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Niu Y, Zhang T, Chen M, Chen G, Liu Z, Yu R, Han X, Chen K, Huang A, Chen C, Yang Y. Analysis of the Complete Mitochondrial Genome of the Bitter Gourd ( Momordica charantia). PLANTS (BASEL, SWITZERLAND) 2023; 12:1686. [PMID: 37111909 PMCID: PMC10143269 DOI: 10.3390/plants12081686] [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: 01/13/2023] [Revised: 03/16/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Bitter gourd (Momordica charantia L.) is a significant vegetable. Although it has a special bitter taste, it is still popular with the public. The industrialization of bitter gourd could be hampered by a lack of genetic resources. The bitter gourd's mitochondrial and chloroplast genomes have not been extensively studied. In the present study, the mitochondrial genome of bitter gourd was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of bitter gourd is 331,440 bp with 24 unique core genes, 16 variable genes, 3 rRNAs, and 23 tRNAs. We identified 134 SSRs and 15 tandem repeats in the entire mitochondrial genome of bitter gourd. Moreover, 402 pairs of repeats with a length greater than or equal to 30 were observed in total. The longest palindromic repeat was 523 bp, and the longest forward repeat was 342 bp. We found 20 homologous DNA fragments in bitter gourd, and the summary insert length was 19,427 bp, accounting for 5.86% of the mitochondrial genome. We predicted a total of 447 potential RNA editing sites in 39 unique PCGs and also discovered that the ccmFN gene has been edited the most often, at 38 times. This study provides a basis for a better understanding and analysis of differences in the evolution and inheritance patterns of cucurbit mitochondrial genomes.
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Affiliation(s)
- Yu Niu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muxi Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhaohua Liu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Renbo Yu
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Xu Han
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Kunhao Chen
- Guangdong Helinong Biological Seeds Co., Ltd., Shantou 515800, China
- Guangdong Helinong Agricultural Research Institute Co., Ltd., Shantou 515800, China
| | - Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Yan Yang
- Tropical Crops Genetic Resources Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
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Parvathi MS, Antony PD, Kutty MS. Multiple Stressors in Vegetable Production: Insights for Trait-Based Crop Improvement in Cucurbits. FRONTIERS IN PLANT SCIENCE 2022; 13:861637. [PMID: 35592574 PMCID: PMC9111534 DOI: 10.3389/fpls.2022.861637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Vegetable production is a key determinant of contribution from the agricultural sector toward national Gross Domestic Product in a country like India, the second largest producer of fresh vegetables in the world. This calls for a careful scrutiny of the threats to vegetable farming in the event of climate extremes, environmental degradation and incidence of plant pests/diseases. Cucurbits are a vast group of vegetables grown almost throughout the world, which contribute to the daily diet on a global scale. Increasing food supply to cater to the ever-increasing world population, calls for intensive, off-season and year-round cultivation of cucurbits. Current situation predisposes these crops to a multitude of stressors, often simultaneously, under field conditions. This scenario warrants a systematic understanding of the different stress specific traits/mechanisms/pathways and their crosstalk that have been examined in cucurbits and identification of gaps and formulation of perspectives on prospective research directions. The careful dissection of plant responses under specific production environments will help in trait identification for genotype selection, germplasm screens to identify superior donors or for direct genetic manipulation by modern tools for crop improvement. Cucurbits exhibit a wide range of acclimatory responses to both biotic and abiotic stresses, among which a few like morphological characters like waxiness of cuticle; primary and secondary metabolic adjustments; membrane thermostability, osmoregulation and, protein and reactive oxygen species homeostasis and turnover contributing to cellular tolerance, appear to be common and involved in cross talk under combinatorial stress exposures. This is assumed to have profound influence in triggering system level acclimation responses that safeguard growth and metabolism. The possible strategies attempted such as grafting initiatives, molecular breeding, novel genetic manipulation avenues like gene editing and ameliorative stress mitigation approaches, have paved way to unravel the prospects for combined stress tolerance. The advent of next generation sequencing technologies and big data management of the omics output generated have added to the mettle of such emanated concepts and ideas. In this review, we attempt to compile the progress made in deciphering the biotic and abiotic stress responses of cucurbits and their associated traits, both individually and in combination.
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Affiliation(s)
- M. S. Parvathi
- Department of Plant Physiology, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - P. Deepthy Antony
- Centre for Intellectual Property Rights, Technology Management and Trade, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - M. Sangeeta Kutty
- Department of Vegetable Science, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, Liu M, Yang X, Zhang W, Deng Z, Li W, Si L. Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber. Sci Rep 2021; 11:3872. [PMID: 33594240 PMCID: PMC7886880 DOI: 10.1038/s41598-021-83313-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
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Affiliation(s)
- Yawo Mawunyo Nevame Adedze
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China.
| | - Xia Lu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Yingchun Xia
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Qiuyue Sun
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Chofong G Nchongboh
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Brunswick, Germany
| | - Md Amirul Alam
- Faculty of Sustainable Agriculture, Horticulture and Landscaping Program, University Malaysia Sabah, Sandakan Campus, 90509, Sandakan, Sabah, Malaysia
| | - Menghua Liu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Xue Yang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenting Zhang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Zhijun Deng
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenhu Li
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Longting Si
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
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A high-quality cucumber genome assembly enhances computational comparative genomics. Mol Genet Genomics 2019; 295:177-193. [PMID: 31620884 DOI: 10.1007/s00438-019-01614-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023]
Abstract
Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.
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Pawełkowicz M, Pryszcz L, Skarzyńska A, Wóycicki RK, Posyniak K, Rymuszka J, Przybecki Z, Pląder W. Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PLANT REPRODUCTION 2019; 32:193-216. [PMID: 30719568 PMCID: PMC6500512 DOI: 10.1007/s00497-019-00362-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Transcriptome data and qPCR analysis revealed new insight into genes regulatory mechanism related to cucumber sex determination. Cucumber (Cucumis sativus L.) is an economically important crop cultivated worldwide. Enhancing the genomic resources for cucumber may enable the regulation of traits relevant to crop productivity and quality. Sequencing technologies and bioinformatics tools provide opportunities for the development of such resources. The aims of this study were to identify and characterize the genes involved in sex determination and flower morphogenesis in cucumber isogenic lines that differed regarding flower sex type. We obtained transcripts for 933 genes related to shoot apex development, among which 310 were differentially expressed genes (DEGs) among the male, female, and hermaphroditic lines. We performed gene ontology and molecular network analyses and explored the DEGs related to already known processes like: hormone synthesis and signaling, lipid and sugar metabolism; and also newly discovered processes related to cell wall, membrane, and cytoskeleton modifications; ion homeostasis which appears to be important for ethylene perception and signaling, and genes expression mediated by transcription factors related to floral organ identities. We proposed a new model of regulatory mechanism network of sex development in cucumber. Our results may be useful for clarifying the molecular genetics and the functional mechanisms underlying the sex determination processes.
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Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Leszek Pryszcz
- Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Rafał K Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
- Philip Morris International R&D, Philip Morris Products S.A., 2000, Neuchâtel, Switzerland
| | - Kacper Posyniak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Jacek Rymuszka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
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Transcriptome Analyses Provide Novel Insights into Heat Stress Responses in Chieh-Qua ( Benincasa hispida Cogn. var. Chieh-Qua How). Int J Mol Sci 2019; 20:ijms20040883. [PMID: 30781658 PMCID: PMC6413116 DOI: 10.3390/ijms20040883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/02/2022] Open
Abstract
Temperature rising caused by global warming has imposed significant negative effects on crop qualities and yields. To get the well-known molecular mechanism upon the higher temperature, we carefully analyzed the RNA sequencing-based transcriptomic responses of two contrasting chieh-qua genotypes: A39 (heat-tolerant) and H5 (heat-sensitive). In this study, twelve cDNA libraries generated from A39 and H5 were performed with a transcriptome assay under normal and heat stress conditions, respectively. A total of 8705 differentially expressed genes (DEGs) were detected under normal conditions (3676 up-regulated and 5029 down-regulated) and 1505 genes under heat stress (914 up-regulated and 591 down-regulated), respectively. A significant positive correlation between RNA-Seq data and qRT-PCR results was identified. DEGs related to heat shock proteins (HSPs), ubiquitin-protein ligase, transcriptional factors, and pentatricopeptide repeat-containing proteins were significantly changed after heat stress. Several genes, which encoded HSPs (CL2311.Contig3 and CL6612.Contig2), cytochrome P450 (CL4517.Contig4 and CL683.Contig7), and bHLH TFs (CL914.Contig2 and CL8321.Contig1) were specifically induced after four days of heat stress. DEGs detected in our study between these two contrasting cultivars would provide a novel basis for isolating useful candidate genes of heat stress responses in chieh-qua.
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Słomnicka R, Olczak-Woltman H, Korzeniewska A, Gozdowski D, Niemirowicz-Szczytt K, Bartoszewski G. Genetic mapping of psl locus and quantitative trait loci for angular leaf spot resistance in cucumber ( Cucumis sativus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:111. [PMID: 30174539 PMCID: PMC6105252 DOI: 10.1007/s11032-018-0866-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/06/2018] [Indexed: 05/16/2023]
Abstract
One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.
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Affiliation(s)
- Renata Słomnicka
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Helena Olczak-Woltman
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Aleksandra Korzeniewska
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Dariusz Gozdowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
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Wang B, Lv XQ, He L, Zhao Q, Xu MS, Zhang L, Jia Y, Zhang F, Liu FL, Liu QL. Whole-Transcriptome Sequence Analysis of Verbena bonariensis in Response to Drought Stress. Int J Mol Sci 2018; 19:E1751. [PMID: 29899256 PMCID: PMC6032440 DOI: 10.3390/ijms19061751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 11/16/2022] Open
Abstract
Drought is an important abiotic factor that threatens the growth and development of plants. Verbena bonariensis is a widely used landscape plant with a very high ornamental value. We found that Verbena has drought tolerance in production practice, so in order to delve into its mechanism of drought resistance and screen out its drought-resistance genes, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze Verbena transcription response to drought stress. By high-throughput sequencing with Illumina Hiseq Xten, a total of 44.59 Gb clean data was obtained from T01 (control group) and T02 (drought experiment group). After assembly, 111,313 unigenes were obtained, and 53,757 of them were annotated by compared databases. In this study, 4829 differentially expressed genes were obtained, of which 4165 were annotated. We performed GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses, and explored a lot of differently expressed genes related to plant energy production, hormone synthesis, cell signal transduction, and metabolism to understand the stress response of Verbena in drought stress. In addition, we also found that a series of TFs related to drought-resistance of Verbena and provide excellent genetic resources for improving the drought tolerance of crops.
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Affiliation(s)
- Bei Wang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Xue-Qi Lv
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Ling He
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Qian Zhao
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Mao-Sheng Xu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Yin Jia
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
| | - Feng-Luan Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, The Chinese Academy of Science, Shanghai Chenshan Botanical Garden, 3888 Huagong Road, Songjiang District, Shanghai 201602, China.
| | - Qing-Lin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu 611130, Sichuan, China.
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Han Y, Wang X, Zhao F, Gao S, Wei A, Chen Z, Liu N, Zhang Z, Du S. Transcriptomic analysis of differentially expressed genes in flower-buds of genetic male sterile and wild type cucumber by RNA sequencing. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:359-367. [PMID: 29692544 PMCID: PMC5911260 DOI: 10.1007/s12298-018-0515-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 05/21/2023]
Abstract
Cucumber (Cucumis sativus L.) pollen development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. Previous studies in our laboratory showed that male sterility was controlled by a single recessive nuclear gene, and occurred in pollen mother cell meiophase. To fully explore the global gene expression and identify genes related to male sterility, a RNA-seq analysis was adopted in this study. Young male flower-buds (1-2 mm in length) from genetic male sterility (GMS) mutant and homozygous fertile cucumber (WT) were collected for two sequencing libraries. Total 545 differentially expressed genes (DEGs), including 142 up-regulated DEGs and 403 down-regulated DEGs, were detected in two libraries (Fold Change ≥ 2, FDR < 0.01). These genes were involved in a variety of metabolic pathways, like ethylene-activated signaling pathway, sporopollenin biosynthetic pathway, cell cycle and DNA damage repair pathway. qRT-PCR analysis was performed and showed that the correlation between RNA-Seq and qRT-PCR was 0.876. These findings contribute to a better understanding of the mechanism that leads to GMS in cucumber.
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Affiliation(s)
- Yike Han
- Department of Vegetable Science, China Agricultural University, Beijing, 100193 China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Breeding Enterprise, Tianjin Kernel Cucumber Research Institute, 295 Baidi Road, Tianjin, 300192 China
| | - Xianyun Wang
- College of Life, Nankai University, Tianjin, 300071 China
| | - Fengyue Zhao
- College of Life, Nankai University, Tianjin, 300071 China
| | - Shang Gao
- The Richard and Loan Hill Department of Bioengineering, University of Illinois, Chicago, IL 0661 USA
| | - Aimin Wei
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Breeding Enterprise, Tianjin Kernel Cucumber Research Institute, 295 Baidi Road, Tianjin, 300192 China
| | - Zhengwu Chen
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Breeding Enterprise, Tianjin Kernel Cucumber Research Institute, 295 Baidi Road, Tianjin, 300192 China
| | - Nan Liu
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Breeding Enterprise, Tianjin Kernel Cucumber Research Institute, 295 Baidi Road, Tianjin, 300192 China
| | - Zhenxian Zhang
- Department of Vegetable Science, China Agricultural University, Beijing, 100193 China
| | - Shengli Du
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Key Laboratory of Vegetable Breeding Enterprise, Tianjin Kernel Cucumber Research Institute, 295 Baidi Road, Tianjin, 300192 China
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Ma C, Yang J, Cheng Q, Mao A, Zhang J, Wang S, Weng Y, Wen C. Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing. PLoS One 2018; 13:e0190691. [PMID: 29304061 PMCID: PMC5755913 DOI: 10.1371/journal.pone.0190691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Determinate cucumber is a type of short vines, fewer nodes, and terminal flowers, it is suitable for high-density planting and available harvesting in field cultivation, whereas the indeterminate cucumber is preferred to cultivate in greenhouses. However, many biotic or abiotic stresses could lead indeterminate cucumber to be determinate in greenhouse cultivation, which may decrease yield and fruit quality. Therefore, it is urgent and essential to investigate the key factors forming determinate and terminal flowering in cucumber. In this study, two close background inbred lines were selected and conducted the miRNA and mRNA high throughput sequencing. Interestingly, ethylene-associated miRNAs and mRNAs were intensively obtained, indicating that the plant hormone ethylene is a key factor impacting determinate and terminal flowering in cucumber. The ethylene metabolites analysis showed that significant higher ethylene was observed in determinate line than that in the indeterminate line. The RT-qPCR validation of ethylene related miRNAs Cas-miR172, Cas-miR396, and Cas-miR414 and their target mRNAs showed a significant negative correlation. These data suggested that ethylene-associated miRNAs might affect determinate and terminal flower phenotypes by regulating their target genes expression. This study not only provides a potential molecular mechanism for determinate formation in cucumber but also establishes a method to demonstrate important physiological processes through the comprehensive association of miRNA and mRNA high-throughput sequencing.
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Affiliation(s)
- Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Qing Cheng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- College of Horticulture, China Agricultural University, Beijing, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Institute of Agro-food Science and Technology, Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison WI, United States of America
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, United States of America
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- * E-mail:
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12
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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