Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Sprint:Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 5 2022 Feb 28 - Mar 11
Description
To understand the significance of our results, we need to learn the current state of knowledge in the field.
For this task, assemble and summarize original research articles published in the last two to three years that investigated how salt stress affects methylation patterns in plants.
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Nowlan Freese
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Nowlan Freese
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Field | Original Value | New Value |
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Epic Link | IGBF-3039 [ 21553 ] |
Nowlan Freese
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Nowlan Freese
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Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Ann Loraine
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Ann Loraine
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Ann Loraine
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Nowlan Freese
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Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Nowlan Freese
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Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
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Ann Loraine
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Sprint | Spring 2 2022 Jan 18 - Jan 28 [ 137 ] | Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 137, 138 ] |
Ann Loraine
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Rank | Ranked higher |
Nowlan Freese
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Attachment | 3059.enl [ 17090 ] |
Ann Loraine
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Sprint | Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 137, 138 ] | Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 137, 138, 139 ] |
Ann Loraine
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Rank | Ranked higher |
Ann Loraine
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Sprint | Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 137, 138, 139 ] | Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 5 2022 Feb 28 - Mar 11 [ 137, 138, 140 ] |
Ann Loraine
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Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
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Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
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Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
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Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
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Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
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Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
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Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Ann Loraine
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Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Ann Loraine
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Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance
We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity.
Following our previous studies [13] we have furthered investigated the patterns of DNA methylation in 'Pokkali', a rice variety that simultaneously shows a great capacity to tolerate salinity stress and to rapidly shape DNA methylation levels when exposed to salinity.
The percentage of uniquely mapped reads was considerably higher on the non-immunoprecipitated sample (approximately 50%) contrasting with approximately 25% for the immunoprecipitated samples (Table 1). Regarding the genome coverage, approximately 7.5% of cytosines were covered by at least one uniquely mapped read (Table 1).
The analysis of differential methylation based on MeDIP-Seq data, using the MEDIPS program, as mentioned in the methods section, enabled the identification of 53 DMRs between control and salt stress samples. The DMRs that were close to each other (less than 500 bp) were merged originating 22 DMRs (ranging from 100 to 1000 bp) (Table 2). Although all methylation contexts were present (CG, CHG, and CHH), in DMR2 the methylation was mainly in the CHH context, while in DMR15 the CHG context was predominant.
The DMRs were analyzed according to their position relative to the nearest gene, and more than 70% of the DMRs were in close proximity to genes (less than 2 kbp away) (Figure 2A). Furthermore, over 75% of the DMRs identified were associated with transposable elements and repetitive sequences (Figure 2B).
The functional annotation of genes flanking or overlapping salt-induced DMRs was performed using Blast2GO [35] and multilevel pie charts were generated for the three main classes: cellular component, biological process, and molecular function (Figure S4).