- All of the encoded proteins contained typical SERK domains. - The chromosomal locations, gene/protein structures, synteny, promoter sequences, protein – protein interactions, and physicochemical characteristics of MdSERK genes were analyzed. - Bioinformatics analyses demonstrated that gene duplications have likely contributed to the expansion and evolution of SERK genes in the apple genome. - Quantitative real-time PCR analyses revealed that the MdSERK genes showed different expression patterns in various tissues. - Eight MdSERK genes were responsive to stress signals, such as methyl jasmonate, salicylic acid, abscisic acid, and salt (NaCl). - The expression levels of seven MdSERK genes were significantly upregulated by brassinosteroid and auxin. - In addition, several MdSERK genes showed higher expression levels in standard trees of ‘ Nagafu 2 ’ (CF)/CF than in dwarf trees of CF. - Malling 9 ’ (M.9), and in CF than in the spur-type bud mutation “ Yanfu 6 ” (YF).. - Conclusion: This study represents the first comprehensive investigation of the apple SERK gene family. - The first SERK gene was identified in Dau- cus carota, and was shown to play an important role in the. - the SPP domain is involved in the interaction between pro- teins and cell walls [7]. - AtSERK3 is involved in the containment of dead cells after microbial infection [21], and AtSERK4 functions redundantly with AtSERK3 to regulate a BR-independent cell-death pathway [22].. - We determined the expression patterns of MdSERK genes in response to stress signals, BR and auxin treatments, and in different graft combinations and apple varieties. - All of the putative genes matched to at least one EST (Additional file 1: Table S2). - Most of the MdSERK proteins were found to be stable with a low instability index (<. - We also detected Ala and Val in the MdSERK proteins. - All MdSERK proteins were predicted to be local- ized in the cell membrane (Additional file 1: Table S4).. - The 12 genes were distributed across eight of the 17 Malus × domestica chromosomes (Fig. - The number of MdSERK genes ranged from one to three genes per chromosome. - three of the five Leu-rich repeats (all except for LRR4 and LRR5) were also conserved (highlighted with a yel- low box). - The promoter regions (about 1.5 kb) of MdSERK genes (Additional file 6: Figure S5) were found to contain im- portant cis-acting elements associated with stress and hormone-related responses. - At least one stress-specific activation element was present in the promoter of all MdSERK genes. - one to two CGTCA motifs in all MdSERK genes;. - Five of the 10 MdSERK genes were. - 4 Synteny of MdSERK genes. - Location of MdSERK genes on apple chromosomes (Md1 – 17). - Apple SERK expression profiles in different tissues The tissue-specific expression patterns of MdSERK genes were analyzed in various tissues of M. - 5 Synteny analysis of SERK genes between apple and Arabidopsis.. - 6 Expression profiles of apple SERK genes in different tissues. - MdSERK6/11 showed the highest expression levels in the phloem. - The expression levels of MdSERK4 and MdSERK12 were higher in the xylem and phloem of the stem than in other tissues. - MdSERK3 was strongly expressed in the root, and the highest expression levels of MdSERK8–10 were in the leaf.. - To elucidate the potential roles and functions of the MdSERK genes in apple, expression profile data for different tissues (seedlings, roots, stems, flowers, fruit, and leaves) with two biological replicates were down- loaded from the ArrayExpress database (E-GEOD- 42873) (Additional file 8: Figure S7). - Almost all MdSERK genes (except for MdSERK8–9 and MdS ERK11) were expressed at higher levels in the flower of M74, fruit of M20_100 daf (100 days after flower- ing) and M.20_harvest, leaf of M49, and fruit of M74_harvest than in other tissues. - MdSERK8–9 and MdSERK11 showed low expression levels in almost all tissues, especially in seedlings of Golden delicious (GD), compared with the other MdSERK genes.. - To investigate the roles of MdSERK genes in stress re- sponses, MdSERK gene expression patterns in young leaves were separately analyzed after methyl jasmonate (MeJA), SA, ABA, and salt treatments (Fig. - The expression level of MdSERK2/5 increased by 0.2- to 5-fold from 3 to 12 h in the MeJA-treated plants.. - were higher in the ABA treatment group than in the con- trol group throughout the whole experiment. - The transcript levels of MdSERK6/11 in leaves were about and 11.5- fold higher in the NaCl-treated group than in the control group. - The transcript levels of the other MdSERK genes were neither increased nor decreased in response to stress treatments (data not shown).. - 8a), and the level of auxin (indole-3- acetic acid, IAA) in the auxin-treated group increased to about 4, 12.3, and 12.4 μg·g − 1 FW at 0, 2, and 3 weeks, respectively, after the auxin treatment (Fig. - The plants in the BR treatment groups were about 4 cm taller than those in the control group at 4 weeks after. - The MdSERK expression levels were evaluated in the shoot tips of M. - The transcript levels of several MdSERK genes were significantly upregulated at most time points after the BR treatment. - 10 Expression of SERK genes in response to brassinosteroid (BR) and auxin treatments. - other MdSERK genes either increased or decreased at dif- ferent time points in response to BR and auxin treatments (data not shown).. - To investigate whether MdSERKs are involved in regulating apple tree height, MdSERK ex- pression patterns were analyzed in the shoot tips of the two grafting combinations (Fig. - The expression pat- terns of the remaining MdSERK genes were irregular after bud break (data not shown).. - Seven MdSERK genes showed high ex- pression levels in CF. - MdSERK2/5 and MdSERK3 were in- duced at and 145 DABB in the shoot tips of CF. - Genome-wide identification and characteristics analysis of SERK genes in apple. - Quantitative reverse transcription polymerase chain reaction analysis of apple SERK genes in (a) CF/CF and CF/M9 after bud break and 155 days), and in (b) YF and CF after bud break and 145 days). - Structural analyses of the MdSERK proteins revealed conservation in the proportion of α helices, β sheets, extended strands, and random coils (Additional file 3: Figure S2. - Evolutionary and syntenic relationships of SERK genes In the unrooted phylogenetic tree, the putative apple SERK proteins were grouped into different classes (Fig.. - There were several sister pairs in the combined tree, including four apple/apple pairs. - Gene duplication events may have played a significant role in the expansion of the apple SERK gene family. - One tandem and five segmental duplications were found among the MdSERK genes (Fig. - This event may have played an im- portant role in the expansion of MdSERK genes [44], and may explain why there are more MdSERK genes than AtSERK genes.. - Both AtSERK4 and AtSERK5-Ler are involved in the response to cell death and stem elongation . - Expression and potential functional analysis of MdSERK genes. - The 12 analyzed MdSERK genes were expressed differ- ently among the roots, xylem, and phloem of stems, and the leaves and shoot tips of M. - Almost all of the analyzed MdSERK genes showed higher expression levels in the xylem, phloem, or shoot tips than in other organs.. - The highest expres- sion levels of MdSERK genes were in the flowers, fruit, and leaves, indicating that they may play important roles in flower, fruit, and leaf development. - The ex- perimental and digital investigation data indicated that MdSERK genes are involved in many aspects of apple development. - Some MdSERK genes were induced by several signals, includ- ing MeJA, SA, ABA, and salt stress (Fig. - These results indicate that there may be a complicated mechanism by which auxin regulates SERK genes in apple, and that these MdSERK genes might have a positive role in regulating apple tree growth by mediating BR and auxin signals.. - These results indicated that MdSERK1 and MdSERK8–9 may be involved in the regulation of the dwarf pheno- type of CF/M.9 trees through auxin signaling, and that MdSERK4 may also play an important role in apple tree growth. - However, few studies have focused on the roles of SERK proteins in the dwarfing mechanism of apple rootstocks. - Our study has highlighted potential roles of MdSERK genes in the dwarfism of apple trees. - At least one GARE or auxin-response motif was identified in the promoters of MdSERK2–3,. - These results indicate that MdSERK genes may be involved in the response to GA and auxin signals to regulate the growth of YF trees. - This study represents the first genome-wide analysis of the apple SERK family. - Eight MdSERK genes (MdSERK2–6 and MdSERK10–12), especially MdSERK2 and MdSERK5, were predicted to play important roles in stress responses. - Future research should focus on validating the functions of MdSERK genes in various stress responses, and their roles in controlling apple tree size.. - Details of the chromosomal locations of MdSERK genes were obtained through BLASTN searches of the GDR database (GDR. - The MdSERK genes were mapped to chromosomes using MapDraw [64]. - The seedlings were held firmly in the holes by sponges. - The growth conditions of the trees were the same as those described in the ‘ Stress treatment ’ section.. - All samples were collected in the same manner,. - Primers specific for MdSERK genes were designed using Primer 6 and Primer 3 (Additional file 1: Table S1). - hupehensis seedlings in the control group to investigate the tissue expression patterns of MdSERK genes. - Synteny analysis of MdSERK genes. - Transmembrane helices of the MdSERK proteins were predicted with TMHMM server v2.0. - Intron/exon organization of apple SERK genes. - Phylogenetic analysis and intron/exon organization of apple SERK genes. - Promoter sequences of selected apple SERK genes. - Promoter (1.5-kb) sequences of 12 MdSERK genes were analyzed with PlantCARE and MEME software. - Mingyu Han revised the final version of the manuscript.. - Subcellular localization and oligomerization of the Arabidopsis thaliana somatic embryogenesis receptor kinase 1 protein. - The Arabidopsis kinase-associated protein phosphatase controls internalization of the somatic embryogenesis receptor kinase 1. - Somatic embryogenesis receptor-like kinase 5 in the ecotype Landsberg erecta of Arabidopsis is a functional RD LRR-RLK in regulating brassinosteroid signaling and cell death control. - MdWRKY9 overexpression confers intensive dwarfing in the M26 rootstock of apple by directly inhibiting brassinosteroid synthetase MdDWF4 expression. - Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. - Gibberellin-responsive elements in the promoter of a barley high-pI alpha-amylase gene. - bioinformatics analysis of the somatic embryogenesis receptor kinases. - Structural characterization and expression analysis of the SERK/SERL gene family in rice (Oryza sativa). - Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. - Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh. - Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh. - Evolutionary and expression analyses of the apple basic leucine zipper transcription factor family
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