Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game

Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.

Three bona fide plant-specific SAGA subunits and their regulatory function

Nucleosomal histone tails are subject to a vast repertoire of covalent modifications that alter the physical accessibility of their associated DNA,impacting gene expression.Specifically,the acetylation of histones is associated with transcriptional activation,as it has been shown to reduce their affinity for DNA(Grant,2001).The dynamic changes on histone acetylation levels throughout development are the result of active acetylation and deacetylation processes,mediated by histone acetyltransferases(HATs)and deacetylases,respectively.

Arahidopsis CHLOROPHYLLASE 1 protects young leaves from long-term photodamage by facilitating FtsH-mediated D1 degradation in photosystemⅡrepair

The proteolytic degradation of the photodamaged D1 core subunit during the photosystemⅡ(PSⅡ)repair cycle is well understood,but chlorophyll turnover during D1 degradation remains unclear.Here,we report that Arabidopsis thaliana CHLOROPHYLLASE 1(CLH1)plays important roles in the PSII repair process.The abundance of CLH1 and CLH2 peaks in young leaves and is induced by high-light exposure.Seedlings of clh1 single and clh1-1/2-2 double mutants display increased photoinhibition after long-term high-light exposure,whereas seedlings overexpressing CLH1 have enhanced light tolerance compared with the wild type.CLH1 is localized in the developing chloroplasts of young leaves and associates with the PSⅡ-dismantling complexes RCC1 and RC47,with a preference for the latter upon exposure to high light.Furthermore,degradation of damaged D1 protein is retarded in young clh1-1/2-2 leaves after 18-h highlight exposure but is rescued by the addition of recombinant CLH1 in vitro.Moreover,overexpression of CLH1 in a variegated mutant(var2~2)that lacks thylakoid protease FtsH2,with which CLH1 interacts,suppresses the variegation and restores D1 degradation.A var2-2 clh1-1/2-2triple mutant shows more severe variegation and seedling death.Taken together,these results establish CLH1 as a long-sought chlorophyll dephytylation enzyme that is involved in PSⅡrepair and functions in long-term adaptation of young leaves to high-light exposure by facilitating FtsH-mediated D1 degradation.