diff --git a/README.md b/README.md index 9085051fe02734d5cefe94de966ad577958f6f9f..7cdcacc26260b9ac330a48fe91176c9010905214 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., Dyballaâ€Rukes, N., Metzger, S., & Stetter, M. G. (2024). Isoformâ€resolved genome annotation enables mapping of tissueâ€specific betalain regulation in amaranth. *New Phytologist*. \ No newline at end of file diff --git a/assays/BSA_RNAseq/isa.assay.xlsx b/assays/BSA_RNAseq/isa.assay.xlsx index a551c1ab2d0da79bd13c36d36ce078866cda24d8..dcbe7e11f655b473bbd4470980261d4e30793c69 100644 Binary files a/assays/BSA_RNAseq/isa.assay.xlsx and b/assays/BSA_RNAseq/isa.assay.xlsx differ diff --git a/assays/BSA_WGS/isa.assay.xlsx b/assays/BSA_WGS/isa.assay.xlsx index b2b18ecaecf4841752a8cd0258de8a9819a1311d..708d706adcd7f143addf1eeb87bb5214a640c12c 100644 Binary files a/assays/BSA_WGS/isa.assay.xlsx and b/assays/BSA_WGS/isa.assay.xlsx differ diff --git a/assays/betalain_LCMS_quantification/isa.assay.xlsx b/assays/betalain_LCMS_quantification/isa.assay.xlsx index ecfb8f6f17edcffa801b2bf4a6438734f0e10f07..67f8304b23ee0bf003ea554d74c45996011ceb56 100644 Binary files a/assays/betalain_LCMS_quantification/isa.assay.xlsx and b/assays/betalain_LCMS_quantification/isa.assay.xlsx differ diff --git a/assays/betalain_photometric_quantification/isa.assay.xlsx b/assays/betalain_photometric_quantification/isa.assay.xlsx index 7bd7647eb7976a150ab391267c8ef4d8a773349a..57d7d78fa302be380171eadfe10235665f2d3c85 100644 Binary files a/assays/betalain_photometric_quantification/isa.assay.xlsx and b/assays/betalain_photometric_quantification/isa.assay.xlsx differ diff --git a/assays/isoform_sequencing/isa.assay.xlsx b/assays/isoform_sequencing/isa.assay.xlsx index 8a876ea8629280fae0073dd1e4806f0d5202ebcd..1060b500708c8c4b594f3196fb1a506b87060688 100644 Binary files a/assays/isoform_sequencing/isa.assay.xlsx and b/assays/isoform_sequencing/isa.assay.xlsx differ diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 8739007236608fcb69d11e2d928a9b9db0adfc29..2d835947552628c62c5c2927d58dc852227fb339 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/BSA_parent_betalain_quant/isa.study.xlsx b/studies/BSA_parent_betalain_quant/isa.study.xlsx index 4748cb4aae1dc7eaa0f7121d9569db1877117b67..eb8b731c41385af409e714442c38e1025ebd109d 100644 Binary files a/studies/BSA_parent_betalain_quant/isa.study.xlsx and b/studies/BSA_parent_betalain_quant/isa.study.xlsx differ diff --git a/studies/Bulk_segregant_analysis/isa.study.xlsx b/studies/Bulk_segregant_analysis/isa.study.xlsx index d12033aaca743373ba731accf012284f679f0e15..2f088d40bd3fed4ddbec2868b90d4916e5c33902 100644 Binary files a/studies/Bulk_segregant_analysis/isa.study.xlsx and b/studies/Bulk_segregant_analysis/isa.study.xlsx differ diff --git a/studies/additional_data/isa.study.xlsx b/studies/additional_data/isa.study.xlsx index 3d36f199ac7bee0c4e0e989ae48a9733ca040f07..450a4499cb6798d4178af96ca512e97b464fa5bc 100644 Binary files a/studies/additional_data/isa.study.xlsx and b/studies/additional_data/isa.study.xlsx differ diff --git a/studies/isoform_sequencing/isa.study.xlsx b/studies/isoform_sequencing/isa.study.xlsx index 259c3740ce4ac1b8edc9efc84c58ab28dc07ccbd..3ef18c901f510deea90212415420b35040a579f0 100644 Binary files a/studies/isoform_sequencing/isa.study.xlsx and b/studies/isoform_sequencing/isa.study.xlsx differ