa Y, Minami E, Okada K, Yamane H, Kaku H, Shibuya N. Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice. Plant Journal, 2010, 64: 204-214.

[14]Monaghan J, Zipfel C. Plant pattern recognition receptor complexes at the plasma membrane. Current Opinion in Plant Biology, 2012, 15: 349-457.

[15]Yamaguchi K, Yamada K, Ishikawa K, Yoshimura S, Hayashi N, Uchihashi K, Ishihama N, Kishi-Kaboshi M, Takahashi A, Tsuge S, Ochiai H, Tada Y, Shimanoto K, Yoshioka H, Kawasaki T. A receptor-like cytoplasmic kinase targeted by a plant pathogen effector is directly phosphorylated by the chitin receptor and mediates rice immunity. Cell Host & Microbe, 2013, 13: 347-357.

[16]Wan J, Zhang X C, Neece D, Ramonell K M, Clough S, Kim S, Stacey M G, Stacey G. A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell, 2008, 20: 471-481.

[17]Miya A, Albert P, Shinya T, Desaki Y, Ichimura K, Shirasu K, Narusaka Y, Kawakami N, Kaku H, Shibuya N. CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104: 19613-19618.

[18]Brotman Y, Landau U, Pnini S, Lisec J, Balazadeh S, Mueller-Roeber B, Ziberstein A, Willmitzer L, Chet L, Viterbo A. The LysM receptor-like kinase LysM RLK1 is required to activate defense and abiotic-stress responses induced by overexpression of fungal chitinases in Arabidopsis plants. Molecular Plant, 2012, 5: 1113-1124.

[19]Wan J, Tanaka K, Zhang X C, Son G H, Brechenmacher L, Nguyen T H, Stacey G. LYK4, a lysin motif receptor-like kinase, is important for chitin signaling and plant innate immunity in Arabidopsis. Plant Physiology, 2012, 160: 396-406.

[20]Faulkner C, Petutsbury E, Benitez-Alfonso Y, Beck M, Robatzek S, Lipka V, Maule A. LYM2-dependent chitin perception limits molecular flux via plasmodesmata. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(22): 9166-9170.

[21]Willmann R, Lajunen H M, Erbs G, Newman M A, Kolb D, Tsuda K, Katagiri F, Hliegmann J, Bono J J, Cullinore J V, Jehle A K, Götz F, Kulik A, Molinaro A, Lipka V, Gust A A, Nürnberger T. Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial peptidoglycan sensing and immunity to bacterial infection. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 19824-19829.

[22]Liu B, Li J F, Ao Y, Qu J, Li Z, Su J, Zhang Y, Liu J, Feng D, Qi K, He Y, Wang J, Wang H B. Lysin motif-containing proteins LYP4 and LYP6 play dual roles in peptidoglycan and chitin perception in rice innate immunity. Plant Cell, 2012, 24: 3406-3419.

[23]Tanaka S, Ichikawa A, Yamada K, Tsuji G, Nishiuchi T, Mori M, Koga H, Nishizawa Y, Cornell R O, Kubo Y. HvCEBiP, a gene homologous to rice chitin receptor CEBiP, contributes to basal resistance of barley to Magnaporthe oryzae. BMC Plant Biology, 2010, 10: 1-11.

[24]Fliegmann J, Uhlenbroich S, Shinya T, Martinez Y, Lefebvre B, Shibuya N. Biochemical and phylogenetic analysis of CEBiP-like LysM domain-containing extracellular proteins in higher plants. Plant Physiology and Biochemistry, 2011, 49: 709-720.

[25]Zeng L, Velásquez A C, Munkvold K R, Zhang J, Martin G B. A tomato LysM receptor-like kinase promotes immunity and its kinase activaty is inhibited by AvrPtoB. Plant Journal, 2012, 69: 92-103.

[26]Madsen E B, Madsen L H, Radutoiu S, Olbryt M, Rakwalska M, Szczyglowskl K, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J. A recepto kinase gene of the LysM type is involved in legume perception of rhizobial signals. Nature, 2003, 425: 637-640.

[27]Broghammer A, Krusell L, Blaise M, Sauer J, Sullivan J T, Maolanon N, Vinther M, Lorentzen A, Madsen E B, Jensen K J, Roepstorff P, Thirup S, Ronson C W, Thygesen M B, Stougaard J. Legume receptors perceive the rhizobial lipochitin oligosaccharide signal molecules by direct binding. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(34): 13859-13864.

[28]Li Y Z, Wu B J, Yu Y L, Yang G D, Wu C A, Zheng C C. Genome-wide analysis of the RING finger gene family in apple. Molecular Genetics and Genomics, 2011, 286: 81-94.

[29]许瑞瑞, 张世忠, 曹慧, 束怀瑞. 苹果WRKY转录因子家族基因生物信息学分析. 园艺学报, 2012, 39(10): 2049-2060.

Xu R R, Zhang S Z, Cao H, Shu H R. Bioinformatics Analysis of WRKY transcription factor genes family in apple. Acta Horticulturae Sinica, 2012, 39(10): 2049-2060. (in Chinese)

[30]Poole R L. The TAIR database. Methods Molecular Biology, 2007, 406: 179-212.

[31]Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 2012, 40: 597-603.

[32]Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 2011, 28(10): 2731-2739.

[33]Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, 2001, 25: 402-408.

[34]Rairdan G, Moffett P. Brothers in arms? Common and contrasting themes in pathogen perception by plant NB-LRR and animal NACHT-LRR proteins. Microbes Infect, 2007, 9: 677-686.

[35]秘彩莉, 刘旭, 张学勇. F-box 蛋白质在植物生长发育中的功能. 遗传, 2006, 28(10): 1337-1342.

Mi L C, Liu X, Zhang X Y. The function of F-box protein in plant growth and development. Hereditas, 2006, 28(10): 1337-1342. (in Chinese)

[36]Velasco R, Zharkikh A, Bumgarner R E, Gardiner S E, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. 2010. The genome of the domesticated apple（Malus × domestica Borkh.). Nature Genetic, 2010, 42: 833-839.

[37]Wang Y, Tan X, Paterson A H. Different patterns of gene structure divergence following gene duplication in Arabidopsis. BMC Genomics, 2013, 14: 652.
[1] SU YiFan, YANG ZhanXu, WANG Di, MAO JunCheng, WEI MengMeng, CHEN Ze, BAI XinRan, CHU TianGe, MA ChangNing, QIAO MingFei, SUN Quan, HU DaGang. Effects of 2, 4-Epibrassinolide on Postharvest Storage Quality and Physiological Performance of Apple [J]. Scientia Agricultura Sinica, 2026, 59(7): 1536-1551.
[2] YANG CaiLi, LI YongZhou, HE LiangLiang, SONG YinHua, ZHANG Peng, LIU ZhaoXian, LI PengHui, LIU SanJun. Genome-Wide Identification and Analysis of TPS Gene Family and Functional Verification of VvTPS4 in the Formation of Monoterpenes in Grape [J]. Scientia Agricultura Sinica, 2025, 58(7): 1397-1417.
[3] TENG MengXin, XU Ya, HE Jing, WANG Qi, QIAO Fei, LI JingYang, LI XinGuo. Identification and Functional Analysis of Ca2+-ATPase Gene Family in Banana [J]. Scientia Agricultura Sinica, 2025, 58(7): 1418-1433.
[4] ZHANG LinLin, GONG Rui, CUI YanLing, ZHONG XiongHui, LI Ye, LI RanHong, QIAN ZongWei. Effect Analysis of SmWRKY30 in Eggplant Resistance to Ralstonia solanacearum by Virus Induced Gene Silencing (VIGS) [J]. Scientia Agricultura Sinica, 2025, 58(3): 548-563.
[5] CONG QiQi, ZHANG JingYi, MENG XiangLong, DAI PengBo, LI Bo, HU TongLe, WANG ShuTong, CAO KeQiang, WANG YaNan. Identification of Hypovirus in Apple Ring Rot Fungus Botryosphaeria dothidea and Detection of Virus-Carrying Status in China [J]. Scientia Agricultura Sinica, 2025, 58(3): 478-492.
[6] PAN Yuan, WANG De, LIU Nan, MENG XiangLong, DAI PengBo, LI Bo, HU TongLe, WANG ShuTong, CAO KeQiang, WANG YaNan. Evaluation of the Effectiveness of Two High-Throughput Sequencing Techniques in Identifying Apple Viruses and Identification of Two Novel Viruses [J]. Scientia Agricultura Sinica, 2025, 58(2): 266-280.
[7] YI ZeHui, WANG Ying, SONG HuiXia, ZHAO Jing, MAO LiPing. Genome-Wide Identification and Expression Analysis of Peroxiredoxins Gene Family in Asparagus officinalis [J]. Scientia Agricultura Sinica, 2025, 58(18): 3728-3743.
[8] QI XiangYu, LI XinRu, CHEN ShuangShuang, FENG Jing, CHEN HuiJie, LIU XinTong, JIN YuYan, DENG YanMing. Identification of the FLA Gene Family and Functional Analysis of JsFLA2 in Jasminum sambac [J]. Scientia Agricultura Sinica, 2025, 58(17): 3516-3530.
[9] WANG Wei, WU ChuanLei, HU XiaoYu, LI JiaJia, BAI PengYu, WANG GuoJi, MIAO Long, WANG XiaoBo. Genome-Wide Identification of Soybean LOX Gene Family and the Effect of GmLOX15A1 Gene Allele on 100-Seed Weight [J]. Scientia Agricultura Sinica, 2025, 58(1): 10-29.
[10] TAN FangDai, HE YingXia, LIU JiaYue, LI AiHua, TAO YongSheng. Multidimensional Characterization of Astringency Quality in Dry Red Wine and Its Effects [J]. Scientia Agricultura Sinica, 2024, 57(21): 4342-4355.
[11] ZHANG Yi, LIU Ying, CHENG CunGang, LI YanQing, LI Zhuang. Effects of Combined Application Proportion of Cow Manure and Chemical Fertilizer on Soil Organic Carbon Pool and Enzyme Activity in Apple Orchard [J]. Scientia Agricultura Sinica, 2024, 57(20): 4107-4118.
[12] YIN JunLiang, LI JingYi, HAN Shuo, YANG PeiHua, MA JiaWei, LIU YiQing, HU HaiJun, ZHU YongXing. Identification of Ginger (Zingiber officinale Roscoe) NHX Gene Family Members and Characterization of Their Expression Patterns in Silicon Alleviating Salt Stress [J]. Scientia Agricultura Sinica, 2024, 57(19): 3848-3869.
[13] ZHOU HanMi, MA LinShuang, SUN QiLi, CHEN JiaGeng, LI JiChen, SU YuMin, CHEN Cheng, WU Qi. Optimization of Integrated Water and Nitrogen Regulation System in Apple Based on Multi-Objective Comprehensive Evaluation [J]. Scientia Agricultura Sinica, 2024, 57(18): 3654-3670.
[14] ZENG YanXin, GONG HaoNan, YOU ChunXiang, LU JingSheng, GAO WenSheng, WANG XiaoFei. Effects of Different Rootstocks on Growth and Fruit Quality of Young Ruixianghong Apple Trees with Multi-Stem Shape [J]. Scientia Agricultura Sinica, 2024, 57(14): 2847-2861.
[15] ZHANG HaiQing, ZHANG HengTao, GAO QiMing, YAO JiaLong, WANG YaRong, LIU ZhenZhen, MENG XiangPeng, ZHOU Zhe, YAN ZhenLi. Transcriptome Analysis for Screening Key Genes Related to Regulating Branching Ability in Apple [J]. Scientia Agricultura Sinica, 2024, 57(10): 1995-2009.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd