The evolutionary trajectories and gene regulatory roles of nuclear‐integrated plastid DNA: clues for enhancing environmental adaptation in Caryophyllales

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)

Published: March 31, 2025

SUMMARY Environmental stimuli can induce the transfer of chloroplast DNA to nuclear genome, resulting in nuclear‐integrated plastid DNAs (NUPTs). However, their role plant adaptability remains unclear. Species within Caryophyllales order, known for adaptation extreme environments, provide an ideal model studying evolutionary dynamics and functions NUPTs. In this study, we analyzed NUPTs 24 species investigate evolution regulatory roles gene expression, particularly response environmental stimuli. We found significant interspecies variation NUPT abundance, ranging from 566 insertions Amaranthus cruentus 3585 Beta vulgaris , with sizes spanning 100 bp over kb. Approximately 62% were inserted last 20 million years, while some exhibit insertion peaks dating back 49 years. presence/absence polymorphisms six related suggest that deletions are dynamic processes influenced by phylogeny. predominantly integrate into intergenic regions but also insert genes promoters, certain acting as hotspots. Notably, introduce numerous environmental‐responsive cis ‐acting elements promoter regions. Genes promoters significantly enriched response. Further luciferase assays Spinacia oleracea demonstrated regulate expression responses, indicating potential adaptive evolution. Overall, our study provides insights influence on function

Language: Английский

Genome sequence of the wild species, Spinacia tetrandra, including a phased sequence of the extensive sex‐linked region, revealing partial degeneration in evolutionary strata with unusual properties

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

Summary Genetic degeneration is a striking feature of Y chromosomes, often involving losses many genes carried on the X chromosome. However, time course gene remains unclear. Sex chromosomes plants evolved more recently than animals' highly degenerated ones, making them ideal for studying timing. To investigate Spinacia sex chromosome evolution and degeneration, we compared genome sequences cultivated oleracea , with small Y‐linked region Chr4, its two wild relatives. In spinach closest relative turkestanica duplication (YDR) introduced male‐determining factor into Chr4's low‐recombining pericentromeric region. other words, turnover event occurred in these species' recent common ancestor. The homologous Chr4 distantly related S. tetrandra has c . 133 Mb completely sex‐linked partially region, possibly reflecting ancestral state. Sequence divergence analysis suggests that ‘evolutionary strata’ shortly before lineages split. Consistent hypothesis, YDR species not within older stratum. We discuss unexpected findings genetic genomic rearrangements, repetitive sequence density are all greatest younger

Language: Английский

Pan‐genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach

Plant Biotechnology Journal, Journal Year: 2024, Volume and Issue: 22(11), P. 3102 - 3117

Published: Aug. 2, 2024

Summary Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, identification characterization SVs Spinacia species rare due to lack a pan‐genome. Here, we report eight chromosome‐scale assemblies cultivated spinach its two wild After integration with five existing assemblies, constructed comprehensive pan‐genome identified 193 661 pan‐SVs, which were genotyped 452 accessions. Our pan‐SVs enabled genome‐wide association study signals associated sex clarified evolutionary direction spinach. Most sex‐linked (86%) biased occur on Y chromosome during evolution region, resulting reduced Y‐linked gene expression. The frequency among accessions further illustrated contribution these domestication, such as bolting time seed dormancy. Furthermore, compared SNPs, act efficient genomic selection (GS) because their ability capture missing heritability information higher prediction accuracy. Overall, this provides valuable resource for genomics highlights potential utility pan‐SV crop improvement breeding programmes.

Language: Английский