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Yang S, Yu X, Gao X, Fatima K, Tahir Ul Qamar M. Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns. Front Genet 2024; 15:1393487. [PMID: 38798703 PMCID: PMC11116618 DOI: 10.3389/fgene.2024.1393487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024] Open
Abstract
In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.
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Affiliation(s)
- Sheng Yang
- Pomology Institute, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, China
| | - Xiaomei Yu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Xinke Gao
- College of Horticulture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
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Ma Y, Sun J, Zhang X, Sadaqat M, Tahir Ul Qamar M, Liu T. Comparative genomics analysis of pheophorbide a oxygenase ( PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear ( Pyrus bretschneideri). Front Genet 2024; 15:1396744. [PMID: 38689648 PMCID: PMC11058654 DOI: 10.3389/fgene.2024.1396744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein-protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.
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Affiliation(s)
- Yuchen Ma
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Jiao Sun
- Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong, China
- Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong, China
| | - Xiao Zhang
- Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong, China
- Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Shanxi Datong University, Datong, China
| | - Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Tingting Liu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
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Song B, Yu J, Li X, Li J, Fan J, Liu H, Wei W, Zhang L, Gu K, Liu D, Zhao K, Wu J. Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement. Genome Biol 2024; 25:87. [PMID: 38581061 PMCID: PMC10996114 DOI: 10.1186/s13059-024-03220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. RESULTS Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. CONCLUSIONS Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jinshan Yu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Hainan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weilin Wei
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Lingchao Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dongliang Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China.
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Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna RR, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey SB, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. A chromosome-scale assembly for 'd'Anjou' pear. G3 (BETHESDA, MD.) 2024; 14:jkae003. [PMID: 38190814 PMCID: PMC10917493 DOI: 10.1093/g3journal/jkae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica 'Honeycrisp' apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d'Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.
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Affiliation(s)
- Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mary Akinyuwa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Nick Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Brannan Cliver
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harrison Estes
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | | | - Omar Hasannin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer Hutchison
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wren Jenkins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Madelene Loftin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Lauren Lopes
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Erika Moore-Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152-3530, USA
| | | | | | - Jinesh Patel
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Parbati Thapa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Martin Waldinger
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jie Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiong Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Leslie Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Heidi Hargarten
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - James Mattheis
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Huiting Zhang
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Teresa Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - LoriBeth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Loren Honaas
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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5
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Morimoto T, Narazaki R, Okabe H, Zhang L, Nishimura K, Itai A. Introduction of a diverse genetic background of Pyrus into Malus through intergeneric hybridization. Mol Genet Genomics 2024; 299:21. [PMID: 38429502 DOI: 10.1007/s00438-024-02131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Wide hybridizations across species and genera have been employed to enhance agriculturally important traits in crops. Within the tribe Maleae of the Rosaceae family, different genera and species exhibit several traits useful for increasing diversity and gene pool through hybridization. This study aimed to develop and characterize intergeneric hybrid individuals between Malus and Pyrus. Through seed germination, shoot multiplication, and rooting in vitro, acclimatized seedlings showing vegetative growth on their own roots were obtained from crosses of Malus × domestica pollinated by Pyrus communis, P. bretschneideri, and the Pyrus interspecific hybrid (P. communis × P. pyrifolia). Comparative analysis of leaf morphology, flow cytometry, and molecular genotyping confirmed the hybrid status of the individuals. Genome-wide genotyping revealed that all the hybrid individuals inherited genomic fragments symmetrically from the Malus and Pyrus parents. To the best of our knowledge, this is the first report on the development of intergeneric hybrid seedlings between Malus × domestica and P. bretschneideri. Furthermore, the Pyrus interspecific hybrid individual served as a bridge plant for introducing the genetic background of P. pyrifolia into Malus × domestica. The results of this study provided a crucial foundation for breeding through intergeneric hybridization between Malus and Pyrus, facilitating the incorporation of valuable traits from diverse gene pools.
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Affiliation(s)
- Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan.
| | - Ryuya Narazaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Hiroaki Okabe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Lumin Zhang
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- Institute of Tropical Eco-agriculture, Yunnan Academy of Agricultural Sciences, Yunnan, China
| | - Kazusa Nishimura
- Graduate School of Environmental, Natural Science and Technology, Okayama University, Life, Okayama, Japan
| | - Akihiro Itai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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6
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Zhang J, Wen M, Dai R, Liu X, Wang C. Comparative Physiological and Transcriptome Analyses Reveal Mechanisms of Salicylic-Acid-Reduced Postharvest Ripening in 'Hosui' Pears ( Pyrus pyrifolia Nakai). PLANTS (BASEL, SWITZERLAND) 2023; 12:3429. [PMID: 37836170 PMCID: PMC10575155 DOI: 10.3390/plants12193429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Postharvest ripening of sand pear fruit leads to quality deterioration, including changes in texture, flavor, and fruit color. Salicylic acid (SA), an important defense-related hormone, delays fruit ripening and maintains fruit quality, but the underling mechanism remains unclear. Herein, we evaluated the efficacy of SA in delaying the ripening process of Pyrus pyrifolia cv. 'Hosui' pear fruit, as evidenced by the reduction in fruit weight loss, inhibition of firmness loss, cell wall degradation and soluble sugars, and retention of total phenols. Based on comparative transcriptomic data, a total of 3837 and 1387 differentially expressed genes (DEGs) were identified during room-temperature storage of control fruit and between SA-treated and control fruit, respectively. Further KEGG analysis revealed that the DEGs were mainly implicated in plant hormone signal transduction, starch and sugar metabolism, and cell wall modification. Moreover, exogenous SA treatment also altered the expression of many transcription factor (TF) families, including those in the ethylene-responsive factor (ERF), NAM, ATAF, CUC (NAC), basic helix-loop-helix (bHLH), basic leucine zipper (bZIP), and v-myb avian myeloblastosis viral oncogene homolog (MYB) families. Together, the results offer important insights into the role of SA-responsive genes in controlling fruit ripening in sand pears.
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Affiliation(s)
| | | | | | | | - Chunlei Wang
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou 225009, China; (J.Z.); (M.W.); (R.D.); (X.L.)
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7
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Chen S, Sun M, Xu S, Xue C, Wei S, Zheng P, Gu K, Qiao Z, Liu Z, Zhang M, Wu J. The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp. BMC PLANT BIOLOGY 2023; 23:430. [PMID: 37710163 PMCID: PMC10503127 DOI: 10.1186/s12870-023-04406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.
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Affiliation(s)
- Shulin Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Manyi Sun
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaozhuo Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Cheng Xue
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai'an, 271000, China
| | - Pengfei Zheng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwen Qiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Mingyue Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jun Wu
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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8
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Liu HN, Shu Q, Lin-Wang K, Espley RV, Allan AC, Pei MS, Li XL, Su J, Wu J. DNA methylation reprogramming provides insights into light-induced anthocyanin biosynthesis in red pear. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111499. [PMID: 36265764 DOI: 10.1016/j.plantsci.2022.111499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation, an epigenetic mark, is proposed to regulate plant anthocyanin biosynthesis. It well known that light induces anthocyanin accumulation, with bagging treatments commonly used to investigate light-controlled anthocyanin biosynthesis. We studied the DNA methylome landscape during pear skin coloration under various conditions (fruits re-exposed to sunlight after bag removal). The DNA methylation level in gene body/TE and its flanking sequence was generally similar between debagged and bagged treatments, however differentially methylated regions (DMRs) were re-modelled after light-exposure. Both DNA demethylase homologs and the RNA-directed DNA methylation (RdDM) pathways contributed to this re-distribution. A total of 310 DEGs were DMR-associated during light-induced anthocyanin biosynthesis between debagged and bagged treatments. The hypomethylated mCHH context was seen within the promoter of PyUFGT, together with other anthocyanin biosynthesis genes (PyPAL, PyDFR and PyANS). This enhanced transcriptional activation and promoted anthocyanin accumulation after light re-exposure. Unlike previous reports on bud sports, we did not detect DMRs within the MYB10 promoter. Instead, we observed the genome-wide re-distribution of methylation patterns, suggesting different mechanisms underlying methylation patterns of differentially accumulated anthocyanins caused by either bud mutation or environment change. We investigate the dynamic landscape of genome-scale DNA methylation, which is the combined effect of DNA demethylation and RdDM pathway, in the process of light-induced fruit colour formation in pear. This process is regulated by methylation changes on promoter regions of several DEGs. These results provide a DMR-associated DEGs set and new insight into the mechanism of DNA methylation involved in light-induced anthocyanin biosynthesis.
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Affiliation(s)
- Hai-Nan Liu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China.
| | - Qun Shu
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand.
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand.
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Mao-Song Pei
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China.
| | - Xiao-Long Li
- College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China.
| | - Jun Su
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Song B, Li X, Cao B, Zhang M, Korban SS, Yu L, Yang W, Zhao K, Li J, Wu J. An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus. BMC Biol 2022; 20:215. [PMID: 36183077 PMCID: PMC9526952 DOI: 10.1186/s12915-022-01409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the wild relatives of pear originated in southwest China, this fruit crop was independently domesticated and improved in Asia and Europe, and there are major phenotypic differences (e.g., maturity and fruit firmness) between Asian and European pears. RESULTS: In this study, we examined the genomes of 113 diverse pear accessions using an identity-by-descent (IBD) approach to investigate how historical gene flow has shaped fruit firmness traits in Asian and European pears. We found a 3-Mbp IBD-enriched region (IBD-ER) that has undergone "convergent domestication" in both the Asian and European pear lineages, and a genome-wide association study (GWAS) of fruit firmness phenotypes strongly implicated the TRANSLOCON AT THE INNER CHLOROPLAST ENVELOPE55 (TIC55) locus within this 3-Mbp IBD-ER. Furthermore, we identified a tandem duplication that includes a 12-bp insertion located in the first exon of TIC55 that is uniquely present in Asian pears, and expression analysis showed that the pear TIC55 gene is highly expressed in Asian pear, while it is weakly or not expressed in European pear; this could contribute to the differences in fruit firmness between Asian and European pear fruits. CONCLUSIONS Our findings provide insights into how pear fruit softening has been impacted during domestication, and we identified candidate genes associated with fruit softening that can contribute to the breeding and improvement of pear and other fruit crops.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaolong Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Present Address: Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Beibei Cao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14850, USA
| | - Wenxi Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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