The Cucumber Genome—An Update

2021 ◽  
pp. 25-35
Author(s):  
Yiqun Weng
Keyword(s):  
Cucumber Genome

scholarly journals Chromosome-scale genome assembly of Cucumis hystrix—a wild species interspecifically cross-compatible with cultivated cucumber

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaodong Qin ◽  
Zhonghua Zhang ◽  
Qunfeng Lou ◽  
Lei Xia ◽  
Ji Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Disease Resistance Gene ◽  
Introgression Breeding ◽  
Interspecific Introgression ◽  
Cucumber Genome ◽  
Cucumis Hystrix

AbstractCucumis 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.

scholarly journals Comprehensive genomic analysis and expression profiling of the BTB and TAZ (BT) genes in cucumber (Cucumis sativus L.)

2019 ◽  
Vol 56 (No. 1) ◽  
pp. 15-23 ◽  
Author(s):  
Yong Zhou ◽  
Guanghua Li ◽  
Lin Zhang ◽  
Jie Xu ◽  
Lifang Hu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Biological Processes ◽  
Quantitative Real Time Pcr ◽  
Cucumis Sativus L ◽  
Btb Domain ◽  
Qrt Pcr ◽  
Cucumber Genome ◽  
Bt Genes

BTB-TAZ (BT) proteins are plant-specific transcription factors containing a BTB domain and a TAZ domain. They play vital roles in various biological processes and stress responses. In this study, a total of three BT genes (CsBT1–3) were identified from cucumber genome, and they were unevenly distributed in two of the seven chromosomes. Phylogenetic analysis of the BT proteins from cucumber, Arabidopsis, apple, tomato, and rice revealed that these proteins could be distinctly divided into two groups in accordance with their motif distributions. We also determined the structures of BT genes from cucumber, Arabidopsis, and rice to demonstrate their differences. The quantitative real-time PCR (qRT-PCR) results showed that the CsBT genes displayed differential expression patterns in cucumber tissues, and their expression was regulated by cold, salt, and drought stresses. These findings suggest that CsBT genes may participate in cucumber development and responses to various abiotic stresses.

scholarly journals The sea cucumber genome provides insights into morphological evolution and visceral regeneration

PLoS Biology ◽  
2017 ◽  
Vol 15 (10) ◽  
pp. e2003790 ◽  
Author(s):  
Xiaojun Zhang ◽  
Lina Sun ◽  
Jianbo Yuan ◽  
Yamin Sun ◽  
Yi Gao ◽  
...  
Keyword(s):  
Sea Cucumber ◽  
Morphological Evolution ◽  
Cucumber Genome

Identification and expression analysis of LEA gene family members in cucumber genome

2016 ◽  
Vol 80 (2) ◽  
pp. 225-241 ◽  
Author(s):  
Yasemin Celik Altunoglu ◽  
Pinar Baloglu ◽  
Esra Nurten Yer ◽  
Sefa Pekol ◽  
Mehmet Cengiz Baloglu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members ◽  
Lea Gene ◽  
Cucumber Genome

Development of genome viewer (Web Omics Viewer) for managing databases of cucumber genome

2012 ◽  
Author(s):  
M. Wojcieszek ◽  
P. Róż ◽  
M. Pawełkowicz ◽  
R. Nowak ◽  
Z. Przybecki
Keyword(s):  
Genome Viewer ◽  
Cucumber Genome

scholarly journals An Integrated Genetic and Cytogenetic Map of the Cucumber Genome

PLoS ONE ◽  
2009 ◽  
Vol 4 (6) ◽  
pp. e5795 ◽  
Author(s):  
Yi Ren ◽  
Zhonghua Zhang ◽  
Jinhua Liu ◽  
Jack E. Staub ◽  
Yonghua Han ◽  
...  
Keyword(s):  
Cytogenetic Map ◽  
Cucumber Genome

scholarly journals Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

2020 ◽  
Author(s):  
Duo Lv ◽  
Gang Wang ◽  
Yue Chen ◽  
Liang-Rong Xiong ◽  
Jing-Xian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Kinase Gene ◽  
Cucumis Sativus L ◽  
Lectin Receptor ◽  
Genome Wide ◽  
Cucumber Genome ◽  
And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

scholarly journals Genome-Wide Identification and Expression Analyses of the Fibrillin Family Genes Reveal Their Involvement in the Photoprotection in Cucumber

2018 ◽  
Author(s):  
Inyoung Kim ◽  
Sang-Choon Lee ◽  
Eun-Ha Kim ◽  
Kiwhan Song ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Dna Sequences ◽  
Light Stress ◽  
High Light ◽  
Light Conditions ◽  
Transcript Levels ◽  
Photosynthetic Organisms ◽  
Conserved Domain ◽  
Genome Wide ◽  
Cucumber Genome

Fibrillin (FBN) is a plastid lipid-associated protein found in photosynthetic organisms from cyanobacteria to plants. In this study, 10 CsaFBN genes were identified in genomic DNA sequences of cucumber (Chinese long and Gy14) through database searches using the conserved domain of FBN and the 14 FBN genes of Arabidopsis. Phylogenetic analysis of CsaFBN protein sequences showed that there was no counterpart of Arabidopsis and rice FBN5 in the cucumber genome. FBN5 is essential for growth in Arabidopsis and rice; its absence in cucumber may be because of incomplete genome sequences or that another FBN carries out its functions. Among the 10 CsaFBN genes, CsaFBN1 and CsaFBN9 were the most divergent in terms of nucleotide sequences. Most of the CsaFBN genes were expressed in the leaf, stem, and fruit. CsaFBN4 showed the highest mRNA expression levels in various tissues, followed by CsaFBN6, CsaFBN1, and CsaFBN9. High-light stress combined with low temperature decreased photosynthetic efficiency and highly induced transcript levels of CsaFBN1, CsaFBN6, and CsaFBN11, which decreased after 24 h treatment. Transcript levels of the other seven genes were changed only slightly. This result suggests that CsaFBN1, CsaFBN6, and CsaFBN11 may be involved in photoprotection under high-light conditions at low temperature.

scholarly journals The DefH9-iaaM-containing construct efficiently induces parthenocarpy in cucumber

2006 ◽  
Vol 11 (2) ◽  
Author(s):  
Zhimin Yin ◽  
Robert Malinowski ◽  
Agnieszka Ziółkowska ◽  
Hans Sommer ◽  
Wojciech Plcader ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Seed Set ◽  
Single Gene ◽  
Marker Gene ◽  
Practical Significance ◽  
F1 Hybrids ◽  
Cucumber Genome ◽  
Seedless Fruits ◽  
Transgenic Lines ◽  
Independent Transformation

AbstractParthenocarpy (seedless fruits) is a desirable trait that has been achieved in many plant cultivars. We generated parthenocarpic cucumber fruits by introducing the chimeric DefH9-iaaM construct into the cucumber genome using an Agrobacterium tumefaciens-mediated protocol. The construct consists of the DefH9 promoter from Antirrhinum majus and the iaaM coding sequence from Pseudomonas syringae. Transgenic plants were obtained from nine independent transformation events: half of these were tetraploid and did not produce seeds following self-pollination, while the remaining half were capable of displaying parthenocarpy in the subsequent reproductive generation. Of the fruits produced by the transgenic lines, 70–90% were parthenocarpic. The segregation of the marker gene in the transgenic T1 progeny indicated single gene inheritance. The seed set in the transgenic lines and their F1 hybrids was lower than in the non-transgenic control plants. Some of the methodological details and the practical significance of the results are discussed.

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