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Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato

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Abstract

BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein–protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies. The SlBTB proteins contains 1–3 BTB domains, and several other types of functional domains, including KCTD (Potassium channel tetramerization domain-containing), the MATH (meprin and TRAF homology), ANK (Ankyrin repeats), NPR1 (nonexpressor of pathogenesis-related proteins1), NPH3 (Nonphototropic Hypocotyl 3), TAZ zinc finger, C-terminal Kelch, Skp1 and Arm (Armadillo/beta-catenin-like repeat) domains are also found in some tomato BTB proteins. Moreover, their expression patterns in tissues/stages, in response to different abiotic stress treatments and hormones were also investigated. This study provides the first comprehensive analysis of BTB gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of BTB genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

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Sources of samples were as follows: leaf, root, flower (Fl), flower bud, 1, 2, 3 cm fruit, mature green (MG) fruit, breaker (Br) fruit, and fruit at 10 days. Blank indicates no raw reads detected in the RNA-seq data

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Acknowledgements

This work was supported by grants from the Basic and Frontier Research Project of Chongqing (No. cstc2015jcyjA80030), The National Natural Science Foundation of China (Nos. 31301779 and 31401884), Natural Science Foundation of Youth in Jiangsu Province (No. BK20140739).

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  1. Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China

    Jinhua Li, Xiaoxing Su, Wei Yang, Yu Pan, Chenggang Su & Xingguo Zhang

  2. Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Yinlei Wang

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  1. Jinhua Li
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Contributions

The work presented here was carried out in collaboration between all authors. JL and XZ conceived the study; XS and WY performed the experiments, JL collected and analyzed the data; CS, YP and YW provided reagents and tools; JL written the manuscript; all authors read and approved of the final manuscript.

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Correspondence to Xingguo Zhang.

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All authors declare that they have no conflict of interest. Jinhua Li declares that he has no conflict of interest. Xiaoxing Su declares that she has no conflict of interest. Yinlei Wang declares that he has no conflict of interest. Wei Yang declares that he has no conflict of interest. Yu Pan declares that she has no conflict of interest. Chenggang Su declares that he has no conflict of interest. Xingguo Zhang declares that he has no conflict of interest.

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Figure S1 Amino acid sequence comparison of BTB genes in tomato (PDF 93 KB)

Table S1 Primers used for the qPCR analysis (DOCX 17 KB)

13258_2017_604_MOESM3_ESM.xlsx

Table S2 The differences about the cis-elements in the promoter sequence of BTB genes between S. pennellii and M82 (XLSX 194 KB)

Table S3 The amounts of the cis-elements that were identified of BTB genes in tomato (XLSX 40 KB)

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Li, J., Su, X., Wang, Y. et al. Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato. Genes Genom 40, 1–15 (2018). https://doi.org/10.1007/s13258-017-0604-x

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