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Genome-wide analysis and identification of the SMXL gene family in apple (Malus × domestica)

Abstract

Strigolactones (SLs) are a recently discovered type of plant hormone that controls various developmental processes. The DWARF53 (D53) protein in rice and the SMAX1-LIKE (SMXL) family in Arabidopsis repress SL signaling. In this study, bioinformatics analyses were performed, and 236 SMXL proteins were identified in 28 sequenced plants. A phylogenetic analysis indicated that all potential SMXL proteins could be divided into three groups and that the SMXL proteins may have originated in Bryophytes. An analysis of the SMXL chromosomal locations suggested that gene duplication events at different times led to expansion of the SMXL family members in Angiospermae. Subsequently, the gene structure and protein modeling of MdSMXLs showed that they are highly conserved. The expression patterns of MdSMXLs indicated that they were expressed in different organs of apple (stems, roots, leaves, flowers, and fruits) at varying levels and that MdSMXLs may participate in the SL signaling pathway and the response to abiotic stress. This study provides a valuable foundation for additional investigations into the function of the SMXL gene family in plants.

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Funding

This work was supported by grants from the National Natural Science Foundation of China (31601742, U1706202), the Ministry of Agriculture of China (CARS-28), Shandong Province (SDAIT-06-03), and the Ministry of Education of China (IRT15R42).

Author information

Correspondence to Xiao-Fei Wang or Yu-Jin Hao.

Additional information

Communicated by E. Dirlewanger

Electronic supplementary material

Supplementary Table 1

Primers used for quantitative real-time PCR of the SMXL genes in apple. (DOC 34 kb)

Supplementary Figure S1

Phylogenetic relationships between Arabidopsis and apple SMXL proteins calculated using the neighbor-joining (NJ) method. A total of 1000 bootstrapping replicates was calculated for each node. The proteins were classified into three distinct subgroups (classes I, II, and III), which are distinguished by their background color. The distance (indicated by ‘0.05’) is the percent sequence divergence. (JPG 597 kb)

Supplementary Figure S2

Phylogenetic relationships between Arabidopsis and apple SMXL proteins calculated using the maximum likelihood (ML) method. The proteins were classified into three distinct subgroups (classes I, II, and III), which are marked by a colored background. The distance (indicated by ‘0.2’) is the percent sequence divergence. (JPG 682 kb)

Supplementary Figure S3

Exon/intron structure of SMXL/D53 genes in Arabidopsis and Oryza sativa. Introns and exons are represented by shrunken lines and red boxes, respectively. The length in base pairs is indicated for each intron and exon. (JPG 743 kb)

Supplementary Figure S4

Sequence alignment of the conserved domains of the SMXL proteins in apple. (JPG 3876 kb)

Supplementary Figure S5

Three-dimensional structure analysis of the SMXLs. A, The three-dimensional structure of the ClpB protein. B, The confidence and coverage of the amino acid sequence of MdSMXLs compared to ClpB. (JPG 2195 kb)

Supplementary Figure S6

MdSMXL expression in response to different abiotic stressors. Expression patterns of MdSMXLs under drought, ABA, salt, and temperature (4 °C) stress. HemI (Version1.0) was used to draw the heatmaps. The color scale representing the relative signal values is shown above. (JPG 1720 kb)

Supplementary Figure S7

Arabidopsis microarray data showing the response of SMXLs to abiotic stress. (JPG 7024 kb)

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Li, R., An, J., You, C. et al. Genome-wide analysis and identification of the SMXL gene family in apple (Malus × domestica). Tree Genetics & Genomes 14, 61 (2018). https://doi.org/10.1007/s11295-018-1275-8

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Keywords

  • Strigolactones
  • SMXL gene family
  • Genome-wide identification
  • Expression analysis
  • Apple