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Genome-Wide Analysis of the Pectin Methylesterase Gene Family in Potato

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Abstract

Pectin methylesterase (PME) is a type of protein encoded by a multi-gene family and participates in seed germination, fruit ripening and stress response. To further study the function of the PME gene family in potato, this paper screened and identified potato PME gene family by bioinformatics methods, and analysed the structure, physicochemical properties, conserved domains and evolutionary relationships of the gene sequences. The results showed that the identified 54 potato PME genes can be divided into Group I (only PME domain) and Group II (both PME domain and PMEI domain). The phylogenetic tree constructed by the maximum likelihood method indicated that potato PME genes consisted of five subfamilies. The protein sequences of potato PME genes were compared with clustalx2.1 software. Most of these sequences were identified to have five conserved structural regions including Gx Yx E (Region I), QAVAxR (Region II), QDTL (Region III), GxxDFIFG (Region IV) and YLGRxWx (Region V). Conserved motifs of potato PME amino acid sequences were analysed by MEME online software. Motif1 contains three of the five conserved structural regions and motif2 and motif8 each contain one, indicating that these sequences are more conservative. The structure of 54 potato PME gene sequences was analysed by the GSDS website. It was found that there were only two parts, exon or coding sequence (CDS) between untranslated regions (UTRs), without intron structures in these sequences, indicating that the structure is relatively simple. It will provide a reference for the study on the function of potato PME gene.

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Funding

This study was supported by grants from the National Natural Science Foundation of China (Grant Nos. 31660352, 31660350), Innovation Project of Guangxi Postgraduate Education (YCBZ2019015), Guangxi Innovation Team Project of Tubers of Modern Agricultural Industrial Technology System of China (nycytxgxcxtd-11-01), and the Science & Technology Development Fund of Guangxi Academy of Agricultural Sciences (Grant Nos. Guinongke2017JZ11).

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Authors and Affiliations

  1. College of Agronomy, Guangxi University, Nanning, 530004, People’s Republic of China

    Yingqiu Li & Long-Fei He

  2. Guangxi Academy of Agricultural Sciences, Cash Crops Research Institute, Nanning, 530007, People’s Republic of China

    Huyi He

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  1. Yingqiu Li
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  2. Huyi He
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  3. Long-Fei He
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Correspondence to Huyi He or Long-Fei He.

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Li, Y., He, H. & He, LF. Genome-Wide Analysis of the Pectin Methylesterase Gene Family in Potato. Potato Res. 64, 1–19 (2021). https://doi.org/10.1007/s11540-020-09453-1

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