Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.)

Wang, Liang; Gao, Yingqi; Wang, Songming; Zhang, Qiqi; Yang, Shouping

doi:10.1186/s12870-021-03355-1

Cited by 9 publications

(8 citation statements)

References 102 publications

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“…Some studies have shown that the expansion of plant gene families is mainly facilitated by segmental and tandem duplication events [27,28]. Segmental duplication frequently occurs during polyploidization and chromosomal rearrangements, resulting in the presence of repeated chromosomal blocks in the genome; tandem duplications are clusters of multiple adjacent homologous gene family members (two or more members) on a chromosome [29].…”

Section: Chromosomal Location Of Ntftsh Gene and Gene Segment Duplica...mentioning

confidence: 99%

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

et al. 2022

BMC Genomics

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Background The filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key gene for plant chloroplast development and photosynthesis regulation. In addition, the ftsH gene is also involved in plant response to stress. At present, the research and analysis of the ftsH gene family are conducted in microorganisms such as Escherichia coli and Oenococcus and various plants such as Arabidopsis, pear, rice, and corn. However, analysis reports on ftsH genes from tobacco (Nicotiana tabacum L.), an important model plant, are still lacking. Since ftsH genes regulate plant growth and development, it has become necessary to systematically study this gene in an economically important plant like tobacco. Results This is the first study to analyze the ftsH gene from Nicotiana tabacum L. K326 (NtftsH). We identified 20 ftsH genes from the whole genome sequence, renamed them according to their chromosomal locations, and divided them into eight subfamilies. These 20 NtftsH genes were unevenly distributed across the 24 chromosomes. We found four pairs of fragment duplications. We further investigated the collinearity between these genes and related genes in five other species. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified differential expression patterns of NtftsH in different tissues and under various abiotic stress conditions. Conclusions This study provides a comprehensive analysis of the NtftsH gene family. The exon–intron structure and motif composition are highly similar in NtftsH genes that belong to the same evolutionary tree branch. Homology analysis and phylogenetic comparison of ftsH genes from several different plants provide valuable clues for studying the evolutionary characteristics of NtftsH genes. The NtftsH genes play important roles in plant growth and development, revealed by their expression levels in different tissues as well as under different stress conditions. Gene expression and phylogenetic analyses will provide the basis for the functional analysis of NtftsH genes. These results provide a valuable resource for a better understanding of the biological role of the ftsH genes in the tobacco plant.

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Section: Chromosomal Location Of Ntftsh Gene and Gene Segment Duplica...mentioning

confidence: 99%

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

et al. 2022

BMC Genomics

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“…The red and dark purple boxes denote high levels of expression and low levels of expression, respectively. LF, leaf; RT, root; ST, stem; FW, flower; MGF, mature green fruit; FCF, full-colored fruit Sénéchal et al 2014b;Wang et al 2021). In this study, we identified 48 PME genes from the sweet orange genome (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Plenty of PME genes in many plant species are dominantly expressed in whole flowers or specific floral tissues such as anthers, pollen, pollen grains, pollen tubes or corn silk (Kim et al 2010;Kim et al 2015;Louvet et al 2006;Moran Lauter et al 2017;Wang et al 2021;Wen et al 2020;Zhang et al 2019), indicating that they have a specific biological function in reproductive development. Arabidopsis QUARTET1 (QRT1, AT5G55590), which encodes a PME isoform, plays a key role in the separation of pollen grains from pollen tetrads after microsporogenesis in the pollen mother cell (Francis et al 2006).…”

Section: Discussionmentioning

confidence: 99%

“…In higher plant species, PME isoforms are encoded by a large multigene family that is differentially expressed in different tissues and in response to environmental stresses (Louvet et al 2006;Sénéchal et al 2014b;Wang et al 2021;Wen et al 2020;Zhang et al 2019). In recent years, whole-genome sequencing technologies and bioinformatic analyses have led to the genome-wide identification and characterization of the PME gene family in diverse plant species: 66 in Arabidopsis (Louvet et al 2006), 89 in poplar (Geisler-Lee et al 2006), 43 in rice (Jeong et al 2015), 43 in maize (Zhang et al 2019), 57 in tomato (Wen et al 2020) and 127 in soybean (Wang et al 2021). The lower number of PME genes in grasses is closely related to the finding that methyl-esterified HGA is less abundant in grass species of the Poaceae family than in dicotyledonous species (Wu et al 2018).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and expression profiling of the pectin methylesterase gene family in Citrus sinensis (L.) Osbeck

Kim¹,

Oh²,

Kim

et al. 2022

J Plant Biotechnol

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Pectin methylesterase (PME) plays an important role in vegetative and reproductive development and biotic/abiotic stress responses by regulating the degree of methyl-esterification of pectic polysaccharides in the plant cell wall. PMEs are encoded by a large multigene family in higher land plant genomes. In general, the expression of plant PME genes shows tissue-or cell-specific patterns and is induced by endogenous and exogenous stimuli. In this study, we identified PME multigene family members (CsPMEs) from the sweet orange genome and report detailed molecular characterization and expression profiling in different citrus tissues and two fruit developmental stages. We also discussed the possible functional roles of some CsPME genes by comparing them with the known functions of PMEs from other plant species. We identified 48 CsPME genes from the citrus genome. A phylogenetic tree analysis revealed that the identified CsPMEs were divided into two groups/types. Some CsPMEs showed very close phylogenetic relationships with the PMEs whose functions were formerly addressed in Arabidopsis, tomato, and maize. Expression profiling showed that some CsPME genes are highly or specifically expressed in the leaf, root, flower, or fruit. Based on the phylogenetic relationships and gene expression profiling results, we suggest that some CsPMEs could play functional roles in pollen development, pollen tube growth, cross incompatibility, root development, embryo/ seed development, stomata movement, and biotic/abiotic stress responses. Our results shed light on the biological roles of individual CsPME isoforms and contribute to the search for genetic variations in citrus genetic resources.

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“…For the protein structures, Type-I PME and Type-II PME proteins share the PME domains, and Type-I PME proteins also contains the PRO-region, an additional N-terminal region similar to the PMEI domain [9]. Recently, PME genes have been discovered in various plant species, such as 66 PME genes, which were identified from Arabidopsis thaliana [10], 53 from Citrus sinensis [11], 61 from Glycine max [12], 54 from Fragaria vesca [12], and 56 from Solanum tuberosum [13]. The PME genes are tightly linked to various functions of plants, such as fruit maturity and softening [14,15], seed germination and development [16], pollen development [17,18], stem elongation [19], root hair formation [19], and stress response [20,21].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study

Zhang

Wang

et al. 2022

Horticulturae

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Pectins are major components of cell walls in plants. Pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs) play crucial roles in pectin synthesis and metabolism. Overall, 28 putative DkPMEs and 29 putative DkPMEIs were identified from the D. kaki genome. According to phylogenetic analysis, DkPME/DkPMEI proteins can be classified into four and five clades, respectively. Motif and gene structure analysis showed that DkPME/DkPMEI are highly conserved in the same clades, which indicates that the function of these DkPME/DkPMEI were similar. Besides, DkPME/DkPMEI genes were distributed unevenly on their corresponding chromosomes. Synteny analysis showed that PME or PMEI gene usually matched with more than one DkPME/DkPMEI in D. oleifera, D. lotus, and A. thaliana, implying that the function of these genes in D. kaki may be diverse. Expression analysis showed that DkPME/DkPMEI from the same clade exhibited diverse expression patterns, indicating that these genes might have diverse functions. Functional protein–protein interaction network analysis showed that DkPMEI21 and DkPMEI15 were core nodes and were, respectively, positive and negative regulators for carbohydrate metabolism, stress responses, and sugar signaling. This study provides a theoretical basis for the functional characteristics, evolutionary relationship, and role of these gene families in developing persimmon fruit.

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Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.)

Cited by 9 publications

References 102 publications

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

Genome-wide identification and expression profiling of the pectin methylesterase gene family in Citrus sinensis (L.) Osbeck

Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study

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