Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth DOI Creative Commons
T. WINKLER, Susanne Vollmer, Nadine Dyballa‐Rukes

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 25, 2023

Summary • Betalains are coloring pigments produced in some families of the order Caryophyllales, where they replace anthocyanins as pigments. While betalain pathway itself is well studied, tissue-specific regulation remains mostly unknown. We enhance high-quality Amaranthus hypochondriacus reference genome and produce a substantially more complete annotation, incorporating isoform details. annotate anthocyanin genes along with their regulators amaranth map genetic control pathway. Our improved annotation allowed us to identify causal mutations that lead knock-out red betacyanins natural accessions amaranth. reveal flower color via previously uncharacterized MYB transcription factor, AhMYB2 . Downregulation leads reduced expression key enzyme loss color. represents most date valuable resource for research. High similarity regulator partially conserved interaction motif support co-option possible reason mutual exclusiveness two

Language: Английский

Origin and evolution of the bread wheat D genome DOI Creative Commons
Emile Cavalet-Giorsa, Andrea González-Muñoz, Naveenkumar Athiyannan

et al.

Nature, Journal Year: 2024, Volume and Issue: 633(8031), P. 848 - 855

Published: Aug. 14, 2024

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories proteins for the human diet. Compared with its wild ancestors, modern bread shows lower genetic diversity, caused by polyploidisation, domestication breeding bottlenecks

Language: Английский

Citations

17
Isoform‐resolved genome annotation enables mapping of tissue‐specific betalain regulation in amaranth DOI Creative Commons
T. WINKLER, Susanne Vollmer, Nadine Dyballa‐Rukes

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: 243(3), P. 1082 - 1100

Published: April 8, 2024

Summary Betalains are coloring pigments produced in some families of the order Caryophyllales, where they replace anthocyanins as pigments. While betalain pathway itself is well studied, tissue‐specific regulation remains mostly unknown. We enhance high‐quality Amaranthus hypochondriacus reference genome and produce a substantially more complete annotation, incorporating isoform details. annotate anthocyanin genes along with their regulators amaranth map genetic control pathway. Our improved annotation allowed us to identify causal mutations that lead knock‐out red betacyanins natural accessions amaranth. reveal flower color via previously uncharacterized MYB transcription factor, AhMYB2 . Downregulation leads reduced expression key enzyme loss color. represents most date valuable resource for research. High similarity regulator partially conserved interaction motif support co‐option possible reason mutual exclusiveness two

Language: Английский

Citations

5
Domestication shaped the chromatin landscape of grain amaranth DOI Creative Commons
Corbinian Graf, T. WINKLER, Peter J. Maughan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Plant domestication has had profound impacts on the morphology and genetic diversity of crops. Beyond sequence diversity, changes in chromatin structure can play an important role plant adaptation. However, interplay between landscape remains unclear. We present a high-quality genome assembly map ancient pseudo-cereal, amaranth. Using ATAC-sequencing multiple accessions three grain amaranth species two wild relatives, we show that overall amount accessible is highly conserved, about 2.5% all switched states, with higher fraction repeatedly opening during processes. These differentially regions, crops their ancestor, were species-specific significantly associated selective sweeps - reflecting repeated independent Our findings reveal dynamic landscape, highlighting additional layer

Language: Английский

Citations

0
Genome-Wide Resequencing Revealed the Genetic Diversity of Fraxinus platypoda Oliv. in Northwestern China DOI Open Access
Ying Liu,

Wanting Ge,

Qiuling Zhao

et al.

Forests, Journal Year: 2025, Volume and Issue: 16(5), P. 860 - 860

Published: May 21, 2025

Fraxinus platypoda Oliv. (Oleaceae), an ecologically and economically valuable tree species with key distribution areas in northwestern China, faces conservation challenges due to its fragmented groups scarce individual numbers. To investigate the genetic consequences of this demographic crisis, we analyzed 65 individuals from 11 natural region using whole-genome resequencing. We identified a total 60,503,092 single nucleotide polymorphisms (SNPs), after further filtering, retained 3,394,299 SNPs for subsequent analysis. Population structure analysis (Neighbor-Joining tree, STRUCTURE, kinship coefficients) revealed two distinct clusters (K = 2), principal component (PCA) confirming subdivision. Cluster I, composed eight Groups 3, 5, 8, 11, is highly differentiated II may be ancestral it. Among groups, 3 show high diversity differentiation, Tajima’s D > 0, indicating long evolutionary history balancing selection. The remaining nine have low diversity, frequent gene flow, < suggesting directional A mantel test showed no significant link between variation geographic isolation (p 0.460). differentiation I flow are maintained by factors like reproductive systems. highlighted as important resources deserving priority protection. This study offers genomic data conserving future adaptability research.

Language: Английский

Citations

0
Origin and evolution of the bread wheat D genome DOI Creative Commons
Emile Cavalet-Giorsa, Andrea González-Muñoz, Naveenkumar Athiyannan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 29, 2023

Abstract Bread wheat ( Triticum aestivum ) is a globally dominant crop and major source of calories proteins for the human diet. Compared to its wild ancestors, modern bread shows lower genetic diversity caused by polyploidisation, domestication, breeding bottlenecks 1,2 . Wild relatives represent reservoirs, harbouring beneficial alleles that have not been incorporated into wheat. Here, we establish analyse pangenome resources Tausch’s goatgrass, Aegilops tauschii , donor D genome. This new facilitated cloning disease resistance gene haplotype analysis across complex locus, allowing us discern from paralogous copies. We also reveal composition history genome, involving previously unreported contributions genetically geographically discrete Ae. subpopulations. Together, our results genome demonstrate potential in improvement.

Language: Английский

Citations

3
Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth DOI Creative Commons
T. WINKLER, Susanne Vollmer, Nadine Dyballa‐Rukes

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 25, 2023

Summary • Betalains are coloring pigments produced in some families of the order Caryophyllales, where they replace anthocyanins as pigments. While betalain pathway itself is well studied, tissue-specific regulation remains mostly unknown. We enhance high-quality Amaranthus hypochondriacus reference genome and produce a substantially more complete annotation, incorporating isoform details. annotate anthocyanin genes along with their regulators amaranth map genetic control pathway. Our improved annotation allowed us to identify causal mutations that lead knock-out red betacyanins natural accessions amaranth. reveal flower color via previously uncharacterized MYB transcription factor, AhMYB2 . Downregulation leads reduced expression key enzyme loss color. represents most date valuable resource for research. High similarity regulator partially conserved interaction motif support co-option possible reason mutual exclusiveness two

Language: Английский

Citations

1