Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes

Soil salinity is a growing concern for global crop production and the sustainable development of humanity.Therefore,it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerance genes to enhance crop tolerance to salt stress.Suaeda glauca,a halophyte species well adapted to the seawater environment,possesses a unique ability to absorb and retain high salt concentrations within its cells,particularly in its leaves,suggesting the presence of a distinct mechanism for salt tolerance.In this study,we performed de novo sequencing of the S.glauca genome.The genome has a size of 1.02 Gb(consisting of two sets of haplotypes)and contains 54761 annotated genes,including alleles and repeats.Comparative genomic analysis revealed a strong synteny between the genomes of S.glauca and Beta vulgaris.Of the S.glauca genome,70.56%comprises repeat sequences,with retroelements being the most abundant.Leveraging the allele-aware assembly of the S.glauca genome,we investigated genome-wide allele-specific expression in the analyzed samples.The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression.Moreover,a systematic analysis of the ABCE gene families shed light on the formation of S.glauca’s flower morphology,suggesting that dysfunction of A-class genes is responsible for the absence of petals in S.glauca.Gene family expansion analysis demonstrated significant enrichment of Gene Ontology(GO)terms associated with DNA repair,chromosome stability,DNA demethylation,cation binding,and red/far-red light signaling pathways in the co-expanded gene families of S.glauca and S.aralocaspica,in comparison with glycophytic species within the chenopodium family.Time-course transcriptome analysis under salt treatments revealed detailed responses of S.glauca to salt tolerance,and the enrichment of the transition-upregulated genes in the leaves associated with DNA repair and chromosome stability,lipid biosynthetic process,and isoprenoid metabolic process.Additionally,genome-wide analysis of transcription factors indicated a significant expansion of FAR1 gene family.However,further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S.glauca.

Photooligomerization Determines Photosensitivity and Photoreactivity of Plant Cryptochromes

Plant and non-plant species possess cryptochrome(CRY)photoreceptors to mediate blue light regulation of development or the circadian clock.The blue light-dependent homooligomerization of Arabidopsis CRY2 is a known early photoreaction necessary for its functions,but the photobiochemistry and function of light-dependent homooligomerization and heterooligomerization of cryptochromes,collectively referred to as CRY photooligomerization,have not been well established.Here,we show that photooligomerization is an evolutionarily conserved photoreaction characteristic of CRY photoreceptors in plants and some non-plant species.Our analyses of the kinetics of the forward and reverse reactions of photooligomerization of Arabidopsis CRY1 and CRY2 provide a previously unrecognized mechanism underlying the different photosensitivity and photoreactivity of these two closely related photoreceptors.We found that photooligomerization is necessary but not sufficient for the functions of CRY2,implying that CRY photooligomerization is presumably accompanied by additional function-empowering conformational changes.We further demonstrated that the CRY2-CRY1 heterooligomerization plays roles in regulating functions of Arabidopsis CRYs in vivo.Taken together,these results suggest that photooligomerization is an evolutionarily conserved mechanism determining the photosensitivity and photoreactivity of plant CRYs.