Genome-wide identification and comparative analysis of the cation proton antiporters family in pear and four other Rosaceae species

Zhou, Hongsheng; Qi, Kaijie; Xing, Liu; Yin, Hong; Wang, Peng; Chen, Jianqing; Wu, Juyou; Zhang, Shaoling

doi:10.1007/s00438-016-1215-y

Cited by 36 publications

(30 citation statements)

References 57 publications

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“…Analysis of chromosomal distribution revealed that ZmCPA s were evenly distributed on the 10 chromosomes of maize. Similarly, the CPA genes were derived from all chromosomes in wheat [41], and 15 out of 17 chromosomes in pear [38], respectively. Phylogenetic tree was generated using full-length CPA protein sequences of maize, rice and Arabidopsis .…”

Section: Discussionmentioning

confidence: 99%

“…The homologous proteins were found tightly clustered due to high homology among them. Classification of the CPA superfamily genes into NHX, KEA and CHX subfamilies and their further categorization into various groups such as N1-N3, K1-K2 and C1-C4 has also been previously performed in Arabidopsis , pear [13, 38].…”

Section: Discussionmentioning

confidence: 99%

“…OsCHX14 played an important role in K + homeostasis during flowering in rice [37]. PbrCHX16 of pear also plays significant role in pollen tube growth [38].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance

Kong

Luo

et al. 2020

Preprint

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BackgroundSodium toxicity and potassium insufficient are important factors affecting the growth and development of maize in saline soil. The monovalent cation proton antiporter (CPA) superfamily comprises Na+/H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) subfamily proteins, which play vital functions in maize salt tolerance.ResultsA total of 35 ZmCPA genes were identified in maize, and they were phylogenetically classified into 13 ZmNHXs, 16 ZmCHXs and 6 ZmKEAs. ZmCPA genes have a conserved gene structure, with the determined introns range from 11 to 25, 0 to 5 and 16 to 19 in ZmNHXs, ZmCHXs, ZmKEAs, respectively. All proteins have transmembrane domains, with an average transmembrane number of 8, 10, and 10 in ZmNHX, ZmCHX and ZmKEA proteins, respectively. Transient expression in maize protoplasts showed that ZmCHX16 and ZmNHX8 are located in the cell membrane. All ZmCHX subfamily genes showed lower expression compared to ZmNHX and ZmKEA subfamilies. Diverse expression in the 60 tissues and modulated expression in response to salt stress suggested ZmCPAs’ role in maize development and salt stress. Yeast complementary experiment revealed the function of ZmNHX8, ZmCHX8, -12, -14, -16 and ZmKEA6 in salt tolerance. Maize mutants zmnhx8 and zmkea6 further validated the important function of ZmNHX8 and ZmKEA6 in salt tolerance. Phosphorylation sites and cis-acting regulation elements analyses indicated that phosphorylation and transcriptional regulation may be involved in salt tolerance of ZmCPA genes.ConclusionsOur study provides comprehensive information about ZmCPA gene superfamily, which would be useful in their future functional characterization.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance

Kong

Luo

et al. 2020

Preprint

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“…All the BAHD members of strawberry, peach and European pear experienced purifying selection. Similar results Hydrated pollen, Pollen tube and Stop growth pollen [64,65]. Then, the gene expression heatmap was drawn using TB-Tools [69].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus☓ bretschneideri)

Liu

Qiao

et al. 2019

Preprint

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Background: The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. However, the copy numbers, expression characteristics and associations with fruit aroma formation of the BAHD genes remain unclear. Results: In total, 717 BAHD genes were obtained from the genomes of seven Rosaceae, ( Pyrus bretschneideri , Malus domestica , Prunus avium , Prunus persica , Fragaria vesca , Pyrus communis and Rubus occidentalis ). Based on the classifications in model plants, we divided the BAHD family genes into seven groups, I-a, I-b, II-a, II-b, III-a, IV and V. An intra-species synteny analysis detected 78 syntenic gene pairs among the seven Rosaceae species. Dispersed gene duplication occurred frequently in all the investigated species. Different modes of duplicated gene pairs identified in each investigated species revealed that the Ka/Ks ratios were less than one, indicating that they evolved through purifying selection. Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, we selected five genes for verification as assessed by qRT-PCR. Pbr020016.1 , Pbr019034.1 , Pbr014028.1 and Pbr029551.1 are important candidate genes involved in aroma formation during pear fruit development. Conclusion: We have thoroughly annotated the BAHD superfamily genes and performed a comprehensive comparative analysis of their colinearity, phylogenetic relationships and gene duplication patterns in seven Rosaceae species, and we also obtained four candidate genes involved in aroma synthesis in pear fruit. These results provide a theoretical basis for future studies of the specific biological functions of BAHD superfamily members and the improvement of pear fruit quality. Keywords : BAHD, pear, evolution, Rosaceae, transcriptome, volatile esters

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“…Duplication events have been widely studied in Rosaceae species by the analysis of various gene families including F-box genes (Wang et al 2013), heat shock factors (Qiao et al 2015), MYB and WRKY transcription factors (Huang et al 2015;Li et al 2016), lipoxygenases (Li et al 2014), sugar transporters (Li et al 2015), and cation proton antiporters (Zhou et al 2016). In this study, based on the chromosome location of each PDI gene, the synteny of chromosome segments containing PDI gene(s) was analyzed among three different phenotypical species: drupe (peach), pome apple, and berry (strawberry).…”

Section: Phylogeny and Duplication Events Of Pdi Genes In Fruit Treesmentioning

confidence: 99%

Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits

Ke¹,

Cheng²,

Liu³

et al. 2018

Can. J. Plant Sci.

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Protein disulfide isomerase (PDI) is an important enzyme for protein folding in endoplasmic reticulum. The PDI gene family has been systematically studied in Arabidopsis, barley, rice, and bread wheat; however, little is known about this gene family and their roles during fruit development and ripening in fruit trees. In this study, 63 PDI genes were isolated from 8 fruit trees. Phylogenetic trees showed that these genes were clustered into six different groups, designated as A to F. In the groups, the PDI genes had significant differences in gene structure and conserved regions. The chromosome location of each PDI gene was determined in complete genome-assembly fruit trees and the synteny of chromosome segments was detected among peach, pear, and strawberry. Expression profiles of PDI genes in peach, pear, and strawberry showed that nearly all genes in group D and E were more highly expressed in developmental and ripening fruit tissues than those in other groups, while all genes in group A and B presented the lowest levels of expression in fruits of each stage. Moreover, qRT-PCR analyses revealed that these expressed genes were stable expressed in pear and peach fruits, as well as the reported reference genes. Eventually, PbPDI.F1 presented the highest expression stability in pear fruit while PpPDI.F displayed stronger stability than other genes in peach fruit. Thus, these two genes, which were clustered in group F, are good reference genes for gene expression studies during fruit development and ripening.

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Genome-wide identification and comparative analysis of the cation proton antiporters family in pear and four other Rosaceae species

Cited by 36 publications

References 57 publications

Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance

Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance

Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus☓ bretschneideri)

Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits

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