A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development

Cornus wilsoniana W.is a woody oil plant with high oil content and strong hypolipidemic effects,making it a valuable species for medicinal,landscaping,and ecological purposes in China.To advance genetic research on this species,we employed PacBio together with Hi-C data to create a draft genome assembly for C.wilsoniana.Based on an 11-chromosome anchored chromosome-level assembly,the estimated genome size was determined to be 843.51 Mb.The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb,respectively.Furthermore,30474 protein-coding genes were annotated.Comparative genomics analysis revealed that C.wilsoniana diverged from its closest species∼12.46 million years ago(Mya).Furthermore,the divergence between Cornaceae and Nyssaceae occurred>62.22 Mya.We also found evidence of whole-genome duplication events and whole-genome triplicationγ,occurring at∼44.90 and 115.86 Mya.We further inferred the origins of chromosomes,which sheds light on the complex evolutionary history of the karyotype of C.wilsoniana.Through transcriptional and metabolic analysis,we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio.We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect f lower morphology in C.wilsoniana.Overall,this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C.wilsoniana.

Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis

The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.