CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

Sun, Yu; Zhang, Quanbao; Liu, Bing; Lin, Kui; Zhang, Zhonghua; Pang, Erli

doi:10.1186/s12870-020-2312-y

Cited by 9 publications

(7 citation statements)

References 48 publications

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“…Alternative splicing (AS) is a significant mechanism for regulating the expression of genes in eukaryotes [ 22 ]. AS refers to one mRNA precursor producing diverse transcripts, which is thought of as an important post-transcriptional mechanism for increasing the diversity of transcripts and proteins [ 23 ]. AS plays a major role in affecting protein function; therefore, it is necessary to systematically identify AS events.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

et al. 2021

IJMS

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It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp ‘Yunma No.1’ were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

et al. 2021

IJMS

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“…In recent years, tea plant multi-omics sequencing data have been published [ 32 , 33 ], but the integration and comprehensive utilization of these data is more difficult than other species due to the tea plant genome size of about 3 Gb and high heterozygosity [ 34 , 35 ]. In this study, we integrated more than 20 Tb of sequencing data from multiple data sources to build a powerful database of tea plant variation.…”

Section: Discussionmentioning

confidence: 99%

TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis)

An¹,

Zhang²,

Jiang³

et al. 2022

BMC Plant Biol

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Genome variation not only plays an important role in plant phenotypic modeling and adaptive evolution, but also enhances population genetic diversity and regulates gene expression. The tea tree (Camellia sinensis) has a large genome (~ 3.0 Gb), making the identification of genome-wide variants time-consuming and expensive. With the continuous publication of a large number of different types of population sequencing data, there is a lack of an open platform to integrate these data and identify variants in the tea plant genome.To integrate the genetic variation confidence in the tea plant population genome, 238 whole-genome resequencing, 213 transcriptome sequencing, and 96 hybrid F1 individuals with a total of more than 20 Tb were collected for mutation site identification. Based on these variations information, we constructed the first tea tree variation web service database TeaPVs (http://47.106.184.91:8025/ and http://liushang.top:8025/). It supports users to search all SNP, Indel, SV mutations and SSR/Polymorphic SSR sequences by location or gene ID. Furthermore, the website also provides the functions of gene expression search of different transcriptome, sequence blast, sequence extraction of CDS and mutation loci, etc.The features of the TeaPVs database make it a comprehensive tea plant genetic variation bioinformatics platform for researchers, and will also be helpful for revealing new functional mutations in the tea plant genome and molecular marker-assisted breeding.

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“…Numerous databases have been created to store, mine, analyze, and disseminate vast transcriptomic and genetic datasets and to provide a central portal for research and breeding communities. The genomics and functional genomics databases specially constructed for the Cucurbitaceae, including cucumber, include the Cucurbit Genomics Database (CuGenDB, http://www.cucurbitgenomics.org/, accessed on 15 December 2021) [61] and the cucumber alternative splicing (CuAS) database (http://cmb.bnu.edu.cn/alt_iso/index.Php, accessed on 20 December 2021) [62].…”

Section: Information Resources For Cucumber Researchmentioning

confidence: 99%

“…Meanwhile, the CuAS database includes AS transcripts from cucumber and annotations that include genomic information, AS events, isoform functions, isoform features, and tissue-specific splicing events. CuAS can be used to explore the relationships between functional features and predicted AS transcripts [62].…”

Section: Information Resources For Cucumber Researchmentioning

confidence: 99%

Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement

Han

Ma²,

Zhang

et al. 2022

Plants

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Cucumbers are rich in vitamins and minerals. The cucumber has recently become one of China’s main vegetable crops. More specifically, the adjustment of the Chinese agricultural industry’s structure and rapid economic development have resulted in increases in the planting area allocated to Chinese cucumber varieties and in the number of Chinese cucumber varieties. After complete sequencing of the “Chinese long” genome, the transcriptome, proteome, and metabolome were obtained. Cucumber has a small genome and short growing cycle, and these traits are conducive to the application of molecular breeding techniques for improving fruit quality. Here, we review the developments and applications of molecular markers and genetic maps for cucumber breeding and introduce the functions of gene families from the perspective of genomics, including fruit development and quality, hormone response, resistance to abiotic stress, epitomizing the development of other omics, and relationships among functions.

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CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

Cited by 9 publications

References 48 publications

Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis)

Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement

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