Plant and Cell Physiology’s 2018 Database Issue and Beyond

Ohyanagi, Hajime; Nakamura, Yasukazu; Yano, Kentarô

doi:10.1093/pcp/pcy002

Cited by 3 publications

(2 citation statements)

References 8 publications

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“…The identified peach variants, both SNP and InDels, are available at the PeachVar-DB portal 9 that provides an easy access to the information mined from peach Whole Genome Re-Sequencing (WGRS) data. Full description of this work can be found in [ 26 ].…”

Section: Resultsmentioning

confidence: 99%

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

et al. 2020

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Background: The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the "Big Data" era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. Results: Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call "ELIXIR-IT HPC@CINECA", offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of~8 Millions of CPU/hours and, for data storage,1 00 TB of permanent and~300 TB of temporary space.

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Section: Resultsmentioning

confidence: 99%

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

et al. 2020

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“…Melon ( Cucumis melo L.) is an economically valuable annual horticultural crop in the cucurbitaceae family. [ 1 ] Most consumers love it due to its distinctive aroma. However, melon production has some challenges, such as soil‐borne diseases, [ 2 ] poor root tolerance to cold, and other environmental factors.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis provides an insight into the function of CmGH9B3, a key gene of β‐1, 4‐glucanase, during the graft union healing of oriental melon scion grafted onto squash rootstock

Zhu,

Hu,

Min

et al. 2024

Biotechnology Journal

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The melon (Cucumis melo L.) is a globally cherished and economically significant crop. The grafting technique has been widely used in the vegetative propagation of melon to promote environmental tolerance and disease resistance. However, mechanisms governing graft healing and potential incompatibilities in melons following the grafting process remain unknown. To uncover the molecular mechanism of healing of grafted melon seedlings, melon wild type (Control) and TRV‐CmGH9B3 lines were obtained and grafted onto the squash rootstocks (C. moschata). Anatomical differences indicated that the healing process of the TRV‐CmGH9B3 plants was slower than that of the control. A total of 335 significantly differentially expressed genes (DEGs) were detected between two transcriptomes. Most of these DEGs were down‐regulated in TRV‐CmGH9B3 grafted seedlings. GO and KEGG analysis showed that many metabolic, physiological, and hormonal responses were involved in graft healing, including metabolic processes, plant hormone signaling, plant MAPK pathway, and sucrose starch pathway. During the healing process of TRV‐CmGH9B3 grafted seedlings, gene synthesis related to hormone signal transduction (auxin, cytokinin, gibberellin, brassinolide) was delayed. At the same time, it was found that most of the DEGs related to the sucrose pathway were down‐regulated in TRV‐CmGH9B3 grafted seedlings. The results showed that sugar was also involved in the healing process of melon grafted onto squash. These results deepened our understanding of the molecular mechanism of GH9B3, a key gene of β‐1, 4‐glucanase. It also provided a reference for elucidating the gene mechanism and function analysis of CmGH9B3 in the process of graft union healing.

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Blue and red light upregulate α-expansin 1 (EXPA1) in transgenic Brassica rapa and its overexpression promotes leaf and root growth in Arabidopsis

et al. 2020

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Plant and Cell Physiology’s 2018 Database Issue and Beyond

Cited by 3 publications

References 8 publications

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

Transcriptomic analysis provides an insight into the function of CmGH9B3, a key gene of β‐1, 4‐glucanase, during the graft union healing of oriental melon scion grafted onto squash rootstock

Blue and red light upregulate α-expansin 1 (EXPA1) in transgenic Brassica rapa and its overexpression promotes leaf and root growth in Arabidopsis

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