Horticultural Plant Journal最新文献

{"title":"Managing virus diseases in citrus: Leveraging high-throughput sequencing for versatile applications","authors":"Hongming Chen, Zhiyou Xuan, Lu Yang, Song Zhang, Mengji Cao","doi":"10.1016/j.hpj.2024.07.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.003","url":null,"abstract":"In this review, the advantages and advances in applying high-throughput sequencing (HTS) in the management of viral diseases in citrus, along with some challenges, are discussed to provide perspectives on future prospects. Since the initial implementation of HTS in citrus virology, a substantial number of citrus viruses have been identified, with a notable increase in the last 7 years. The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology, epidemiology, pathology, evolution, ecology, and biotechnology of citrus viruses. HTS has notably contributed to disease diagnosis, such as the diagnoses of concave gum and impietratura, as well as to the surveillance of new virus risks and the preparation of virus-free materials. However, certain inherent defects in HTS and coupled bioinformatics analysis, such as challenges with sequence assembly and the detection of viral dark matter, require improvement to enhance practical efficiency. In addition, the utilization of HTS for the systematic management of citrus viral diseases remains limited, and drawing insights from other virus–plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"70 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BcAHL24-MF1 promotes photomorphogenesis in Brassica campestris via inhibiting over-elongation of hypocotyl under light conditions","authors":"Huiyan Zhou, Jingwen Chen, Xiaojie Cai, Xiangtan Yao, Xinhua Quan, Songhua Bai, Jinzhuang Ni, Yujing Shao, Li Huang","doi":"10.1016/j.hpj.2024.05.015","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.05.015","url":null,"abstract":"Hypocotyl length is regarded to be a crucial seedling trait, influencing many subsequent plant development processes. However, little is known about this trait in <ce:italic>Brassica campestris</ce:italic> syn. <ce:italic>Brasscia rapa</ce:italic>. Here, we performed a comparative observation on the early hypocotyl development between two cultivars, ‘SZQ’ belonging to pak-choi (<ce:italic>B. campestris</ce:italic> ssp. <ce:italic>chinensis</ce:italic> var. <ce:italic>communis</ce:italic>) with longer hypocotyls, and ‘WTC’ belonging to Tacai (<ce:italic>B</ce:italic>. <ce:italic>campestris</ce:italic> L. ssp. <ce:italic>chinensis</ce:italic> var. <ce:italic>rosularis</ce:italic>) with shortter hypocotyls, and found that the difference in auxin biosynthesis might contribute to the varied hypocotyl phenotype between these two cultivars. By applying GWAS analysis using a total of 226 <ce:italic>B. campestris</ce:italic> accessions, we identified that the AT-Hook motif nuclear localized (AHL) gene <ce:italic>BcAHL24-MF1</ce:italic> contributed to the natural variation in hypocotyl length. Functional variation of BcAHL24-MF1 was attributed to four haplotypes featuring four SNPs within the promoter region, of which Hap I accumulated more transcripts with shorter hypocotyls. Constitutive overexpression of <ce:italic>BcAHL24-MF1</ce:italic> in <ce:italic>B. campestris</ce:italic> caused decreased hypocotyl length under light circumstances and even constant darkness, as BcAHL24-MF1 repressed the PIF-mediated transcriptional activation of auxin biosynthesis genes <ce:italic>BcYUC6-MF2</ce:italic> and <ce:italic>BcYUC8-LF.</ce:italic> Our research uncovered the important role of BcAHL24-MF1 in regulating light-triggered inhibition of hypocotyl elongation, therefore presenting a valuable genetic target for crop breeding.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"172 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BoaCRTISO regulates the color and glossiness of Chinese kale through its effects on pigment, abscisic acid, and cuticular wax biosynthesis","authors":"Chenlu Zhang, Ling Li, Yutong Zhang, Qiannan Liang, Sha Luo, Zhi Huang, Huanxiu Li, Victor Hugo Escalona, Zhifeng Chen, Fen Zhang, Yi Tang, Bo Sun","doi":"10.1016/j.hpj.2024.06.008","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.06.008","url":null,"abstract":"Carotenoid isomerase (CRTISO) is an important enzyme in carotenoid biosynthesis, and it catalyzes the conversion of lycopene precursors to lycopene in several plant species. However, the role of CRTISO in other biochemical processes during plant growth and development remains unclear. Here, we showed that Chinese kale <ce:italic>boacrtiso</ce:italic> mutants have distinctive characteristics, including a yellow-green hue and glossy appearance, and this contrasts with the dark green and glaucous traits observed in wild-type (WT) plants. Analysis of pigments in mutants revealed that the reduction in the content of carotenoids and chlorophylls contributed to the yellow-green coloration observed in mutants. An examination of cuticular waxes in Chinese kale indicated that there was a decrease in both the total wax content and the content of individual waxes in <ce:italic>boacrtiso</ce:italic> mutants (bearing a mutation of <ce:italic>BoaCRTISO</ce:italic>), which may be caused by the decrease of abscisic acid (ABA) content. The expression of carotenoid, chlorophyll, ABA, and wax biosynthesis genes was down-regulated in <ce:italic>boacrtiso</ce:italic> mutants. This finding confirms that <ce:italic>BoaCRTISO</ce:italic> regulates the biosynthesis of pigments, ABA, and cuticular waxes in Chinese kale. Our results provide new insights into the interplay between plant pigment and cuticular wax metabolic pathways in <ce:italic>Brassica</ce:italic> vegetables.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of the main terpenoids biosynthesis and accumulation in fruit trees","authors":"Yujie Hu, Tianyi Zheng, Jie Dong, Wangze Li, Xiaoyu Ma, Jin Li, Yulin Fang, Keqin Chen, Kekun Zhang","doi":"10.1016/j.hpj.2024.08.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.08.002","url":null,"abstract":"Terpenoids are vital secondary metabolites in plants that function as agents for defense and stress resistance. These genes not only play crucial roles in plant growth and development but also function in diverse biological group interactions. Terpenoids released by fruit trees possess defensive properties and constitute a class of aromatic compounds. For some fruits, terpenoids are indispensable indicators for evaluating fruit quality and the economic value. Significant research progress has been made in terpenoids biosynthesis and regulation. In this review, we introduce the main terpenoids of fruit trees, emphasize synthetic enzymes and regulatory factors involved in the mevalonate pathway and the methylerythritol pathway, and analyze <ce:italic>TPS</ce:italic> gene family identification and diversity in several fruit tree species. Moreover, the regulation of terpenes biosynthesis, including the molecular interaction mechanisms of environmental factors and hormone signaling pathways, are comprehensively described. Our objective is to summarize the molecular regulatory network and research foundation of terpenoids biosynthesis, providing a reference for investigations of metabolic pathways and promoting the development of techniques for the regulation and breeding of terpenoids in fruit trees.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Betula platyphylla glucosyltransferase BpGT14;6 is essential for cell wall development and stress response","authors":"Xiaohui Chen, Ruijia Zhang, Jialin Yan, Xinying Jia, Ronghua Liang, Fengkun Sun, Leilei Li, Minghao Ma, Yaguang Zhan, Fansuo Zeng","doi":"10.1016/j.hpj.2024.05.014","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.05.014","url":null,"abstract":"Glycosyltransferases (GTs) constitute a diverse family of synthetic polysaccharides with important roles in plant growth and development. This study characterized the GT14 family gene <ce:italic>BpGT14;6</ce:italic> of birch (<ce:italic>Betula platyphylla</ce:italic> Suk.). <ce:italic>BpGT14;6</ce:italic> was highly expressed in the xylem and stem of birch plants. Subcellular localization analysis suggested that <ce:italic>BpGT14;6</ce:italic> was located in the Golgi apparatus. RNA interference (RNAi) silencing of <ce:italic>BpGT14;6</ce:italic> revealed lower lignin, hemicellulose, and pectin contents compared to wild type (WT) plants. Following treatment with abscisic acid (ABA), compared to WT plants, RNAi-<ce:italic>BpGT14;6</ce:italic> plants were more sensitive to ABA, suffered more membrane lipid damage, and accumulated more reactive oxygen species. The inhibition of <ce:italic>BpGT14;6</ce:italic> expression narrowed the birch xylem and thinned the cell wall, and increased the expression of multiple ABA pathway-related genes in birch under ABA treatment. Compared to WT plants, RNAi-<ce:italic>BpGT14;6</ce:italic> plants showed increased tolerance to drought stress. Promoter analysis revealed that <ce:italic>BpGT14;6</ce:italic> is involved in hormone regulation and adaptation to adversity. Using the 1156 bp <ce:italic>BpGT14;6</ce:italic> promoter as bait, two potential transcription factors, BpWRKY1 and BpARF2, were identified through Y1H screening that may regulate its expression. EMSA confirmed that BpWRKY1 and BpARF2 can directly bind to the W-BOX and AuxRE <ce:italic>cis</ce:italic>-acting elements on the <ce:italic>BpGT14;6</ce:italic> promoter, respectively. The collective results suggest that <ce:italic>BpGT14;6</ce:italic> affects birch xylem and cell wall development by affecting lignin, hemicellulose, and pectin synthesis, and participates in birch adversity adaptation.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"49 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Competitive network of polyamines metabolic and ethylene biosynthesis pathways during gibberellin-induced parthenocarpic grape fruit setting","authors":"Xuxian Xuan, Ziyang Qu, Ehsan Sadeghnezhad, Zhenqiang Xie, Ziyang Qi, Hui Yang, Xiuling Song, Mucheng Yu, Linjia Luo, Rana Badar Aziz, Yanping Zhang, Peijie Gong, Jinggui Fang, Chen Wang","doi":"10.1016/j.hpj.2024.07.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.002","url":null,"abstract":"Polyamines (PAs) and ethylene are involved in the modulation of plant growth and development. However, their roles in fruit-set, especially in exogenous gibberellin (GA<ce:inf loc=\"post\">3</ce:inf>)-induced grape parthenocarpic berries, and the related competitive action mode are poorly understood. For this, we, here performed their content determination, bioinformatics and expression pattern analysis of genes to identify the key ones in the competitive network of polyamines metabolic and ethylene biosynthesis (PMEB) pathways. The content of putrescine (Put) significantly increased; while 1-aminocyclopropanecarboxylic acid (ACC) sharply decreased during the fruit-set process of GA<ce:inf loc=\"post\">3</ce:inf>-induced grape parthenocarpic seedless berries. Totally, twenty-five genes in PMEB pathways, including 20 polyamines metabolic (PM) genes and 5 ethylene biosynthesis (EB) ones were identified in grape, of which 8 PM and 2 EB genes possessed the motifs responsive to phytohormone GA. The expression levels of most PMEB genes kept changing during grape fruit-set generating a competitive action mode of GA<ce:inf loc=\"post\">3</ce:inf>-mediated two metabolic fluxes toward PAs and ethylene synthesis. Exogenous GA<ce:inf loc=\"post\">3</ce:inf> might enhance grape fruit-set of parthenocarpic berries via up-regulation of <ce:italic>VvSAMS4</ce:italic>, <ce:italic>VvSAMDC1/2</ce:italic>, <ce:italic>VvODC1</ce:italic>, <ce:italic>VvSPDS1</ce:italic>, and <ce:italic>VvPAO1</ce:italic> to promote PAs accumulation<ce:italic>,</ce:italic> whereby repressing the ethylene synthesis by down-regulation of <ce:italic>VvACS1</ce:italic> and <ce:italic>VvACO2.</ce:italic> Our findings provide novel insights into GA<ce:inf loc=\"post\">3</ce:inf>-mediated competitive inhibition of ethylene by PAs to promote the fruit-set of parthenocarpic berries in grape, which has important implications for molecular breeding of seedless grape with high fruit-setting rate.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"22 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical characterization of CsCXEs: Carboxylesterase enhances the biosynthesis of green odor volatiles during tea processing","authors":"Sanyan Lai, Ning Yi, Shixin Yin, Yipeng Huang, Tianlin Shen, Qianying Dai, Liping Gao, Xiaolan Jiang, Tao Xia","doi":"10.1016/j.hpj.2024.08.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.08.001","url":null,"abstract":"Tea flavor is a comprehensive representation of its aroma and other characteristics. The formation of volatile odor compounds during tea processing depends on a variety of enzymatic and non-enzymatic activities. (<ce:italic>Z</ce:italic>)-3-hexenol is considered the primary source of the green odor and is also the most important component in tea aroma, significantly affecting the overall aroma. However, the biosynthesis and accumulation of (<ce:italic>Z</ce:italic>)-3-hexenol during tea processing have not been fully analyzed. In this study, we found that withering treatment at different times and withering plus shaking treatment at different degrees promoted the accumulation of important volatile components of green tea odor, especially (<ce:italic>Z</ce:italic>)-3-hexenol by GC–MS. The RNA-seq and qRT-PCR results showed that withering and withering plus shaking treatments enhanced the expression of (<ce:italic>Z</ce:italic>)-3-hexenol-related genes in tea leaves, including synthetic pathway 1 genes (<ce:italic>CsLOX3</ce:italic>, <ce:italic>CsHPL1</ce:italic>, <ce:italic>CsADH4</ce:italic>, and <ce:italic>CsAHD1</ce:italic>), synthetic pathway 2 genes (<ce:italic>CsGLU</ce:italic>), and synthetic pathway 3 genes (<ce:italic>CsCXEs</ce:italic>). Correlation analysis of the key odorants and important genes in the three synthetic pathways revealed that some <ce:italic>CsCXEs</ce:italic> were positively correlated with green odor compounds. The <ce:italic>in vitro</ce:italic> enzyme activity results showed that rCsCXE3 (GWHTASIV011658), and rCsCXE6 (GWHTASIV031480) exhibited hydrolytic activity against three tea acetate compounds [hexyl acetate, (<ce:italic>E</ce:italic>)-2-hexyl acetate, and (<ce:italic>Z</ce:italic>)-3-hexyl acetate], resulting in the production of corresponding alcohol compounds. In summary, withering and shaking treatment during tea processing promoted the expression of <ce:italic>CsCXE3</ce:italic> and <ce:italic>CsCXE6</ce:italic>, thereby enhancing the production of hexenol compounds. These compounds play a crucial role in increasing the green odor of tea.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"249 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the role of MpAL1 in drought stress responses in Malus prunifolia: Insights into AL gene family functionality","authors":"Peien Feng, Jiale Li, Qiuying Ai, Xinchu Li, Jiawei Luo, Yunxiao Liu, Jiakai Liang, Chongrong Chen, Yangjun Zou, Fengwang Ma, Tao Zhao, Yaqiang Sun","doi":"10.1016/j.hpj.2024.07.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.001","url":null,"abstract":"Drought stress significantly impedes apple growth, development, and yield, leading to substantial economic losses within the global apple industry. <ce:italic>Malus prunifolia</ce:italic> (<ce:italic>Mp</ce:italic>), a commonly utilized apple rootstock, has shown promise in augmenting cultivated apple resistance to abiotic stress. Although Alfin-like (ALs) proteins have demonstrated pivotal roles in dicotyledonous plants' response to abiotic stresses, knowledge about AL genes in apple rootstocks is limited, and their functions remain largely elusive. In this study, we identified and characterized 10 <ce:italic>MpAL</ce:italic> gene members in the apple rootstock genome, confirming their localization within the nucleus. Our investigation revealed the significant regulation of <ce:italic>MpALs</ce:italic>' expression under drought and abscisic acid (ABA) stresses in <ce:italic>M. prunifolia</ce:italic>. In this study, one of the members, <ce:italic>MpAL1</ce:italic>, was selected for further exploration in <ce:italic>Arabidopsis</ce:italic> and apple to explore its potential function in response to drought and ABA stresses. The results showed that overexpression-<ce:italic>MpAL1</ce:italic> transgenic apple calli grew significantly better than WT and <ce:italic>MpAL1</ce:italic>-RNAi lines, which regulates the accumulation of H<ce:inf loc=\"post\">2</ce:inf>O<ce:inf loc=\"post\">2</ce:inf> and O<ce:inf loc=\"post\">2</ce:inf><ce:sup loc=\"post\">-</ce:sup> levels. Additionally, transgenic <ce:italic>Arabidopsis</ce:italic> plants overexpressing <ce:italic>MpAL1</ce:italic> exhibited positively regulating anti-oxidant enzymes activities under stress treatments. Further study showed that silencing <ce:italic>MpAL1</ce:italic> in apple plants showed obvious chlorosis in leaves, and accumulation of reactive oxygen species under drought stress. Moreover, our detailed analysis established that <ce:italic>MpAL1</ce:italic> regulates several drought and ABA-responsive genes, exerting an influence on their expression in transgenic apple. Collectively, our findings identify <ce:italic>MpAL1</ce:italic> as a positive regulator that increases drought stress in apple, shedding light on its potential significance in bolstering drought resistance in this fruit crop.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"7 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptomics analysis reveals stage-specific gene expression profiles associated with gamete formation in Allium sativum L.","authors":"Jie Ge, Jide Fan, Yongqiang Zhao, Xinjuan Lu, Canyu Liu, Biwei Zhang, Qingqing Yang, Mengqian Li, Yan Yang, Feng Yang","doi":"10.1016/j.hpj.2024.01.012","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.01.012","url":null,"abstract":"Commercial cultivars of garlic, a popular condiment, are sterile, making genetic variation and germplasm innovation of this plant challenging. Understanding mechanism of gamete sterility in garlic and their key regulatory networks is therefore important for fertility restoration. In this work, we conducted a detailed phenotypic analysis of fertile and sterile garlic genotypes and found that enlargement of topset in the inflorescence of sterile genotypes led to abnormal flowers. Additional cytological observations showed that aberrant meiotic cytokinesis in sterile garlic ultimately resulted in pollen degeneration. Transcriptomics analysis of sterile and fertile genotypes identified possible molecular mechanisms underlying gamete abortion. A total of 100 710 differentially expressed genes (DEGs) between the fertile and sterile garlic flowers at three stages of gamete development were identified, many of which were involved in homologous chromosome synapsis during meiosis, MYB transcription factor regulation, ribosome biogenesis and plant hormone signal transduction. Taken together, these results provide insight into the molecular mechanisms and regulatory networks underlying gamete development in garlic and point to a set of candidate genes for further functional characterization.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"17 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Telomere-to-telomere, gap-free assembly of the Rosa rugosa reference genome","authors":"Dan Liu, Kun Liu, Boqiang Tong, Haili Guo, Kai Qu, Ting Xu, Ren-Gang Zhang, Wei Zhao, Xiaoman Xie, Longxin Wang, Kai-Hua Jia","doi":"10.1016/j.hpj.2024.06.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.06.005","url":null,"abstract":"Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for <ce:italic>Rosa rugosa</ce:italic>, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of <ce:italic>ATHILA</ce:italic>/<ce:italic>Gypsy</ce:italic> long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering <ce:italic>R. rugosa</ce:italic>'s stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in <ce:italic>R. rugosa</ce:italic> but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"32 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}