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  • 11
    Online Resource
    Online Resource
    DataSheet_1.pdf
    Frontiers Media SA ; 2020
    In:  Frontiers in Plant Science Vol. 11 ( 2020-9-25)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 11 ( 2020-9-25)
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2020.570817
    DOI: 10.3389/fpls.2020.570817.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 12
    Online Resource
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    Data_Sheet_1.docx
    Frontiers Media SA ; 2020
    In:  Frontiers in Genetics Vol. 11 ( 2020-12-3)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 11 ( 2020-12-3)
    Abstract: MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090 , encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber ( Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [ Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis -element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita , finding that CsMYB ( Csa6G538700 , Csa1G021940 , and Csa5G641610 ) genes showed up-regulation coincident with upregulation of the “hub” gene LTP ( Csa6G410090 ) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2020.550677
    DOI: 10.3389/fgene.2020.550677.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2606823-0
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  • 13
    Online Resource
    Online Resource
    Genome-Wide Identification of the B-Box Gene Family and Expression Analysis Suggests Their Potential Role in Photoperiod-Mediated β-Carotene Accumulation in the Endocarp of Cucumber (Cucumis sativus L.) Fruit
    MDPI AG ; 2022
    In:  Genes Vol. 13, No. 4 ( 2022-04-08), p. 658-
    Details
    In: Genes, MDPI AG, Vol. 13, No. 4 ( 2022-04-08), p. 658-
    Abstract: Carotenoids are indispensable to plants and essential for human nutrition and health. Carotenoid contents are strongly influenced by light through light-responsive genes such as B-Box (BBX) genes. BBX proteins, a class of zinc-finger transcription factors, mediate many light-signaling pathways, leading to the biosynthesis of important metabolites in plants. However, the identification of the BBX gene family and expression analysis in response to photoperiod-mediated carotenoid accumulation in cucumber remains unexplored. We performed a genome-wide study and determined the expression of cucumber BBX genes (hereafter referred to as CsaBBXs genes) in the endocarp of Xishuangbanna cucumber fruit (a special type of cucumber accumulating a high level of β-carotene in the endocarp) using an RNA-seq analysis of plants previously subjected to two photoperiodic conditions. Here, 26 BBX family genes were identified in the cucumber genome and named serially CsaBBX1 through CsaBBX26. We characterized CsaBBX genes in terms of their phylogenetic relationships, exon-intron structures, cis-acting elements, and syntenic relationships with Arabidopsis thaliana (L.) Heynh. RNA-seq analysis revealed a varied expression of CsaBBX genes under photoperiod treatment. The analysis of CsaBBXs genes revealed a strong positive correlation between CsaBBX17 and carotenoid biosynthetic pathway genes (phytoene synthase, ζ-carotene desaturase, lycopene ε-cyclase, β-carotene hydroxylase-1), thus suggesting its involvement in β-carotene biosynthesis. Additionally, nine CsaBBX genes (CsaBBX 4,5,7,9,11, 13,15,17 and 22) showed a significant positive correlation with β-carotene content. The selected CsaBBX genes were verified by qRT-PCR and confirmed the validity of RNA-seq data. The results of this study established the genome-wide analysis of the cucumber BBX family and provide a framework for understanding their biological role in carotenoid accumulation and photoperiodic responses. Further investigations of CsaBBX genes are vital since they are promising candidate genes for the functional analysis of carotenoid biosynthesis and can provide genetic tools for the molecular breeding of carotenoids in plants.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes13040658
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2527218-4
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  • 14
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    Sparse Kernel Principal Component Analysis via Sequential Approach for Nonlinear Process Monitoring
    Institute of Electrical and Electronics Engineers (IEEE) ; 2019
    In:  IEEE Access Vol. 7 ( 2019), p. 47550-47563
    Details
    In: IEEE Access, Institute of Electrical and Electronics Engineers (IEEE), Vol. 7 ( 2019), p. 47550-47563
    Type of Medium: Online Resource
    ISSN: 2169-3536
    URL: Journal
    URL: Article
    DOI: 10.1109/Access.6287639
    DOI: 10.1109/ACCESS.2019.2909986
    Language: Unknown
    Publisher: Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2019
    detail.hit.zdb_id: 2687964-5
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  • 15
    Online Resource
    Online Resource
    Chromosome-scale genome assembly of Cucumis hystrix —a wild species interspecifically cross-compatible with cultivated cucumber
    Oxford University Press (OUP) ; 2021
    In:  Horticulture Research Vol. 8 ( 2021-12-01)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 8 ( 2021-12-01)
    Abstract: Cucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in “defense response,” and C. hystrix harbored 104 nucleotide-binding site–encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber–C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1038/s41438-021-00475-5
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2781828-7
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  • 16
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    Long-distance control of the scion by the rootstock under drought stress as revealed by transcriptome sequencing and mobile mRNA identification
    Oxford University Press (OUP) ; 2022
    In:  Horticulture Research Vol. 9 ( 2022-01-05)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 9 ( 2022-01-05)
    Abstract: Grafting with pumpkin rootstock is commonly used not only to improve the quality of cucumber fruits but also to confer biotic or abiotic stress tolerance. However, the molecular mechanism of the response of grafted cucumbers to drought stress and the possible roles of mobile mRNAs in improving stress tolerance have remained obscure. Hence, we conducted transcriptome sequencing and combined it with morphophysiological experiments to compare the response of homografts (cucumber as scion and rootstock) and heterografts (cucumber as scion and pumpkin as rootstock) to drought stress. After applying drought stress, homografts and heterografts expressed 2960 and 3088 genes, respectively, in response to the stress. The differentially expressed genes identified in heterografts under drought stress were categorized into different stress-responsive groups, such as carbohydrate metabolism (involved in osmotic adjustment by sugar accumulation), lipid and cell wall metabolism (involved in cell membrane integrity by a reduction in lipid peroxidation), redox homeostasis (increased antioxidant enzyme activities), phytohormone (increased abscisic acid content), protein kinases, and transcription factors, using MapMan software. Earlier and greater H2O2 accumulation in xylem below the graft union was accompanied by leaf abscisic acid accumulation in heterografts in response to drought stress. Greater leaf abscisic acid helped heterografted cucumbers to sense and respond to drought stress earlier than homografts. The timely response of heterografts to drought stress led to the maintenance of higher water content in the leaves even in the late stage of drought stress. The mobile mRNAs identified in heterografts were mostly related to photosynthesis, which would be the possible reason for improved chlorophyll content and maximum photochemical efficiency of photosystem II (Fv/Fm). The existence of some stress-responsive pumpkin (rootstock) mRNAs in cucumber (scion), such as heat shock protein (HSP70, a well-known stress-responsive gene), led to higher proline accumulation than in homografts. Expression of mobile and immobile stress-responsive mRNAs and timely response of heterografts to drought stress could improve drought tolerance in pumpkin-rooted plants.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhab033
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2781828-7
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  • 17
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    Genome-wide analysis of a putative lipid transfer protein LTP_2 gene family reveals CsLTP_2 genes involved in response of cucumber against root-knot nematode ( Meloidogyne incognita )
    Canadian Science Publishing ; 2020
    In:  Genome Vol. 63, No. 4 ( 2020-04), p. 225-238
    Details
    In: Genome, Canadian Science Publishing, Vol. 63, No. 4 ( 2020-04), p. 225-238
    Abstract: Plant lipid transfer proteins (LTPs) are small basic proteins that play important roles in the regulation of various plant biological processes as well as the response to biotic and abiotic stresses. However, knowledge is limited on how this family of proteins is regulated in response to nematode infection in cucumber. In the present study, a total of 39 CsLTP_2 genes were identified by querying databases for cucumber-specific LTP_2 using a Hidden Markov Model approach and manual curation. The family has a five-cysteine motif (5CM) with the basic form CC-Xn-CXC-Xn-C, which differentiates it from typical nsLTPs. The members of CsLTP_2 were grouped into six families according to their structure and their phylogenetic relationships. Expression data of CsLTP_2 genes in 10 cucumber tissues indicated that they were tissue-specific genes. Two genes showed significant expression change in roots of resistant and susceptible lines during nematode infection, indicating their involvement in response to Meloidogyne incognita. This systematic analysis provides a foundation of knowledge for future studies of the biological roles of CsLTP_2 genes in cucumber in response to nematode infection and may help in the efforts to improve M. incognita-resistance breeding in cucumber.
    Type of Medium: Online Resource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/gen-2019-0157
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2020
    detail.hit.zdb_id: 2020635-5
    SSG: 12
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  • 18
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    Online Resource
    Chromosome identification in Cucumis anguria revealed by cross-species single-copy gene FISH
    Canadian Science Publishing ; 2018
    In:  Genome Vol. 61, No. 6 ( 2018-06), p. 397-404
    Details
    In: Genome, Canadian Science Publishing, Vol. 61, No. 6 ( 2018-06), p. 397-404
    Abstract: Cucumis anguria is a potential genetic resource for improving crops of the genus Cucumis, owing to its broad-spectrum resistance. However, few cytogenetic studies on C. anguria have been reported because of its small metaphase chromosomes and the scarcity of distinguished chromosomal landmarks. In this study, 14 single-copy genes from cucumber and rDNAs were used as probes for FISH to identify the individual chromosomes of C. anguria. The distinctive signal distribution patterns of the probes allowed us to distinguish each chromosome of C. anguria (A01–A12). Further, detailed chromosome characteristics were obtained through pachytene chromosome FISH. The lengths of pachytene chromosomes varied from 54.80 to 143.41 μm. The proportion of heterochromatin regions varied from 13.56% to 63.86%. Finally, the chromosomal homeologous relationship between C. anguria and cucumber (C1–C7) was analyzed. The results showed that A06 + A09, A03 + A12, A02 + A04, and A01 + A11 were homeologs of C1, C2, C3, and C6, respectively. Furthemore, chromosomes A08, A10, and A05 were homeologs of C4, C5, and C7, respectively. Chromosome identification and homeologous relationship analysis between C. anguria and cucumber lay the foundation for further research of genome structure evolution in species of Cucumis.
    Type of Medium: Online Resource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/gen-2017-0235
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2018
    detail.hit.zdb_id: 2020635-5
    SSG: 12
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  • 19
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    Online Resource
    The Chloroplast-Localized Phospholipases D α4 and α5 Regulate Herbivore-Induced Direct and Indirect Defenses in Rice    
    Oxford University Press (OUP) ; 2011
    In:  Plant Physiology Vol. 157, No. 4 ( 2011-12-01), p. 1987-1999
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 157, No. 4 ( 2011-12-01), p. 1987-1999
    Abstract: The oxylipin pathway is of central importance for plant defensive responses. Yet, the first step of the pathway, the liberation of linolenic acid following induction, is poorly understood. Phospholipases D (PLDs) have been hypothesized to mediate this process, but data from Arabidopsis (Arabidopsis thaliana) regarding the role of PLDs in plant resistance have remained controversial. Here, we cloned two chloroplast-localized PLD genes from rice (Oryza sativa), OsPLDα4 and OsPLDα5, both of which were up-regulated in response to feeding by the rice striped stem borer (SSB) Chilo suppressalis, mechanical wounding, and treatment with jasmonic acid (JA). Antisense expression of OsPLDα4 and -α5 (as-pld), which resulted in a 50% reduction of the expression of the two genes, reduced elicited levels of linolenic acid, JA, green leaf volatiles, and ethylene and attenuated the SSB-induced expression of a mitogen-activated protein kinase (OsMPK3), a lipoxygenase (OsHI-LOX), a hydroperoxide lyase (OsHPL3), as well as a 1-aminocyclopropane-1-carboxylic acid synthase (OsACS2). The impaired oxylipin and ethylene signaling in as-pld plants decreased the levels of herbivore-induced trypsin protease inhibitors and volatiles, improved the performance of SSB and the rice brown planthopper Nilaparvata lugens, and reduced the attractiveness of plants to a larval parasitoid of SSB, Apanteles chilonis. The production of trypsin protease inhibitors in as-pld plants could be partially restored by JA, while the resistance to rice brown planthopper and SSB was restored by green leaf volatile application. Our results show that phospholipases function as important components of herbivore-induced direct and indirect defenses in rice.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.111.183749
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 20
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    Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis
    Wiley ; 2021
    In:  The Plant Journal Vol. 107, No. 4 ( 2021-08), p. 1243-1259
    Details
    In: The Plant Journal, Wiley, Vol. 107, No. 4 ( 2021-08), p. 1243-1259
    Abstract: To date, elucidating karyotype evolution that has been disrupted by complex chromosome rearrangements remains a major challenge in the study of chromosome evolution. By reconstructing a deduced ancestral chromosome and an evolutionary framework using highly customizable comparative oligo‐painting, we demonstrated the evolutionary histories for eight Cucumis species. Our findings highlight that the evolution of Cucumis genomes is marked by partitioned evolutionary plasticity with the essential function of creating karyotype novelty, expanding our understanding for karyotype evolution.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.v107.4
    DOI: 10.1111/tpj.15381
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020961-7
    SSG: 12
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