Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize

Zhang, Panpan; Wang, Hao; Qin, Xiner; Chen, Kuan; Zhao, Jiuran; Zhao, Yang; Yue, Bing

doi:10.1038/s41598-019-56254-9

Cited by 26 publications

(22 citation statements)

References 68 publications

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“…The number of PME genes are varied in species. Here, we acquired more PME gene members in soybean than those reported in flax (105 members) [ 45 ], Arabidopsis (66 members) [ 18 ], rice (59 members) [ 19 ], strawberry (54 members) [ 2 ] and maize (43 members) [ 20 ]. Plant genome evolutions often along with segmental and tandem duplications that resulted in the expansions of different gene families [ 46 ].…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, whole-genome sequencing technologies promoted the exploration of multiple gene families in diverse species [ 17 ]. Genome-wide identifications and characterizations of PME genes have been carried out in diverse plant species, including Arabidopsis [ 18 ], rice [ 19 ], maize [ 20 ], cotton [ 21 ], tomato [ 16 ] and strawberry [ 2 ]. For the gene structures, all the PME gene members contain the PME domains, and some of them meanwhile harbor the PME inhibitor (PMEI) domains [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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Background Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking. Results We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination. Conclusion In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…Polygalacturaonase was found up-regulated in the fertile line in the stages of pollen grain maturation and pollen tube growth ( Jiang, Lu & Imsabai, 2008 ). PME/PMEI genes were also found highly expressed in male-fertile lines in comparison with their sterile counterparts in Brassica napus ( Zhu et al, 2010 ), cotton ( Suzuki et al, 2013 ), and maize ( Zhang et al, 2019 ). In addition, silencing of an Arabidopsis PMEI gene, At1g10770 , could result in male sterility ( Zhang et al, 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq

Qin

Zhang

Dong

et al. 2020

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Cytoplasmic male sterility (CMS) is extensively used in maize hybrid production, and identification of genes related to fertility restoration for CMS is important for hybrid breeding. The fertility restoration of S type CMS is governed by several loci with major and minor effects, while the mechanism of fertility restoration for CMS-S is still unknown. In this study, BSR-Seq was conducted with two backcrossing populations with the fertility restoration genes, Rf3 and Rf10, respectively. Genetic mapping via BSR-Seq verified the positions of the two loci. A total of 353 and 176 differentially expressed genes (DEGs) between the male fertility and male sterile pools were identified in the populations with Rf3 and Rf10, respectively. In total, 265 DEGs were co-expressed in the two populations, which were up-regulated in the fertile plants, and they might be related to male fertility involving in anther or pollen development. Moreover, 35 and seven DEGs were specifically up-regulated in the fertile plants of the population with Rf3 and Rf10, respectively. Function analysis of these DEGs revealed that jasmonic acid (JA) signal pathway might be involved in the Rf3 mediated fertility restoration for CMS-S, while the small ubiquitin-related modifier system could play a role in the fertility restoration of Rf10.

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“…PMEIs that regulate cell wall elasticity (Wormit and Usadel 2018) are abundantly transcribed and translated in all three species investigated. However, 35 of 49 PMEIs were reported to be specifically transcribed and translated in pollen grains of maize (Zhang et al 2019). Altogether, this suggests that the wall of fast-growing maize pollen tubes remains very elastic during growth, but hints also to the possibility that cell walls of maternal tissues have to be loosened at high speed to allow pollen tube penetration.…”

Section: Correlation Of Secreted Proteins With Pollen Tube Growth Ratmentioning

confidence: 99%

Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides

et al. 2020

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Key message Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides. Abstract Flowering plants (angiosperms) generate pollen grains that germinate on the stigma and produce tubes to transport their sperm cells cargo deep into the maternal reproductive tissues toward the ovules for a double fertilization process. During their journey, pollen tubes secrete many proteins (secreted proteome or secretome) required, for example, for communication with the maternal reproductive tissues, to build a solid own cell wall that withstands their high turgor pressure while softening simultaneously maternal cell wall tissue. The composition and species specificity or family specificity of the pollen tube secretome is poorly understood. Here, we provide a suitable method to obtain the pollen tube secretome from in vitro grown pollen tubes of the basal angiosperm Amborella trichopoda (Amborella) and the Poaceae model maize. The previously published secretome of tobacco pollen tubes was used as an example of eudicotyledonous plants in this comparative study. The secretome of the three species is each strongly different compared to the respective protein composition of pollen grains and tubes. In Amborella and maize, about 40% proteins are secreted by the conventional “classic” pathway and 30% by unconventional pathways. The latter pathway is expanded in tobacco. Proteins enriched in the secretome are especially involved in functions associated with the cell wall, cell surface, energy and lipid metabolism, proteolysis and redox processes. Expansins, pectin methylesterase inhibitors and RALFs are enriched in maize, while tobacco secretes many proteins involved, for example, in proteolysis and signaling. While the majority of proteins detected in the secretome occur also in pollen grains and pollen tubes, and correlate in the number of mapped peptides with relative gene expression levels, some novel secreted small proteins were identified. Moreover, the identification of secreted proteins containing pro-peptides indicates that these are processed in the apoplast. In conclusion, we provide a proteome resource from three distinct angiosperm clades that can be utilized among others to study the localization, abundance and processing of known secreted proteins and help to identify novel pollen tube secreted proteins for functional studies.

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Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize

Cited by 26 publications

References 68 publications

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

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

Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq

Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides

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