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Cheng S, Su L, Guo X, Shao D, Qin Y, Liu X, Chu Q, Zhou X, He Z. Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote. BMC PLANT BIOLOGY 2024; 24:603. [PMID: 38926681 PMCID: PMC11201790 DOI: 10.1186/s12870-024-05317-9] [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: 03/08/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far. RESULTS In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine. CONCLUSIONS These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.
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Affiliation(s)
- Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Xin Guo
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Dalong Shao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Yanmei Qin
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Xuanxuan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Qianwen Chu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, PR China.
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Wang M, Cao Z, Jiang B, Wang K, Xie D, Chen L, Shi S, Yang S, Lu H, Peng Q. Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua. HORTICULTURE RESEARCH 2024; 11:uhae113. [PMID: 38898961 PMCID: PMC11186066 DOI: 10.1093/hr/uhae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/10/2024] [Indexed: 06/21/2024]
Abstract
Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua 'A36' using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.
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Affiliation(s)
- Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Kejian Wang
- China National Rice Research Institute, Hangzhou 310012, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Shaoqi Shi
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Songguang Yang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Hongwei Lu
- China National Rice Research Institute, Hangzhou 310012, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
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Ali Q, Sami A, Haider MZ, Ashfaq M, Javed MA. Antioxidant production promotes defense mechanism and different gene expression level in Zea mays under abiotic stress. Sci Rep 2024; 14:7114. [PMID: 38531994 DOI: 10.1038/s41598-024-57939-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
The growth and productivity of maize are severely affected by soil salinity. The crucial determinants for the future performance of plants are productive for seed germination and seedling establishment; however, both stages are liable to soil salinity. For grain, maize is an economically significant crop sensitive to abiotic stresses. However, little is known about defense responses by the salinity-induced antioxidant and oxidative stress in maize. In our work, the commercially available maize variety Raka-Poshi was grown in pots for 30 days under greenhouse conditions. To evaluate the salt-induced oxidative/antioxidant responses in maize for salt stress 0, 25, 50, 75, 100 and 150 mM concentrations, treatments were provided using sodium chloride (NaCl). All the biochemical indices were calculated under all NaCl concentrations, while drought was induced by up to 50% irrigation water. After 30 days of seed germination, the maize leaves were collected for the measurement of lipid peroxidase or malondialdehyde (MDA), glutathione reductase (GR), guaiacol peroxidase (GPOD), hydrogen peroxide (H2O2), superoxide dismutase (SOD), lipoxygenase (LOX), catalase (CAT), ascorbate peroxidase (APOD) and glutathione-S-transferase (GST). The results revealed a 47% reduction under 150 mM NaCl and 50% drought stress conditions. The results have shown that the successive increase of NaCl concentrations and drought caused an increase in catalase production. With successive increase in NaCl concentration and drought stress, lower levels of H2O2, SOD, and MDA were detected in maize leaves. The results regarding the morphology of maize seedlings indicated a successive reduction in the root length and shoot length under applications of salt and drought stress, while root-to-shoot weights were found to be increased under drought stress and decreased under salt stress conditions During gene expression analysis collectively indicate that, under drought stress conditions, the expression levels of all nine mentioned enzyme-related genes were consistently downregulated.
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Affiliation(s)
- Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Ashfaq
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, 54590, Pakistan.
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Zhao W, Sun X, Wang L, Sun Z, Zhang H, Zhong Q, Yang S. Metabolomics analysis of quality components metabolism during the growth process of pepino ( Solanum muricatum) fruit. PLANT SIGNALING & BEHAVIOR 2023; 18:2283363. [PMID: 37976083 PMCID: PMC10761028 DOI: 10.1080/15592324.2023.2283363] [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: 09/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Pepino (Solanum muricatum), a horticultural crop that has experienced significant growth in the highlands of China over the past two decades, is widely embraced by consumers due to its distinctive taste and nutritional advantages. This study focused on the cultivar 'Qingcanxiang' of pepino grown on the Qinghai-Tibetan Plateau was analyzed using UPLC-QTOF-MS and RNA-seq transcriptome sequencing. Fruit samples were collected at three distinct stages of development, and the results of the metabolomics and transcriptomics were compared and correlated. The study's findings indicate that the 'Qingcanxiang' fruit contained a total of 187 metabolites, comprising 12 distinct categories of compounds, including amino acids and their derivatives, organic acids, sugars and alcohols, phenols and phenolic acids. Of these metabolites, 94 were identified as differential. Significant variations in nutrient composition were observed across the three growth stages of the fruit. Specifically, the stage spanning from the growth to the maturation was identified as the critical stages for nutrient accumulation and flavor development. Transcriptome sequencing analysis revealed a set of highly associated genes between aspartate and quinic acid, namely SIR2, IRAK4, RP-L29, and CCNH. These genes are potentially involved in the regulation of both amino acid and phenolic acid synthesis. Through the application of metabolomics and transcriptomics, this investigation elucidates the alterations in metabolites and the underlying molecular regulatory mechanisms of pepino fruits during three growth stages. The findings furnish a theoretical foundation for the evaluation of nutritional quality and the enhancement of breeding strategies for pepino.
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Affiliation(s)
- Wenwen Zhao
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xuemei Sun
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
| | - Lihui Wang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
| | - Zhu Sun
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
| | - Huajing Zhang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Qiwen Zhong
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Xining, China
- College of Life Sciences, Northwest A&F University, Yangling, China
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5
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Du Z, Qu F, Zhang C, Chen Z, Li Y, Wen L. Multi-Omics Analyses Unravel Metabolic and Transcriptional Differences in Tender Shoots from Two Sechium edule Varieties. Curr Issues Mol Biol 2023; 45:9060-9075. [PMID: 37998745 PMCID: PMC10670898 DOI: 10.3390/cimb45110568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Chaylte vine, the tender shoot of Sechium edule, is popular among vegetable consumers because of its high nutritional content, crisp texture, and unique flavor. Existing studies on the nutrient composition of chaylte vines are mostly simple chemical determinations, which have limited the breeding of specialized cultivars and the development of related industries. Using metabolomics combined with transcriptomics, this study analyzed the metabolic characteristics and related molecular mechanisms of two common varieties of chaylte vines: green-skinned (SG) and white-skinned (SW). Between the two varieties, a total of 277 differentially accumulated metabolites (DAMs) and 739 differentially expressed genes (DEGs) were identified. Furthermore, chemical assays demonstrated that the SW exhibited a higher total flavonoid content and antioxidant capacity. In conclusion, it was found that the SG samples exhibited a higher diversity of flavonoid subclasses compared to the SW samples, despite having a lower total flavonoid content. This inconsistent finding was likely due to the differential expression of the phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) genes in the two varieties. These results laid the foundation for investigating the mechanisms involved in flavonoid regulation and the breeding of specialized S. edule cultivars for chaylte vine production.
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Affiliation(s)
| | | | | | | | - Yurong Li
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (F.Q.); (C.Z.); (Z.C.); (L.W.)
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6
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Cheng S, Liu Y, Su L, Liu X, Chu Q, He Z, Zhou X, Lu W, Jiang C, Zheng W. Physiological, anatomical and quality indexes of root tuber formation and development in chayote (Sechium edule). BMC PLANT BIOLOGY 2023; 23:413. [PMID: 37674150 PMCID: PMC10483781 DOI: 10.1186/s12870-023-04427-0] [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: 04/01/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Chayote is an underutilized species of Cucurbitaceae. It is rich in nutrients such as protein, minerals, phenols and its extracts have anti-cardiovascular and anti-cancer effects, making it a versatile plant for both medicinal and culinary purposes. Although research on its root tuber is limited, they are rich in starch and have a structure similar to that of potatoes, cassava, and sweet potatoes. Therefore, they can serve as potential substitutes for potatoes and offer promising prospects as agricultural and industrial resources. However, the physiological and cellular mechanisms of chayote root tuber formation and development are still unclear. RESULTS In this study, we observed the growth habit of 'Tuershao' (high yield of root tuber). The results revealed that the tuber enlargement period of 'Tuershao' lasts approximately 120 days, with the early enlargement phase occurring during 0-30 days, rapid enlargement phase during 30-90 days, and maturation phase during 90-120 days. Physiological indicators demonstrated a gradual increase in starch content as the tuber developed. The activities of sucrose synthase (SUS) and invertase (VIN) showed a consistent trend, reaching the highest level in the rapid expansion period, which was the key enzyme affecting tuber expansion. Moreover, the special petal like structure formed by the secondary phloem and secondary xylem of the tuber resulted in its enlargement, facilitating the accumulation of abundant starch within the thin-walled cells of this structure. Principal component analysis further confirmed that starch content, SUS and VIN activities, as well as the concentrations of calcium (Ca), iron (Fe), and selenium (Se), were the major factors influencing tuber development. Moreover, the low temperature environment not only promoted the growth of 'Tuershao' tubers but also enhanced the accumulation of nutritional substances. CONCLUSIONS These findings contribute to a deeper understanding of the formation and developmental mechanisms of 'Tuershao' tubers, providing valuable guidance for cultivation practices aimed at improving crop yield.
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Affiliation(s)
- Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuhang Liu
- Horticulture Research Institute, Chengdu Academy of Agricultural and Forest Sciences, Chengdu, 611130, China
| | - Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuanxuan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianwen Chu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wangang Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
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7
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in Cucumber ( Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 ( RALF34) Tell Us? Int J Mol Sci 2023; 24:ijms24098440. [PMID: 37176146 PMCID: PMC10179419 DOI: 10.3390/ijms24098440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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Affiliation(s)
- Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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8
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Song H, Wang Q, Zhang Z, Lin K, Pang E. Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes. HORTICULTURE RESEARCH 2023; 10:uhad038. [PMID: 37799630 PMCID: PMC10548412 DOI: 10.1093/hr/uhad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/20/2023] [Indexed: 10/07/2023]
Abstract
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
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Affiliation(s)
- Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qi Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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9
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Cheng S, Jia M, Su L, Liu X, Chu Q, He Z, Zhou X, Lu W, Jiang C. Genome-Wide Identification of the MADS-Box Gene Family during Male and Female Flower Development in Chayote (Sechium edule). Int J Mol Sci 2023; 24:ijms24076114. [PMID: 37047083 PMCID: PMC10094161 DOI: 10.3390/ijms24076114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
The MADS-box gene plays an important role in plant growth and development. As an important vegetable of Cucurbitaceae, chayote has great edible and medicinal value. So far, there is little molecular research on chayote, and there are no reports on the MADS-box transcription factor of chayote. In this study, the MADS-box gene family of chayote was analyzed for the first time, and a total of 70 MADS-box genes were identified, including 14 type I and 56 type II MICK MADS genes. They were randomly distributed on 13 chromosomes except for chromosome 11. The light response element, hormone response element and abiotic stress response element were found in the promoter region of 70 MADS genes, indicating that the MADS gene can regulate the growth and development of chayote, resist abiotic stress, and participate in hormone response; GO and KEGG enrichment analysis also found that SeMADS genes were mainly enriched in biological regulation and signal regulation, which further proved the important role of MADS-box gene in plant growth and development. The results of collinearity showed that segmental duplication was the main driving force of MADS gene expansion in chayote. RNA-seq showed that the expression levels of SeMADS06, SeMADS13, SeMADS26, SeMADS28, SeMADS36 and SeMADS37 gradually increased with the growth of chayote, indicating that these genes may be related to the development of root tubers of 'Tuershao'. The gene expression patterns showed that 12 SeMADS genes were specifically expressed in the male flower in 'Tuershao' and chayote. In addition, SeMADS03 and SeMADS52 may be involved in regulating the maturation of male flowers of 'Tuershao' and chayote. SeMADS21 may be the crucial gene in the development stage of the female flower of 'Tuershao'. This study laid a theoretical foundation for the further study of the function of the MADS gene in chayote in the future.
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Affiliation(s)
- Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyue Jia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanxuan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianwen Chu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
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10
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Guo S, Ji Y, Zheng Y, Watkins CB, Ma L, Wang Q, Liang H, Bai C, Fu A, Li L, Meng D, Liu M, Zuo J. Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit. FRONTIERS IN PLANT SCIENCE 2023; 14:1142913. [PMID: 36968400 PMCID: PMC10032333 DOI: 10.3389/fpls.2023.1142913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.
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Affiliation(s)
- Susu Guo
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhai Ji
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Christopher B. Watkins
- School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, NY, Ithaca, United States
| | - Lili Ma
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hao Liang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ling Li
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Mingchi Liu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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11
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Shi M, Wang Y, Olvera-Vazquez SG, Iñiguez JC, Thein MS, Watanabe KN. Comparison of Chayote ( Sechium edule (Jacq.) Sw.) Accessions from Mexico, Japan, and Myanmar Using Reproductive Characters and Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:476. [PMID: 36771559 PMCID: PMC9919900 DOI: 10.3390/plants12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Promoting neglected and underutilized crop species is a possible solution to deal with the complex challenges of global food security. Chayote is a Neglected and Underutilized Cucurbit Species (NUCuS), which is recognized as a fruit vegetable in Latin America and is widely grown in Asia and Africa. However, basic biological knowledge about the crop is insufficient in scientific sources, especially outside of its center of origin. In this study, limited observations on reproductive characters were conducted, differentiating accessions from Mexico, Japan, and Myanmar. Cytological evaluation among Mexican and Japanese accessions showed that the relative nuclear DNA content is 1.55 ± 0.05 pg, the estimated genome size is 1511 at 2C/Mbp, and the observed mitotic chromosomal number is 2n = 28. The genetic diversity of 21 chayote accessions was also examined using six microsatellite markers. A global low genetic heterozygosity (Ho = 0.286 and He = 0.408) and three genetic groups were detected. The results established the basis to provide insights into chayote arrival history in Asia by looking at the crop's reproductive morphology, cytology, and genetic diversity status outside its origin center. This could help in developing sustainable utilization and conservation programs for chayote.
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Affiliation(s)
- Miao Shi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Yihang Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Sergio Gabriel Olvera-Vazquez
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
- GQE-Le Moulon, INRAe et University Paris-Saclay, Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette, France
| | - Jorge Cadena Iñiguez
- Colegio de Postgraduados, Campus San Luis Potosí, Salias de Hidalgo, San Luis Potosí 78622, Mexico
| | - Min San Thein
- Department of Agricultural Research, Ministry of Agriculture, Livestock and Irrigation, Yezin, Myanmar
| | - Kazuo N. Watanabe
- Tsukuba Plant Innovation Research Center, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
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12
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Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2023; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
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Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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13
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Fu A, Zheng Y, Guo J, Grierson D, Zhao X, Wen C, Liu Y, Li J, Zhang X, Yu Y, Ma H, Wang Q, Zuo J. Telomere-to-telomere genome assembly of bitter melon ( Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics. HORTICULTURE RESEARCH 2023; 10:uhac228. [PMID: 36643758 PMCID: PMC9832870 DOI: 10.1093/hr/uhac228] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/26/2022] [Indexed: 05/19/2023]
Abstract
Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6-Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19 895 protein-coding genes, of which 45.59% constitute predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.
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Affiliation(s)
| | | | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Changlong Wen
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Ye Liu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Jian Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ying Yu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hong Ma
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Qing Wang
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Jinhua Zuo
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
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14
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Pu Y, Wang C, Jiang Y, Wang X, Ai Y, Zhuang W. Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage. Front Nutr 2023; 10:1029745. [PMID: 36937343 PMCID: PMC10019507 DOI: 10.3389/fnut.2023.1029745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
Chayote (Sechium edulel) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and the corresponding regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, an integrated transcriptome and metabolite analysis of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, exogenous application of phenylalanine increased the total content of flavonoids and promoted some flavonoid biosynthesis-related gene expression in chayote fruits. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.
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Affiliation(s)
- YuTing Pu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - YongWen Jiang
- Tea Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - XiaoJing Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
- *Correspondence: XiaoJing Wang,
| | - YuJie Ai
- Tea Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
- YuJie Ai,
| | - WeiBing Zhuang
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Memorial Sun Yat-sen, Institute of Botany, Nanjing, China
- WeiBing Zhuang,
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15
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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16
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Wang L, Fan L, Zhao Z, Zhang Z, Jiang L, Chai M, Tian C. The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family. Gigascience 2022; 11:giac106. [PMID: 36310248 PMCID: PMC9618406 DOI: 10.1093/gigascience/giac106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/17/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqiang Fan
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Zhenyong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhibin Zhang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mao Chai
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Zhang X, Zhao Y, Kou Y, Chen X, Yang J, Zhang H, Zhao Z, Zhao Y, Zhao G, Li Z. Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae). HORTICULTURE RESEARCH 2022; 10:uhac231. [PMID: 36643751 PMCID: PMC9832869 DOI: 10.1093/hr/uhac231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/01/2022] [Indexed: 06/17/2023]
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26 588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside.
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Affiliation(s)
- Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, 030012, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuemei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, 550018, China
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Zhang Z, Zhang Y, Yuan L, Zhou F, Gao Y, Kang Z, Li T, Hu X. Exogenous 5-aminolevulinic acid alleviates low-temperature injury by regulating glutathione metabolism and β-alanine metabolism in tomato seedling roots. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114112. [PMID: 36155340 DOI: 10.1016/j.ecoenv.2022.114112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Food availability represents a major worldwide concern due to climate change and population growth. Low-temperature stress (LTS) severely restricts the growth of tomato seedlings. Exogenous 5-aminolevulinic acid (ALA) can alleviate the harm of abiotic stress including LTS; however, data on its protective mechanism on tomato seedling roots, the effects of organelle structure, and the regulation of metabolic pathways under LTS are lacking. In this study, we hope to fill the above gaps by exploring the effects of exogenous ALA on morphology, mitochondrial ultrastructure, reactive oxygen species (ROS) enrichment, physiological indicators, related gene expression, and metabolic pathway in tomato seedlings root under LTS. Results showed that ALA pretreatment could increase the activity of antioxidant enzymes and the content of antioxidant substances in tomato seedlings roots under LTS to scavenge the massively accumulated ROS, thereby protecting the mitochondrial structure of roots and promoting root development under LTS. Combined transcriptomic and metabolomic analysis showed that exogenous ALA pretreatment activated the glutathione metabolism and β-alanine metabolism of tomato seedling roots under LTS, further enhanced the scavenging ability of tomato seedling roots to ROS, and improved the low-temperature tolerance of tomato seedlings. The findings provide a new insight into the regulation of the low-temperature tolerance of tomato by exogenous ALA.
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Affiliation(s)
- Zhengda Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Yuhui Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Luqiao Yuan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Fan Zhou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Kang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| | - Xiaohui Hu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling, Shaanxi 712100, China; Shaanxi Protected Agriculture Research Centre, Yangling, Shaanxi 712100, China.
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Su K, Sun J, Han J, Zheng T, Sun B, Liu S. Combined morphological and multi-omics analyses to reveal the developmental mechanism of Zanthoxylum bungeanum prickles. FRONTIERS IN PLANT SCIENCE 2022; 13:950084. [PMID: 36072325 PMCID: PMC9441855 DOI: 10.3389/fpls.2022.950084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum bungeanum Maxim. as an important economic forest, its epidermis bears prickles which complicate the harvesting process and increase the labor costs. To explore the developmental mechanism of prickles, three varieties of Zanthoxylum bungeanum (PZB, SZB, GSZB) were selected for morphological and multi-omics analyses. The absorption spectra of prickles and stems were detected using Fourier-transform infrared spectroscopy (FTIR), and they were found different at 1617, 1110, 3319, and 1999 cm-1. The morphology of prickles and stems were observed using light microscopy and transmission electron microscopy (TEM). The growth direction of cells on the prickle side and stem side were perpendicular to each other, and there was a resembling abscission zone (RAZ) between them. The vacuolar deposits of prickle cells were much more than stem cells, indicating that the lignification degree of prickles was higher than stems. In addition, 9 candidate genes (ZbYABBY2, ZbYABBY1, ZbYABBY5, ZbWRKY, ZbLOG5, ZbAZG2, ZbGh16, ZbIAA33, and ZbGh16X1) were screened out and validated base on transcriptome and qRT-PCA. As well as, 30 key metabolites were found related to prickle development base on metabolome analysis. Among them, 4-hydroxy-2-oxopentanoate, trans-2-hydroxy-cinnamate, trans-cinnamate, polyhydroxy-fatty acid, 10,16-dihydroxypalmitate, cinnamic acid were related to the biosynthesis of cutin, suberine and wax. Indole-3-acetate, tryptamine, anthranilate, fromylanthranilate, N6-(delta2-isopentenyl)-adenine were related to plant hormone signal transduction. Generally, this is the first study to reveal the developmental mechanism of prickles. The results of this study lay the foundation for the breeding of non-prickle Zanthoxylum bungeanum.
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Affiliation(s)
- Kexing Su
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
| | - Jiaqian Sun
- Powerchina Northwest Engineering Corporation Limited, Xi’an, China
- Shaanxi Union Research Center of University and Enterprise for River and Lake Ecosystems Protection and Restoration, Xi’an, China
| | - Jun Han
- Forestry and Grassland Bureau of Xunhua County, Qinghai, China
| | - Tao Zheng
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
| | - Bingyin Sun
- Department of Ecological Engineering, Yangling Vocational and Technical College, Xianyang, China
| | - Shuming Liu
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
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20
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Li X, Cai K, Zhang Q, Pei X, Chen S, Jiang L, Han Z, Zhao M, Li Y, Zhang X, Li Y, Zhang S, Chen S, Qu G, Tigabu M, Chiang VL, Sederoff R, Zhao X. The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis. Gigascience 2022; 11:6619298. [PMID: 35764602 PMCID: PMC9239856 DOI: 10.1093/gigascience/giac057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/20/2022] [Accepted: 05/24/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. FINDINGS Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. CONCLUSIONS Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.
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Affiliation(s)
| | | | | | | | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Luping Jiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Minghui Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yuxi Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Center, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma SE-234 22, Sweden
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiyang Zhao
- Correspondence address. Xiyang Zhao, E-mail:
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Su L, Cheng S, Liu Y, Xie Y, He Z, Jia M, Zhou X, Zhang R, Li C. Transcriptome and Metabolome Analysis Provide New Insights into the Process of Tuberization of Sechium edule Roots. Int J Mol Sci 2022; 23:ijms23126390. [PMID: 35742832 PMCID: PMC9224348 DOI: 10.3390/ijms23126390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chayote (Sechium edule) produces edible tubers with high starch content after 1 year of growth but the mechanism of chayote tuberization remains unknown. ‘Tuershao’, a chayote cultivar lacking edible fruits but showing higher tuber yield than traditional chayote cultivars, was used to study tuber formation through integrative analysis of the metabolome and transcriptome profiles at three tuber-growth stages. Starch biosynthesis- and galactose metabolism-related genes and metabolites were significantly upregulated during tuber bulking, whereas genes encoding sugars will eventually be exported transporter (SWEET) and sugar transporter (SUT) were highly expressed during tuber formation. Auxin precursor (indole-3-acetamide) and ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, were upregulated, suggesting that both hormones play pivotal roles in tuber development and maturation. Our data revealed a similar tuber-formation signaling pathway in chayote as in potatoes, including complexes BEL1/KNOX and SP6A/14-3-3/FDL. Down-regulation of the BEL1/KNOX complex and upregulation of 14-3-3 protein implied that these two complexes might have distinct functions in tuber formation. Finally, gene expression and microscopic analysis indicated active cell division during the initial stages of tuber formation. Altogether, the integration of transcriptome and metabolome analyses unraveled an overall molecular network of chayote tuberization that might facilitate its utilization.
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Affiliation(s)
- Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Yuhang Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Yongdong Xie
- Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agricultural and Forest Sciences, Chengdu 611130, China;
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
- Correspondence:
| | - Mingyue Jia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Ruijie Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
| | - Chunyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (L.S.); (S.C.); (Y.L.); (M.J.); (X.Z.); (R.Z.); (C.L.)
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22
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Niu Y, Li G, Ni S, He X, Zheng C, Liu Z, Gong L, Kong G, Li W, Liu J. The Chromosome-Scale Reference Genome of Macadamia tetraphylla Provides Insights Into Fatty Acid Biosynthesis. Front Genet 2022; 13:835363. [PMID: 35281801 PMCID: PMC8906886 DOI: 10.3389/fgene.2022.835363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 12/28/2022] Open
Abstract
Macadamia is an evergreen tree belonging to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. The M. integrifolia genome was recently sequenced, but the genome of M. tetraphylla has to date not been published, which limits the study of biological research and breeding in this species. This study reports a high-quality genome sequence of M. tetraphylla based on the Oxford Nanopore Technologies technology and high-throughput chromosome conformation capture techniques (Hi-C). An assembly of 750.87 Mb with 51.11 Mb N50 length was generated, close to the 740 and 758 Mb size estimates by flow cytometry and k-mer analysis, respectively. Genome annotation indicated that 61.42% of the genome is composed of repetitive sequences and 34.95% is composed of long terminal repeat retrotransposons. Up to 31,571 protein-coding genes were predicted, of which 92.59% were functionally annotated. The average gene length was 6,055 bp. Comparative genome analysis revealed that the gene families associated with defense response, lipid transport, steroid biosynthesis, triglyceride lipase activity, and fatty acid metabolism are expanded in the M. tetraphylla genome. The distribution of fourfold synonymous third-codon transversion showed a recent whole-genome duplication event in M. tetraphylla. Genomic and transcriptomic analysis identified 187 genes encoding 33 crucial oil biosynthesis enzymes, depicting a comprehensive map of macadamia lipid biosynthesis. Besides, the 55 identified WRKY genes exhibited preferential expression in root as compared to that in other tissues. The genome sequence of M. tetraphylla provides novel insights for breeding novel varieties and genetic improvement of agronomic traits.
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Affiliation(s)
- Yingfeng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guohua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Shubang Ni
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Xiyong He
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Ziyan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Lidan Gong
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guanghong Kong
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
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23
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Fang S, Duan Y, Nie L, Zhao W, Wang J, Zhao J, Zhao L, Wang L. Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon ( Cucumis melo L.). PeerJ 2022; 10:e13088. [PMID: 35287348 PMCID: PMC8917798 DOI: 10.7717/peerj.13088] [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: 10/18/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
Melon (Cucumis melo L.) is an agronomically important vegetable. Most cultivars of melon are andromonoecious and bisexual flowers only emerged from the leaf axil of lateral branches. However, the regulatory mechanism contributing to the occurrence of bisexual flowers were still obscure. In this study, ethephon was applied in two common cultivars of melon. In control without ethephon treatment, no bisexual flower was made in the main stem. However, 6.56 ± 1.42 and 6.63 ± 0.55 bisexual flowers were respectively induced in main stem of 'Yangjiaocui-QX' and 'Lvbao' after ethephon treatment, and induced bisexual flowers distributed in 12-20 nodes of main stem. During the formation of bisexual flowers, 41 metabolites were significantly up-regulated and 98 metabolites were significantly down-regulated. According to the KEGG enrichment analysis of 139 different metabolites, a total of 30 pathways were mapped and KEGG terms of "Phenylalanine, tyrosine and tryptophan biosynthesis", "Phenylalanine metabolism" and "Flavone and flavonol biosynthesis" were significantly enriched. In three significantly enriched KEGG terms, shikimic acid, L-tryptophan, L-phenylalanine, and kaempferol were significantly up-regulated while L-tyrosine, 4-hydroxycinnami acid and luteolin were significantly down-regulated in ET compared to CK. Different metabolites were also classified depend on major class features and 14 classes were acquired. The results of metabonomics and endogenous hormone identification indicated that ethylene could enhance the concentration of salicylic acid, methyl jasmonate, ABA and IAA. This study provided an important theoretical foundation for inducing bisexual flowers in main stem and breeding new varieties of melon in future.
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Affiliation(s)
- Siyu Fang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yaqian Duan
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding, China,Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, China,Collaborative Innovation Center of Vegetative Industry of Hebei Province, Baoding, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, China,Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, China,Collaborative Innovation Center of Vegetative Industry of Hebei Province, Baoding, China
| | - Jiahao Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Liping Zhao
- Bureau of Agriculture and Rural of Dingzhou, Dingzhou, China
| | - Lei Wang
- Bureau of Agriculture and Rural of Dingzhou, Dingzhou, China
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24
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Ma L, Wang Q, Zheng Y, Guo J, Yuan S, Fu A, Bai C, Zhao X, Zheng S, Wen C, Guo S, Gao L, Grierson D, Zuo J, Xu Y. Cucurbitaceae genome evolution, gene function and molecular breeding. HORTICULTURE RESEARCH 2022; 9:uhab057. [PMID: 35043161 PMCID: PMC8969062 DOI: 10.1093/hr/uhab057] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 05/07/2023]
Abstract
The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaogui Guo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yong Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Zhao D, Zhang Y, Lu Y, Fan L, Zhang Z, Chai M, Zheng J. Genome sequence and transcriptome of Sorbus pohuashanensis provides insights into population evolution and leaf sunburn response. J Genet Genomics 2022; 49:547-558. [PMID: 34995812 DOI: 10.1016/j.jgg.2021.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Sorbus pohuashanensis is a potential horticulture and medicinal plant, but its genomic and genetic backgrounds remain unknown. Here, we sequenced and assembled the S. pohuashanensis (Hance) Hedl. reference genome using PacBio long reads. Based on the new reference genome, we resequenced a core collection of 22 Sorbus spp. samples, which were divided into 2 groups (G1 and G2) based on phylogenetic and PCA analyses. These phylogenetic clusters were highly consistent with their classification based on leaf shape. Natural hybridization between the G1 and G2 groups was evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis showed that G1 had a higher diversity than G2 and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and the gene families involved in energy consumption contracted. RNA-seq data suggested that flavonoid biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This study provides new insights into the evolution of Sorbus spp. genomes. In addition, the genomic resources, and the identified genetic variations, especially those related to stress resistance, will help future efforts to produce and breed Sorbus spp.
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Affiliation(s)
- Dongxue Zhao
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Yan Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong 250102, China
| | - Liqiang Fan
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Zhibin Zhang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Mao Chai
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China.
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
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Huang D, Ming R, Xu S, Wang J, Yao S, Li L, Huang R, Tan Y. Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis. DNA Res 2021; 28:6367775. [PMID: 34499150 PMCID: PMC8476931 DOI: 10.1093/dnares/dsab018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/06/2021] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.
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Affiliation(s)
- Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Ruhong Ming
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaochang Yao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Liangbo Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Rongshao Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yong Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
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Chen J, Xue M, Liu H, Fernie AR, Chen W. Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement. PLANT COMMUNICATIONS 2021; 2:100216. [PMID: 34327326 PMCID: PMC8299079 DOI: 10.1016/j.xplc.2021.100216] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingyun Xue
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Pu YT, Luo Q, Wen LH, Li YR, Meng PH, Wang XJ, Tan GF. Origin, Evolution, Breeding, and Omics of Chayote, an Important Cucurbitaceae Vegetable Crop. FRONTIERS IN PLANT SCIENCE 2021; 12:739091. [PMID: 34630492 PMCID: PMC8497889 DOI: 10.3389/fpls.2021.739091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/23/2021] [Indexed: 05/02/2023]
Abstract
Chayote (Sechium edule), a member of the Cucurbitaceae family, is cultivated throughout tropical and subtropical regions of the world and utilized in pharmaceutical, cosmetic and food industries because it is an excellent source of minerals, dietary fibers, protein, vitamins, carotenoids, polysaccharides, phenolic and flavonoid compounds, and other nutrients. Chayote extracts process various medicinal properties, such as anti-cardiovascular, antidiabetic, antiobesity, antiulcer, and anticancer properties. With the rapid advancements of molecular biology and sequencing technology, studies on chayote have been carried out. Research advances, including molecular makers, breeding, genomic research, chemical composition, and pests and diseases, regarding chayote are reviewed in this paper. Future exploration and application trends are briefly described. This review provides a reference for basic and applied research on chayote, an important Cucurbitaceae vegetable crop.
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Affiliation(s)
- Yu-Ting Pu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
| | - Qing Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Lin-Hong Wen
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yu-Rong Li
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ping-Hong Meng
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xiao-Jing Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
- *Correspondence: Xiao-Jing Wang,
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guo-Fei Tan,
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