scholarly journals 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 ◽  
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.

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

2019 ◽  
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. Keywords : BAHD, pear, evolution, Rosaceae, transcriptome, volatile esters

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

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.

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

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

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

scholarly journals Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

2018 ◽  
Author(s):  
Guodong Chen ◽  
Xiaolong Li ◽  
Xin qiao ◽  
Jiaming Li ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Higher Plants ◽  
Chloride Transport ◽  
Structural Characteristics ◽  
Evolutionary Analysis ◽  
Anion Channels ◽  
Genome Wide ◽  
A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

2020 ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background: The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae. Results: A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear ( Pyrus bretschneideri ) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment. Conclusions: This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3400 ◽  
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.

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

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.

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

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

scholarly journals Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

2020 ◽  
Author(s):  
Guodong Chen ◽  
Jizhong Wang ◽  
Xin Qiao ◽  
Cong Jin ◽  
Weike Duan ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Gene Family ◽  
Structural Characteristics ◽  
Purifying Selection ◽  
Related Protein ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Survey

Abstract Background The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants, which play important roles in stress signal transduction and adaptation. Because of these positive regulatory roles in response to adversity, the genes encoding them are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family and the function of these genes has not been explored in Rosaceae. Results A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the main forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assays revealed that the distribution of PbrSnRK2s was very extensive including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatments. Conclusions This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

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