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

Abstract 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 detailed phylogenetic analysis and 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 inter-species synteny analysis revealed the ancient origin of BAHD superfamily with 78 syntenic gene pairs were detected among the seven Rosaceae species. Different types of gene duplication events jointly drive the expansion of BAHD superfamily, and purifying selection dominates the evolution of BAHD genes supported by the small Ka/Ks ratios . Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, four candidate genes were selected for verification as assessed by qRT-PCR. The result implied that 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 identified the BAHD superfamily genes and performed a comprehensive comparative analysis of their phylogenetic relationships, expansion patterns, and expression characteristics 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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Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus bretschneideri)

BMC Plant Biology ◽

10.1186/s12870-019-2230-z ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Chunxin Liu ◽

Xin Qiao ◽

Qionghou Li ◽

Weiwei Zeng ◽

Shuwei Wei ◽

...

Keyword(s):

Comparative Analysis ◽

Candidate Genes ◽

Fruit Quality ◽

Prunus Persica ◽

Prunus Avium ◽

Developmental Stages ◽

Purifying Selection ◽

Pear Fruit ◽

Rosaceae Species ◽

Expression Characteristics

Abstract 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 detailed phylogenetic analysis and 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 inter-species synteny analysis revealed the ancient origin of BAHD superfamily with 78 syntenic gene pairs were detected among the seven Rosaceae species. Different types of gene duplication events jointly drive the expansion of BAHD superfamily, and purifying selection dominates the evolution of BAHD genes supported by the small Ka/Ks ratios. Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, four candidate genes were selected for verification as assessed by qRT-PCR. The result implied that 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 identified the BAHD superfamily genes and performed a comprehensive comparative analysis of their phylogenetic relationships, expansion patterns, and expression characteristics 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.

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

10.21203/rs.2.13258/v2 ◽

2019 ◽

Author(s):

Chunxin Liu ◽

Xin Qiao ◽

Qionghou Li ◽

Weiwei Zeng ◽

Shuwei Wei ◽

...

Keyword(s):

Comparative Analysis ◽

Gene Duplication ◽

Candidate Genes ◽

Fruit Quality ◽

Prunus Persica ◽

Prunus Avium ◽

Developmental Stages ◽

Pear Fruit ◽

Gene Pairs ◽

Rosaceae Species

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

10.21203/rs.2.13258/v1 ◽

2019 ◽

Author(s):

Chunxin Liu ◽

Xin Qiao ◽

Qionghou Li ◽

Weiwei Zeng ◽

Shuwei Wei ◽

...

Keyword(s):

Comparative Analysis ◽

Gene Duplication ◽

Candidate Genes ◽

Fruit Quality ◽

Prunus Persica ◽

Prunus Avium ◽

Purifying Selection ◽

Pear Fruit ◽

Gene Pairs ◽

Rosaceae Species

Abstract Background: The BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulation the fruit quality; catalytic synthesis of terpene, phenolic and esters; improvement of stress resistance. However, the copy number, evolutionary history and potential functions of the BAHD superfamily genes in the genome sequenced Rosaceae species remains unclear. Results: Totally, 755 BAHD genes were obtained from the genomes of seven Rosaceae fruit species (Pyrus bretschneideri, Malus domestica, Prunus avium, Prunus persica, Fragaria vesca, Pyrus communis and Rubus occidentalis). Based on the classification results from model plants, we divided the BAHD family genes into seven subgroups (I-a, I-b, II-a, II-b, III-a, IV, V). Based on intra-species synteny analysis, 61 syntenic gene pairs were detected from the six Rosaceae species. Dispersed gene duplication occurred frequently in all investigated species. Different modes of duplicated gene pairs identified in each investigated species show that the Ka/Ks is less than one, indicating they evolved through purifying selection. Based on the correlation analysis between ester content and expression level of BAHD genes at different development stages, we selected five genes to perform qRT-PCR verification, and the results showed that Pbr020016.1, Pbr019034.1, Pbr014028.1 and Pbr029551.1 are the important candidate genes involved in aroma formation during pear fruit development. Conclusion: We have thoroughly annotated the BAHD superfamily genes and made a comprehensive comparative analysis of their colinearity, phylogenetic relationships and gene duplication patterns in the seven Rosaceae species, and also obtained four candidate genes might be involved in the aroma synthesis in the pear fruit. These presented results provide a theoretical basis for the 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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Genome-Wide Comparative Analysis of the β-glucosidase Family in Five Rosaceae Species and their Potential Role on Lignification of Stone Cells in Chinese White Pear

10.21203/rs.3.rs-46971/v1 ◽

2020 ◽

Author(s):

Han Wang ◽

Yang Zhang ◽

Yu Zhao ◽

Wenlong Han ◽

Jinjin Lu ◽

...

Keyword(s):

Candidate Genes ◽

Prunus Avium ◽

Expression Patterns ◽

Cell Development ◽

Glycoside Hydrolase Family ◽

Pear Fruit ◽

Stone Cell ◽

Rosaceae Species ◽

Genome Wide ◽

A Genome

Abstract Background: The β-glucosidase BGLU in the glycoside hydrolase family 1 (GH1) is involved in the sugar metabolism of the plant and plays an important role in maintaining the normal physiological function of the plant. Recent studies had shown that β-glucosidase was involved in plant lignification. The lignification in pear fruit is closely related to the formation of pear stone cells, but the BGLU genes family has not been identified in pears.Result: A total of 343 BGLU genes were identified from five species of Rosaceae (Pyrus bretschneideri, Prunus mume, Malus domestica, Prunus avium, Fragaria vesca). According to phylogenetic analysis, 50 PbBGLUs were divided into 8 groups. 298 syntenic pairs were found in intra- and inter-species collinear analysis of five Rosaceae species, found that pears and apples had more syntenic pairs than pear and the other three Rosaceae species. The Ka/Ks analysis of duplication PbBGLU genes in pear indicated that the main mode of expansion of the PbBGLUs was segmental replication and was mainly affected by purification. qRT-PCR showed that the three gene expression patterns of PbBGLU1, PbBGLU15 and PbBGLU16 were basically consistent with the change trend of pear fruit lignin and stone cell content, and may be involved in lignification and stone cell development of pear fruit. Subcellular localization showed that these three candidate genes were all located on the cell wall.Conclusion: In this study, a genome-wide analysis of BGLU genes in five Rosaceae species was carried out, and three candidate genes related to lignification and stone cell development of pear fruits were identified, which laid the foundation for a deeper understanding of the function of BGLU genes in pear fruits and potential in changing pear fruit quality.

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Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear

BMC Genomics ◽

10.1186/s12864-020-07032-9 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Qiming Chen ◽

Qionghou Li ◽

Xin Qiao ◽

Hao Yin ◽

Shaoling Zhang

Keyword(s):

Prunus Persica ◽

Prunus Avium ◽

Higher Plants ◽

Structural Characteristics ◽

Pathogenic Fungus ◽

Purifying Selection ◽

Pathogen Resistance ◽

Contributing Factors ◽

Rosaceae Species ◽

Chinese White

Abstract Background Lysin motif-containing proteins (LYP), which act as pattern-recognition receptors, play central roles in growth, node formation, and responses to biotic stresses. The sequence of Chinese white pear genome (cv. ‘Dangshansuli’) along with the seven other species of Rosaceae has already been reported. Although, in these fruit crops, there is still a lack of clarity regarding the LYP family genes and their evolutionary history. Results In the existing study, eight Rosaceae species i.e., Pyrus communis, Prunus persica, Fragaria vesca, Pyrus bretschneideri, Prunus avium, Prunus mume, Rubus occidentalis, and Malus × domestica were evaluated. Here, we determined a total of 124 LYP genes from the underlined Rosaceae species. While eighteen of the genes were from Chinese white pear, named as PbrLYPs. According to the LYPs structural characteristics and their phylogenetic analysis, those genes were classified into eight groups (group LYK1, LYK2, LYK3, LYK4/5, LYM1/3, LYM2, NFP, and WAKL). Dispersed duplication and whole-genome duplication (WGD) were found to be the most contributing factors of LYP family expansion in the Rosaceae species. More than half of the duplicated PbrLYP gene pairs were dated back to the ancient WGD (~ 140 million years ago (MYA)), and PbrLYP genes have experienced long-term purifying selection. The transcriptomic results indicated that the PbrLYP genes expression was tissue-specific. Most PbrLYP genes showed differential expression in leaves under fungal pathogen infection with two of them located in the plasmalemma. Conclusion A comprehensive analysis identified 124 LYP genes in eight Rosaceae species. Our findings have provided insights into the functions and characteristics of the Rosaceae LYP genes and a guide for the identification of other candidate LYPs for further genetic improvements for pathogen-resistance in higher plants.

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Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

PeerJ ◽

10.7717/peerj.3400 ◽

2017 ◽

Vol 5 ◽

pp. e3400 ◽

Cited By ~ 7

Author(s):

Yunpeng Cao ◽

Yahui Han ◽

Dandan Meng ◽

Dahui Li ◽

Qing Jin ◽

...

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Large Scale ◽

Prunus Persica ◽

Genome Duplication ◽

Purifying Selection ◽

Whole Genome ◽

Environmental Selection ◽

Rosaceae Species ◽

High Level

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

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Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing

International Journal of Molecular Sciences ◽

10.3390/ijms20225783 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5783

Author(s):

Yi Feng ◽

Qiran Sun ◽

Guifen Zhang ◽

Ting Wu ◽

Xinzhong Zhang ◽

...

Keyword(s):

Abc Transporter ◽

Abc Transporters ◽

Prunus Persica ◽

Prunus Avium ◽

Structural Features ◽

Apple Rootstocks ◽

Specific Expression ◽

Protein Motifs ◽

Rosaceae Species ◽

Abc Transporter Genes

ATP-binding cassette (ABC) transporters constitute a large, diverse, and ubiquitous superfamily that is involved in a broad range of processes. The completion of genome sequencing provides an opportunity to understand the phylogenetic history of the ABC transporter superfamily among Rosaceae species. This study identified a total of 1323 ABC transporter genes from nine Rosaceae genomes: 191 from Malus domestica, 174 from Pyrus communis, 138 from Prunus persica, 118 from Prunus avium, 141 from Prunus dulcis, 122 from Fragaria vesca, 98 from Rubus occidentalis, 162 from Prunus mume, and 179 from Rosa chinensis. Their chemical characterization, phylogenetic analysis, chromosomal localization, gene structure, gene duplication, and tissue-specific expression were studied. Their subcellular localization, transmembrane structures, and protein motifs were predicted. All the ABC transporter genes were grouped into eight subfamilies on the basis of their phylogenetic relationships and structural features. Furthermore, cis-element and expression analysis of 10 potential phytohormone transporters in MdABCG subfamily genes were also performed. Loss of the W-box in the promoter region of MdABCG28 was found to reduce the gene expression level and was linked to the dwarfing phenotype in apple rootstocks. MdABCG28 overexpression promoted shoot growth of atabcg14 mutants in Arabidopsis.

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Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit

International Journal of Molecular Sciences ◽

10.3390/ijms222212492 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12492

Author(s):

Muhammad Aamir Manzoor ◽

Irfan Ali Sabir ◽

Iftikhar Hussain Shah ◽

Han Wang ◽

Zhao Yu ◽

...

Keyword(s):

Transcription Factors ◽

Comparative Analysis ◽

Gene Family ◽

Prunus Persica ◽

Expression Profiles ◽

Functional Divergence ◽

Composition Analysis ◽

Rosaceae Species ◽

Gata Transcription Factors ◽

Gata Gene

The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.

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Metabolite Fruit Profile Is Altered in Response to Source–Sink Imbalance and Can Be Used as an Early Predictor of Fruit Quality in Nectarine

Frontiers in Plant Science ◽

10.3389/fpls.2020.604133 ◽

2021 ◽

Vol 11 ◽

Author(s):

María Paz Covarrubias ◽

Victoria Lillo-Carmona ◽

Lorena Melet ◽

Gianfranco Benedetto ◽

Diego Andrade ◽

...

Keyword(s):

Organic Acids ◽

Fruit Quality ◽

Fruit Development ◽

Prunus Persica ◽

Developmental Stages ◽

Soluble Sugars ◽

Quality Parameters ◽

Stages Of Development ◽

Early Stages ◽

Source Sink

Peaches and nectarines [Prunus persica (L.) Batsch] are among the most exported fresh fruit from Chile to the Northern Hemisphere. Fruit acceptance by final consumers is defined by quality parameters such as the size, weight, taste, aroma, color, and juiciness of the fruit. In peaches and nectarines, the balance between soluble sugars present in the mesocarp and the predominant organic acids determines the taste. Biomass production and metabolite accumulation by fruits occur during the different developmental stages and depend on photosynthesis and carbon export by source leaves. Carbon supply to fruit can be potentiated through the field practice of thinning (removal of flowers and young fruit), leading to a change in the source–sink balance favoring fruit development. Thinning leads to fruit with increased size, but it is not known how this practice could influence fruit quality in terms of individual metabolite composition. In this work, we analyzed soluble metabolite profiles of nectarine fruit cv “Magique” at different developmental stages and from trees subjected to different thinning treatments. Mesocarp metabolites were analyzed throughout fruit development until harvest during two consecutive harvest seasons. Major polar compounds such as soluble sugars, amino acids, organic acids, and some secondary metabolites were measured by quantitative 1H-NMR profiling in the first season and GC-MS profiling in the second season. In addition, harvest and ripening quality parameters such as fruit weight, firmness, and acidity were determined. Our results indicated that thinning (i.e., source–sink imbalance) mainly affects fruit metabolic composition at early developmental stages. Metabolomic data revealed that sugar, organic acid, and phenylpropanoid pathway intermediates at early stages of development can be used to segregate fruits impacted by the change in source–sink balance. In conclusion, we suggest that the metabolite profile at early stages of development could be a metabolic predictor of final fruit quality in nectarines.

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