Integrated Characterization of Cassava (<i>Manihot esculenta</i>) Pectin Methylesterase (<i>MePME</i>) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses

Plant pectin methylesterases (PMEs) play crucial roles in regulating cell wall modification and response to various stresses. Members of the PME family have been found in several crops, but there is a lack of research into their presence in cassava (<i>Manihot esculent</i>), which is an important crop for world food security. In this research, 89 <i>MePME</i> genes were identified in cassava that were separated into two types (type-Ⅰ and type-Ⅱ) according to the existence or absence of a pro-region (PMEI domain). The <i>MePME</i> gene members were unevenly located on 17 chromosomes, with 19 gene pairs being identified that most likely arose via duplication events. The <i>MePMEs</i> could be divided into ten sub-groups in type-Ⅰ and five sub-groups in type-Ⅱ. The motif analysis revealed 11 conserved motifs in type-Ⅰ and 8 in type-Ⅱ <i>MePMEs</i>. The number of introns in the CDS region of type-Ⅰ <i>MePMEs</i> ranged between one and two, and the number of introns in type-Ⅱ <i>MePMEs</i> ranged between one and nine. There were 21 type-Ⅰ and 31 type-Ⅱ <i>MePMEs</i> that contained signal peptides. Most of the type-Ⅰ <i>MePMEs</i> had two conserved “RK/RLL” and one “FPSWVS” domain between the pro-region and the PME domain. Multiple stress-, hormone- and tissue-specific-related <i>cis</i>-acting regulatory elements were identified in the promoter regions of <i>MePME</i> genes. A total of five co-expressed genes (<i>MePME1</i>, <i>MePME2</i>, <i>MePME27</i>, <i>MePME65</i> and <i>MePME82</i>) were filtered from different abiotic stresses via the use of UpSet Venn diagrams. The gene expression pattern analysis revealed that the expression of <i>MePME1</i> was positively correlated with the degree of cassava postharvest physiological deterioration (PPD). The expression of this gene was also significantly upregulated by 7% PEG and 14 °C low-temperature stress, but slightly downregulated by ABA treatment. The tissue-specific expression analysis revealed that <i>MePME1</i> and <i>MePME65</i> generally displayed higher expression levels in most tissues than the other co-expressed genes. In this study, we obtain an in-depth understanding of the cassava <i>PME</i> gene family, suggesting that <i>MePME1</i> could be a candidate gene associated with multiple abiotic tolerance.