Comprehensive identification and analyses of the Hsf gene family in the whole-genome of three Apiaceae species

Apiaceae is a major family from Apiales and includes many important vegetable and medicinal crops.Heat shock transcription factors(Hsf)play important roles in heat tolerance during plant development.Here,we conducted systematic analyses of the Hsf gene family in three Apiaceae species,including 17 Apium graveolens(celery),32 Coriandrum sativum(coriander),and 14 Daucus carota(carrot).A total of 73 Hsf genes were identified in three representative species,including Arabidopsis thaliana,Vitis vinifera,and Lactuca sativa.Whole-genome duplication played important roles in the Hsf gene family’s expansion within Apiaceae.Interestingly,we found that coriander had more Hsf genes than celery and carrot due to greater expansion and fewer losses.Twenty-seven branches of the phylogenetic tree underwent considerable positive selection in these Apiaceae species.We also explored the expression patterns of Hsf genes in three plant organs.Collectively,this study will serve as a rich gene resource for exploring the molecular mechanisms of heat tolerance.Additionally,this is the first study to report on the Hsf gene family in Apiaceae;thus,our research will provide guidance for future comparative and functional genomic studies on the Hsf gene family and others in Apiaceae.

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Long noncoding RNAs(lncRNAs)are widely present in different species and play critical roles in response to abiotic stresses.However,the functions of lncRNAs in Chinese cabbage under heat stress remain unknown.Here,we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species.The results indicated that lncRNAs were poorly conserved among different species,and only 960 lncRNAs were homologous to 524 miRNA precursors.We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment.In total,18,253 lncRNAs were identified,of which 1229 differentially expressed(DE)lncRNAs were characterized as being heat-responsive.The ceRNA network revealed that 38 lncRNAs,16 miRNAs,and 167 mRNAs were involved in the heat response in Chinese cabbage.Combined analysis of the cis-and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the“protein processing in endoplasmic reticulum”and“plant hormone signal transduction”pathways.Furthermore,the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly.Based on the networks of DE lncRNA-mRNAs,29 and 22 lncRNAs were found to interact with HSP and PYL genes,respectively.Finally,the expression of several critical lncRNAs and their targets was verified by qRT-PCR.Overall,we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage.Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage,and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.