Genome-wide identification, phylogenetic analysis, and expression profiling of polyamine synthesis gene family members in tomato

Taibo Liu; Binbin Huang; Lin Chen; Zhiqiang Xian; Shiwei Song; Riyuan Chen; Yanwei Hao

doi:10.1016/j.gene.2018.03.084

Genome-wide identification, phylogenetic analysis, and expression profiling of polyamine synthesis gene family members in tomato

Gene. 2018 Jun 30:661:1-10. doi: 10.1016/j.gene.2018.03.084. Epub 2018 Mar 29.

Authors

Taibo Liu¹, Binbin Huang², Lin Chen³, Zhiqiang Xian⁴, Shiwei Song⁵, Riyuan Chen⁶, Yanwei Hao⁷

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China. Electronic address: tbliu@scau.edu.cn.
² College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
³ College of Horticulture, South China Agricultural University, Guangzhou 510642, China. Electronic address: chenlin_304@scau.edu.cn.
⁴ School of life sciences, Chongqing University, Chongqing 400000, China; College of Mathematics and Statistics, Chongqing University, Chongqing 400000, China. Electronic address: xianzhiqiang@cqu.edu.cn.
⁵ College of Horticulture, South China Agricultural University, Guangzhou 510642, China. Electronic address: swsong@scau.edu.cn.
⁶ College of Horticulture, South China Agricultural University, Guangzhou 510642, China. Electronic address: rychen@scau.edu.cn.
⁷ College of Horticulture, South China Agricultural University, Guangzhou 510642, China. Electronic address: Yanweihao@scau.edu.cn.

PMID: 29605609
DOI: 10.1016/j.gene.2018.03.084

Abstract

Polyamines (PAs), including putrescine (Put), spermidine (Spd), spermine (Spm), and thermospermine (T-Spm), play key roles in plant development, including fruit setting and ripening, morphogenesis, and abiotic/biotic stress. Their functions appear to be intimately related to their synthesis, which occurs via arginine/ornithine decarboxylase (ADC/ODC), Spd synthase (SPDS), Spm synthase (SPMS), and Acaulis5 (ACL5), respectively. Unfortunately, the expression and function of these PA synthesis-relate genes during specific developmental process or under stress have not been fully elucidated. Here, we present the results of a genome-wide analysis of the PA synthesis genes (ADC, ODC, SPDS, SPMS, ACL5) in the tomato (Solanum lycopersicum). In total, 14 PA synthesis-related genes were identified. Further analysis of their structures, conserved domains, phylogenetic trees, predicted subcellular localization, and promoter cis-regulatory elements were analyzed. Furthermore, we also performed experiments to evaluate their tissue expression patterns and under hormone and various stress treatments. To our knowledge, this is the first study to elucidate the mechanisms underlying PA function in this variety of tomato. Taken together, these data provide valuable information for future functional characterization of specific genes in the PA synthesis pathway in this and other plant species. Although additional research is required, the insight gained by this and similar studies can be used to improve our understanding of PA metabolism ultimately leading to more effective and consistent plant cultivation.

Keywords: Fruit development; Genomic characterization; Plant stress response; Polyamine synthesis; Solanum lycopersicum; Tomato.

MeSH terms

Fruit / genetics
Fruit / metabolism
Gene Expression Profiling / methods
Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant*
Genomics / methods
Metabolic Networks and Pathways / genetics
Phylogeny*
Polyamines / metabolism*
Putrescine / metabolism
Solanum lycopersicum / classification
Solanum lycopersicum / genetics*
Solanum lycopersicum / metabolism*
Stress, Physiological / genetics
Transcriptome*

Substances

Polyamines
Putrescine