From f4e920d3e4e02e1e67d6703775f5b1f4170bd33d Mon Sep 17 00:00:00 2001
From: Tom Winkler <t.winkler@uni-koeln.de>
Date: Thu, 26 Sep 2024 16:36:35 +0200
Subject: [PATCH] changed readme

---
 README.md                                     |  18 ++++++++++++------
 assays/BSA_RNAseq/isa.assay.xlsx              | Bin 9292 -> 9292 bytes
 assays/BSA_WGS/isa.assay.xlsx                 | Bin 9310 -> 9310 bytes
 .../isa.assay.xlsx                            | Bin 9276 -> 9276 bytes
 .../isa.assay.xlsx                            | Bin 10100 -> 10100 bytes
 assays/isoform_sequencing/isa.assay.xlsx      | Bin 9323 -> 9323 bytes
 isa.investigation.xlsx                        | Bin 8416 -> 8416 bytes
 .../BSA_parent_betalain_quant/isa.study.xlsx  | Bin 12583 -> 12583 bytes
 .../Bulk_segregant_analysis/isa.study.xlsx    | Bin 10585 -> 10585 bytes
 studies/additional_data/isa.study.xlsx        | Bin 7504 -> 7504 bytes
 studies/isoform_sequencing/isa.study.xlsx     | Bin 10163 -> 10163 bytes
 11 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 9085051..7cdcacc 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,20 @@
-## Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth
-<br>
+# Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth
+
+
+## Authors
 Tom S. Winkler∗ , Susanne K. Vollmer∗† , Nadine Dyballa-Rukes‡ , Sabine Metzger‡ and Markus G Stetter∗,1
 <br>
 ∗ Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany, † Heinrich Heine University,
 Duesseldorf, Germany, ‡ MS platform, Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne,
 Germany
-<br>
-<br>
-<br>
+
+
+## Study description
+
 - Betalains are coloring pigments produced in some families of the order Caryophyllales, where they replace anthocyanins as coloring pigments. While the betalain pathway itself is well studied, the tissue-specific regulation of the pathway remains mostly unknown. <br>
-- We enhance the high-quality Amaranthus hypochondriacus reference genome and produce a substantially more complete genome annotation, incorporating isoform details. We annotate betalain and anthocyanin pathway genes along with their regulators in amaranth and map the genetic control and tissue-specific regulation of the betalain pathway. <br>
+- We enhance the high-quality *Amaranthus hypochondriacus* reference genome and produce a substantially more complete genome annotation, incorporating isoform details. We annotate betalain and anthocyanin pathway genes along with their regulators in amaranth and map the genetic control and tissue-specific regulation of the betalain pathway. <br>
 - Our improved genome annotation allowed us to identify causal mutations that lead to a knock-out of red betacyanins in natural accessions of amaranth. We reveal the tissue-specific regulation of flower color via a previously uncharacterized MYB transcription factor, AhMYB2. Downregulation of AhMYB2 in the flower leads to reduced expression of key betalain enzyme genes and loss of red flower color. <br>
 - Our improved amaranth reference genome represents the most complete genome of amaranth to date and is a valuable resource for betalain and amaranth research. High similarity of the flower betalain regulator AhMYB2 to anthocyanin regulators and a partially conserved interaction motif support the co-option of anthocyanin regulators for the betalain pathway as a possible reason for the mutual exclusiveness of the two pigments.
+
+## Citation
+Winkler, T. S., Vollmer, S. K., Dyballa‐Rukes, N., Metzger, S., & Stetter, M. G. (2024). Isoform‐resolved genome annotation enables mapping of tissue‐specific betalain regulation in amaranth. *New Phytologist*.
\ No newline at end of file
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diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
index 8739007236608fcb69d11e2d928a9b9db0adfc29..2d835947552628c62c5c2927d58dc852227fb339 100644
GIT binary patch
delta 615
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delta 615
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diff --git a/studies/BSA_parent_betalain_quant/isa.study.xlsx b/studies/BSA_parent_betalain_quant/isa.study.xlsx
index 4748cb4aae1dc7eaa0f7121d9569db1877117b67..eb8b731c41385af409e714442c38e1025ebd109d 100644
GIT binary patch
delta 701
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delta 701
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diff --git a/studies/Bulk_segregant_analysis/isa.study.xlsx b/studies/Bulk_segregant_analysis/isa.study.xlsx
index d12033aaca743373ba731accf012284f679f0e15..2f088d40bd3fed4ddbec2868b90d4916e5c33902 100644
GIT binary patch
delta 687
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delta 687
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diff --git a/studies/additional_data/isa.study.xlsx b/studies/additional_data/isa.study.xlsx
index 3d36f199ac7bee0c4e0e989ae48a9733ca040f07..450a4499cb6798d4178af96ca512e97b464fa5bc 100644
GIT binary patch
delta 615
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delta 615
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diff --git a/studies/isoform_sequencing/isa.study.xlsx b/studies/isoform_sequencing/isa.study.xlsx
index 259c3740ce4ac1b8edc9efc84c58ab28dc07ccbd..3ef18c901f510deea90212415420b35040a579f0 100644
GIT binary patch
delta 687
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delta 687
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-- 
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