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CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri).

ABSTRACT: The synthetic enzyme cinnamyl alcohol dehydrogenase (CAD) is involved in responses to various stresses during plant growth. It regulates the monolignol biosynthesis and catalyzes hydroxyl cinnamaldehyde reduction to the corresponding alcohols. Although the CAD gene families have been explored in some species, little known is in Rosaceae. In this study, we identified 149 genes in Pyrus bretschneideri (PbrCAD), Malus domestica (MDPCAD), Prunus mume (PmCAD) and Fragaria vesca (mrnaCAD). They were phylogenetically clustered into six subgroups. All CAD genes contained ADH-N and ADH-zinc-N domains and were distributed on chromosomes unevenly. Dispersed and WGD/segmental duplications accounted the highest number of evolutionary events. Eight collinear gene pairs were identified among the four Rosaceae species, and the highest number was recorded in pear as five pairs. The five PbrCAD gene pairs had undergone purifying selection under Ka/Ks analysis. Furthermore, nine genes were identified based on transcriptomic and stone cell content in pear fruit. In qRT-PCR, the expression patterns of PbrCAD1, PbrCAD20, PbrCAD27, and PbrCAD31 were consistent with variation in stone cell content during pear fruit development. These results will provide valuable information for understanding the relationship between gene expressions and stone cell number in fruit.

SUBMITTER: Qi K

PROVIDER: S-EPMC8309377 | biostudies-literature |

REPOSITORIES: biostudies-literature

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B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.).

Project description:BackgroundThe B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear.ResultsIn the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members. The transcript analysis revealed that twelve PbBBX genes (48%) were specifically expressed in pear pollen tubes. Furthermore, qRT-PCR analysis indicated that both PbBBX4 and PbBBX13 have potential role in pear fruit development, while PbBBX5 should be involved in the senescence of pear pollen tube.ConclusionsThis study provided a genome-wide survey of BBX gene family in pear, and highlighted its roles in both pear fruits and pollen tubes. The results will be useful in improving our understanding of the complexity of BBX gene family and functional characteristics of its members in future study.

| S-EPMC5606111 | biostudies-literature

Comprehensive genome-wide analysis of the pear (Pyrus bretschneideri) laccase gene (PbLAC) family and functional identification of PbLAC1 involved in lignin biosynthesis.

Project description:The content and size of stone cell clusters affects the quality of pear fruit, and monolignol polymerization and deposition in the cell walls constitute a required step for stone cell formation. Laccase (LAC) is the key enzyme responsible for the polymerization of monolignols. However, there are no reports on the LAC family in pear (Pyrus bretschneideri), and the identity of the members responsible for lignin synthesis has not been clarified. Here, 41 LACs were identified in the whole genome of pear. All Pyrus bretschneideri LACs (PbLACs) were distributed on 13 chromosomes and divided into four phylogenetic groups (I-IV). In addition, 16 segmental duplication events were found, implying that segmental duplication was a primary reason for the expansion of the PbLAC family. LACs from the genomes of three Rosaceae species (Prunus mummer, Prunus persica, and Fragaria vesca) were also identified, and an interspecies collinearity analysis was performed. The phylogenetic analysis, sequence alignments and spatiotemporal expression pattern analysis suggested that PbLAC1, 5, 6, 29, 36 and 38 were likely associated with lignin synthesis and stone cell formation in fruit. The two target genes of Pyr-miR1890 (a microRNA identified from pear fruit that is associated with lignin and stone cell accumulation), PbLAC1 and PbLAC14, were selected for genetic transformation. Interfamily transfer of PbLAC1 into Arabidopsis resulted in a significant increase (approximately 17%) in the lignin content and thicker cell walls in interfascicular fibre and xylem cells, which demonstrated that PbLAC1 is involved in lignin biosynthesis and cell wall development. However, the lignin content and cell wall thickness were not changed significantly in the PbLAC14-overexpressing transgenic Arabidopsis plants. This study revealed the function of PbLAC1 in lignin synthesis and provides important insights into the characteristics and evolution of the PbLAC family.

| S-EPMC6372139 | biostudies-literature

Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis.

Project description:BackgroundThe content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145?days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched.ResultsIn this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis.ConclusionsOur results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.

| S-EPMC6788021 | biostudies-literature

Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri).

Project description:BackgroundThe lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene family has not yet been characterized for the Chinese White Pear.ResultsIn our study, a total of 60 PbrLBDs were identified in the pear genome. The PbrLBD gene family was divided into two classes based on gene structure and phylogenetic analysis: class I (53) and class II (7). Cis-acting element analysis results suggested that PbrLBDs may participate in various biological processes, such as flavonoid biosynthetic and stress response. Synteny analysis results indicated that segmental duplication played a key role in the expansion of the PbrLBD gene family. The mean Ks and 4DTv values showed that the PbrLBD gene family had undergone only one recent whole-genome duplication event occurring at 30-45 MYA. Purifying selection was a primary force during the PbrLBD gene family evolution process. Transcriptome data analysis revealed that 10 PbrLBDs were expressed in all six examined tissues, and 73.33% of members in the PbrLBD gene family were expressed in pear sepal. qRT-PCR was conducted to verify the expression levels of 11 PbrLBDs in these six tissues. Specifically, PbrLBD20, PbrLBD35 and PbrLBD53 genes were down-regulated when anthocyanin concentrations were high, whereas PbrLBD33 was significantly up-regulated in pear when anthocyanin concentrations were high. Furthermore, PbrLBD20, one of the candidate genes related to anthocyanins was localized in the nucleus.ConclusionsOur analysis provides valuable information for understanding the evolution of the PbrLBD gene family, and provides new insights into the regulation of pear pigment metabolism and lays a foundation for the future disclosure of the molecular mechanism of LBD gene regulating flavonoid metabolism.

| S-EPMC7504654 | biostudies-literature

Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri).

Project description:Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR) family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.

| S-EPMC5911567 | biostudies-literature

Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence.

Project description:MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear.

| S-EPMC5598432 | biostudies-literature

Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress.

Project description:BackgroundWRKY transcription factors (TFs) constitute one of the largest protein families in higher plants, and its members contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. WRKY proteins play significant roles in plant development, and in responses to biotic and abiotic stresses. Pear (Pyrus bretschneideri) is one of the most important fruit crops in the world and is frequently threatened by abiotic stress, such as drought, affecting growth, development and productivity. Although the pear genome sequence has been released, little is known about the WRKY TFs in pear, especially in respond to drought stress at the genome-wide level.ResultsWe identified a total of 103 WRKY TFs in the pear genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the pear WRKY (PbWRKY) family was classified into seven groups (Groups 1, 2a-e, and 3). The microsyteny analysis indicated that 33 (32%) PbWRKY genes were tandemly duplicated and 57 genes (55.3%) were segmentally duplicated. RNA-seq experiment data and quantitative real-time reverse transcription PCR revealed that PbWRKY genes in different groups were induced by drought stress, and Group 2a and 3 were mainly involved in the biological pathways in response to drought stress. Furthermore, adaptive evolution analysis detected a significant positive selection for Pbr001425 in Group 3, and its expression pattern differed from that of other members in this group. The present study provides a solid foundation for further functional dissection and molecular evolution of WRKY TFs in pear, especially for improving the water-deficient resistance of pear through manipulation of the PbWRKYs.

| S-EPMC4691019 | biostudies-literature

The Sucrose Synthase Gene Family in Chinese Pear (Pyrus bretschneideri Rehd.): Structure, Expression, and Evolution.

Project description:Sucrose synthase (SS) is a key enzyme involved in sucrose metabolism that is critical in plant growth and development, and particularly quality of the fruit. Sucrose synthase gene families have been identified and characterized in plants various plants such as tobacco, grape, rice, and Arabidopsis. However, there is still lack of detailed information about sucrose synthase gene in pear. In the present study, we performed a systematic analysis of the pear (Pyrus bretschneideri Rehd.) genome and reported 30 sucrose synthase genes. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, gene duplications, promoter regions, collinearity, RNA-Seq data and qRT-PCR were conducted on these sucrose synthase genes. The transcript analysis revealed that 10 PbSSs genes (30%) were especially expressed in pear fruit development. Additionally, qRT-PCR analysis verified the RNA-seq data and shown that PbSS30, PbSS24, and PbSS15 have a potential role in the pear fruit development stages. This study provides important insights into the evolution of sucrose synthase gene family in pear and will provide assistance for further investigation of sucrose synthase genes functions in the process of fruit development, fruit quality and resistance to environmental stresses.

| S-EPMC6100409 | biostudies-literature

Unbiased subgenome evolution following a recent whole-genome duplication in pear (<i>Pyrus bretschneideri</i> Rehd.).

Project description:Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.

| S-EPMC6395616 | biostudies-literature

Genome-wide identification of PbrbHLH family genes, and expression analysis in response to drought and cold stresses in pear (Pyrus bretschneideri).

Project description:BackgroundThe basic helix-loop-helix (bHLH) transcription factors play important roles in many processes in plant growth, metabolism and responses to abiotic stresses. Although, the sequence of Chinese white pear genome (cv. 'Dangshansuli') has already been reported, there is still a lack of clarity regarding the bHLH family genes and their evolutionary history.ResultsIn this work, a genome-wide identification of the bHLH genes in Chinese white pear was performed, and we characterized the functional roles of these PbrbHLH genes in response to abiotic stresses. Based on the phylogenetic analysis and structural characteristics, 197 identified bHLH genes could be well classified into 21 groups. Expansion of PbrbHLH gene family was mainly driven by WGD and dispersed duplication with the purifying selection from the recent WGD. The functional annotation enrichment showed that the majority of PbrbHLHs were enriched in the GO terms and KEGG pathways involved in responds to stress conditions as TFs. Transcriptomic profiles and qRT-PCR revealed that PbrbHLH7, PbrbHLH8, PbrbHLH128, PbrbHLH160, PbrbHLH161 and PbrbHLH195 were significantly up-regulated under cold and drought treatments. In addition, PbrbHLH195-silenced pear seedlings display significant reduced cold tolerance, exhibiting reduced chlorophyll content, as well as increased electrolyte leakage and concentrations of malondialdehyde and H2O2.ConclusionFor the first time, a comprehensive analysis identified the bHLH genes in Chinese white pear and demonstrated that PbrbHLH195 is involved in the production of ROS in response to cold stress, suggesting that members of the PbrbHLH family play an essential role in the stress tolerance of pear.

| S-EPMC7874673 | biostudies-literature

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