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README.md

-- 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.
-- 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.
-- 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.
+# 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
+
+
+## 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>
+- 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

assays/BSA_RNAseq/adapters/custom_adapters.fa

+>read1_1/1
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+>read1_2/1
+AGATCGGAAGAGCACACGTCTGAAC
+>read1_3/1
+TGGAATTCTCGGGTGCCAAGG
+>read1_4/1
+AGATCGGAAGAGCACACGTCT
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+>read1_6/1
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+>read2_1/2
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+>read2_2/2
+AGATCGGAAGAGCGTCGTGTAGGGA
+>read2_3/2
+TGGAATTCTCGGGTGCCAAGG
+>read2_4/2
+AGATCGGAAGAGCACACGTCT
+>read2_5/2
+CTGTCTCTTATACACATCT
+>read2_6/2
+AGATGTGTATAAGAGACAG

assays/BSA_RNAseq/adapters/readme.txt

+## raw_data/BSA_rnaseq/adapters/
+
+Sequencing adapters used for reads trimming