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

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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

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