Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)

Manzoor, Muhammad Aamir; Cheng, Xi; Li, Guohui; Su, Xueqiang; Abdullah, Muhammad; Cai, Yongping

doi:10.1016/j.compbiolchem.2020.107346

Cited by 22 publications

(17 citation statements)

References 37 publications

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“…In this research, The PavMYB family was extensively studied with analysis of phylogeny, gene structures, promoter regions, gene duplication events, sequence characteristics, chromosomal locations, GO annotations and expression patterns. Sweet cherry has fewer PavMYB genes (69) than, Oryza sativa (155) [14], Zea mays (132) [13], Setaria italic (209) [77], Malus pumila Mill (229) [79], while greater than Ginkgo biloba (45) [80]. These results illustrated that the R2R3-MYB gene family expansion occurred as compared to Ginkgo biloba.…”

Section: Expression Analysismentioning

confidence: 98%

“…Finally, the sequences were eliminated which omitted the central or entire MYB_DNAbinding domain. The MYB protein sequence were further subjected to the WoLF PSOPT (http:/www.genscript.com/wolf-psort.html) and Expasy software (https://web.expasy.org/protparam/) for analyzing the subcellular localization and molecular characteristics (length of amino acids, molecular weights and isoelectric points) correspondingly [44,45].…”

Section: Identi Cation Database Search and Characteristics Of The Myb Genes In P Aviummentioning

confidence: 99%

“…CLC sequence viewer version 7 (CLC Bio, QIAGEN A/S, Aarhus, Denmark) was used to verify these locations along chromosomes of the downloaded rosaceae genome (httpp://www.rosaceae.org/). Finally, Mapinspect software (http://mapinspect.software.com) [45,56,57] was being used to analyze the data.…”

Section: Intron-exon Conserved Motif and Domain Analysismentioning

confidence: 99%

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MYB Transcription Factor Family in Sweet Cherry (Prunus avium L.): Genome-wide Investigation, Evolution, Structure, Characterization and Expression Patterns

Sabir

Manzoor

Shah

et al. 2021

Preprint

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Back groundMYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown. ResultsIn the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) and whole-genome duplication (WGD) events might play an important role in the expansion of the MYB genes family. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Moreover, different subfamilies contained different cis-acting elements, conserved motifs analysis and introns-exons structures, representing functional divergence in the MYB family. Subsequently, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. Subsequently, the quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit. ConclusionOur comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.

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Section: Expression Analysismentioning

confidence: 98%

Section: Identi Cation Database Search and Characteristics Of The Myb Genes In P Aviummentioning

confidence: 99%

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MYB Transcription Factor Family in Sweet Cherry (Prunus avium L.): Genome-wide Investigation, Evolution, Structure, Characterization and Expression Patterns

Sabir

Manzoor

Shah

et al. 2021

Preprint

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“…The fruit samples 39 days after flowering were collected from a 42-year-old pear plant, which was grown in a research horticulture orchard in Dangshan, Anhui, China. The exogenous hormonal sprayed on the whole surface of fruits with 200 μM salicylic acid (SA), 500 μM abscisic acid (ABA), and 500 μM Methyl jasmonate (MeJA) according to a previously described method [50,77]. All fruit samples were harvested at 39 DAF and collected on 0 h, 1 h, 2 h, 3 h. Immediately all fruit samples were frozen in liquid nitrogen and transformed into − 80°C for storage until further experiments.…”

Section: Plant Materials and Treatmentsmentioning

confidence: 99%

“…Chinese pear (Pyrus. bretschneideri) fruit crop is cultivated worldwide, especially in China, and has become most popular or essential due to its high medicinal and nutritional value [49,50]. Although bZIP members have been identified in various model plants, this gene family has not been comprehensively studied in Pyrus.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

Manzoor

et al. 2021

BMC Plant Biol

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Background In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. Results In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. Conclusions Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.

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Structure and Function of Heavy Metal Transporting ATPases in Brassica Species

Memon

Meraklı²

2023

Phytoremediation

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Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)

Cited by 22 publications

References 37 publications

MYB Transcription Factor Family in Sweet Cherry (Prunus avium L.): Genome-wide Investigation, Evolution, Structure, Characterization and Expression Patterns

MYB Transcription Factor Family in Sweet Cherry (Prunus avium L.): Genome-wide Investigation, Evolution, Structure, Characterization and Expression Patterns

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

Structure and Function of Heavy Metal Transporting ATPases in Brassica Species

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