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Phylogenetic analysis of upland cotton MATE gene family reveals a conserved subfamily involved in transport of proanthocyanidins

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Abstract

The multidrug and toxic compound extrusion (MATE) protein belongs to a secondary transporter family, which plays a role in transporting different kinds of substrates like phytohormones and secondary metabolites. In plant, MATE transporters related to the endogenous and exogenous mechanisms of detoxification for secondary metabolites such as alkaloids, flavonoids, anthocyanins and other secondary metabolites have been studied. However, a genome-wide analysis of the MATE family is rarely reported in upland cotton (Gossypium hirsutum L.). In the study, a total of 72 GhMATEs were identified from the genome of upland cotton, which were classified into four subfamilies with possible diverse functions such as transport of proanthocyanidins (PAs), accumulation of alkaloids, extrusion of xenobiotic compounds, regulation of disease resistance and response to abiotic stresses. Meanwhile, the gene structure, evolutionary relationship, physical location, conservative motifs, subcellular localization and gene expression pattern of GhMATEs have been further analysed. Three of these MATE genes (GhMATE12, GhMATE16 and GhMATE38) were identified as candidate genes due to their functions in transport of PA similar to GhTT12. These results provide a new perspective on upland cotton MATE gene family for their potential roles in transport of PA and a theoretical basis for further analyzing the function of MATE genes and improving the fiber quality of brown cotton.

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Acknowledgements

We thank Dr. Da-Hui Li for assisting the experimental technology and revising the original manuscript, and are thankful for Prof. Zhao-Rong Deng to offer the biochemical reagents. This work was sponsored by State Key Laboratory of Cotton Biology Open Fund (No. CB2018A01 to J.-S. G.) and the National Natural Science Foundation of China (Grant Nos. 31672497 to J.-S. G.; 31572468 to Y. M.). It was also supported by the National Key Research and Development Program of China (No. 2016YFD0300205-3 to Z.-R. D.).

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Authors and Affiliations

  1. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China

    Lei Xu, Zhi-Lin Shen, Wen Chen, Guo-Yang Si, Yan Meng, Ning Guo, Xu Sun, Yong-Ping Cai, Yi Lin & Jun-Shan Gao

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  1. Lei Xu
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  2. Zhi-Lin Shen
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Contributions

J-SG, YL and YM conceived the idea, LX, WC, G-YS and Z-LS analysed the data, J-SG, LX and Z-LS wrote the manuscript, NG, Y-PC and XS assisted in sequence analysis. All authors reviewed the manuscript.

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Correspondence to Jun-Shan Gao.

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Supplement Fig. S1

Chromosomal location and gene duplication of 72 MATE genes on 20 chromosomes of upland cotton. The name of chromosome is indicated at the top of each bar. The scale on the left is in Mb. The MATE gene on the left side of each chromosome corresponds to the approximate location on each chromosome. The segmentally duplicated genes are connected by dashed lines. (TIF 4285 KB)

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Xu, L., Shen, ZL., Chen, W. et al. Phylogenetic analysis of upland cotton MATE gene family reveals a conserved subfamily involved in transport of proanthocyanidins. Mol Biol Rep 46, 161–175 (2019). https://doi.org/10.1007/s11033-018-4457-4

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