An improved draft genome sequence of hybrid Populus alba×Populus glandulosa

Populus alba × P.glandulosa clone 84 K,derived from South Korea,is widely cultivated in China and used as a model in the molecular research of woody plants because of hi gh gene transformation efficiency.Here,we combined63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the genome.Due to the hi gh heterozygosity level at 2.1% estimated by k-mer analysis,we exploited TrioCanu for genome assembly.The PacBio clean subreads of P.alba × P.glandulosa were separated into two parts according to the similarities,compared with the parental genomes of P.alba and P.glandulosa.The two parts of the subreads were assembled to two sets of subgenomes comprising subgenome A(405.31 Mb,from P.alba)and subgenome G(376.05 Mb,from P.glandulosa) with the contig N50 size of 5.43 Mb and 2.15 Mb,respectively.A high-quality P.alba × P.glandulosa genome assembly was obtained.The genome size was 781.36 Mb with the contig N50 size of 3.66 Mb and the longest contig was 19.47 Mb.In addition,a total of 176.95 Mb(43.7%),152.37 Mb(40.5%)of repetitive elements were identified and a total of 38,701 and 38,449 protein-coding genes were predicted in subgenomes A and G,respectively.For functional annotation,96.98% of subgenome A and 96.96% of subgenome G genes were annotated with public databases.This de novo assembled genome will facilitate systematic and comprehensive study,such as multi-omics analysis,in the model tree P.alba X P.glandulosa.

The SOC1-like gene BoMADS50 is associated with the flowering of Bambusa oldhamii

Bamboo is known for its edible shoots and beautiful texture and has considerable economic and ornamental value.Unique among traditional flowering plants,many bamboo plants undergo extensive synchronized flowering followed by large-scale death,seriously affecting the productivity and application of bamboo forests.To date,the molecular mechanism of bamboo flowering characteristics has remained unknown.In this study,a SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1(SOC1)-like gene,BoMADS50,was identified from Bambusa oldhamii.BoMADS50 was highly expressed in mature leaves and the floral primordium formation period during B.oldhamii flowering and overexpression of BoMADS50 caused early fl owering in transgenic rice.Moreover,BoMADS50 could interact with APETALA1/FRUITFULL(AP1/FUL)-like proteins(BoMADS 14-1/2,BoMADS15-1/2)in vivo,and the expression of BoMADS50 was signi ficantly promoted by BoMADS14-1,further indicating a synergistic effect between BoMADS50 and BoAP1/FUL-like proteins in regulating B.oldhamii flowering.We also identi fi ed four additional transcripts of BoMADS50(BoMADS50-1/2/3/4)with different nucleotide variations.Although the protein-CDS were polymorphic,they had flowering activation functions similar to those of BoMADS50.Yeast one-hybrid and transient expression assays subsequently showed that both BoMADS50 and BoMADS50-1 bind to the promoter fragment of itself and the SHORT VEGETATIVE PHASE(SVP)-like gene BoSVP,but only BoMADS50-1 can positively induce their transcription.Therefore,nucleotide variations likely endow BoMADS50-1 with strong regulatory activity.Thus,BoMADS50 and BoMADS50-1/2/3/4 are probably important positive flowering regulators in B.oldhamii.Moreover,the functional conservatism and speci ficity of BoMADS50 and BoMADS50-1 might be related to the synchronized and sporadic flowering characteristics of B.oldhamii.

Fine-tuning brassinosteroid biosynthesis via 3′UTR-dependent decay of CPD mRNA modulates wood formation in Populus

Brassinosteroids(BRs)are plant hormones that regulate wood formation in trees.Currently,little is known about the post-transcriptional regulation of BR synthesis.Here,we show that during wood formation,fine-tuning BR synthesis requires 3′UTR-dependent decay of Populus CONSTITUTIVE PHOTOMORPHOGENIC DWARF 1(PdCPD1).Overexpression of PdCPD1 or its 3′UTR fragment resulted in a significant increase of BR levels and inhibited secondary growth.In contrast,transgenic poplars repressing PdCPD13′UTR expression displayed moderate levels of BR and promoted wood formation.We show that the Populus GLYCINE-RICH RNA-BINDING PROTEIN1(PdGRP1)directly binds to a GU-rich element in 3′UTR of Pd CPD1,leading to its mRNA decay.We thus provide a post-transcriptional mechanism underlying BRs synthesis during wood formation,which may be useful for genetic manipulation of wood biomass in trees.

PagGRF12a interacts with PagGIF1b to regulate secondary xylem development through modulating PagXND1a expression in Populus alba×P.glandulosa

Growth-regulating factors(GRFs)are important regulators of plant development and growth,but their possible roles in xylem development in woody plants remain unclear.Here,we report that Populus alba×Papulus glandulosa PagGRF12a negatively regulates xylem development in poplar.PagGRF12a is expressed in vascular tissues.Compared to non-transgenic control plants,transgenic poplar plants overexpressing PagGRF12a exhibited reduced xylem width and plants with repressed expression of PagGRF12a exhibited increased xylem width.Xylem NAC domain 1(XND1)encodes a NAC domain transcription factor that regulates xylem development and transcriptional analyses revealed that PagXND1a is highly upregulated in PagGRF12a-overexpressing plants and downregulated in PagGRF12a-suppressed plants,indicating that PagGRF12a may regulate xylem development through PagXND1a.Transient transcriptional assays and chromatin immunoprecipitation-polymerase chain reaction assays confirmed that PagGRF12a directly upregulates PagXND1a.In addition,PagGRF12a interacts with the GRF-Interacting Factor(GIF)PagGIF1b,and this interaction enhances the effects of PagGRF12a on PagXND1a.Our results indicate that PagGRF12a inhibits xylem development by upregulating the expression of PagXND1a.

Plant Biosystems Design Research Roadmap 1.0

Human life intimately depends on plants for food,biomaterials,health,energy,and a sustainable environment.Various plants have been genetically improved mostly through breeding,along with limited modification via genetic engineering,yet they are still not able to meet the ever-increasing needs,in terms of both quantity and quality,resulting from the rapid increase in world population and expected standards of living.A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches.This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems.Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes.From this perspective,we present a comprehensive roadmap of plant biosystems design covering theories,principles,and technical methods,along with potential applications in basic and applied plant biology research.We highlight current challenges,future opportunities,and research priorities,along with a framework for international collaboration,towards rapid advancement of this emerging interdisciplinary area of research.Finally,we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception,trust,and acceptance.