Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development

Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.

Comparative analysis of the TCP gene family in celery,coriander and carrot(family Apiaceae)

Apiaceae is one of the most important families in Apiales and includes many economically important vegetables and medicinal plants.The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1/2(TCP)gene family plays an important role in regulating plant growth and development,but it has not been widely studied in Apiaceae.In the present study,we identified 215 TCP family genes in six species of plant,of which 122 genes were present in three Apiaceae including 29 in celery(Apium graveolens),43 in coriander(Coriandrum sativum),and 50 in carrot(Daucus carota).Whole-genome duplication likely contributed to TCP gene family expansion in Apiaceae.There were more paralogs in carrot than in coriander and celery,which was attributable to the greater number of tandem and proximal duplicated genes on chromosome 1.Nine microRNAs were found to regulate 20 TCP genes in the three Apiaceae species,with miR-319 having the most target genes.Several TCP genes showed high expression in the root,petiole and leaf of celery and coriander.These results provide a basis for comparative and functional genomic analyses of TCP genes in Apiaceae and other plants.

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.

Research progress on biological functions of lncRNAs in major vegetable crops

With the advances in genomics and bioinformatics,particularly the extensive application of high-throughput sequencing technology,a large number of non-coding RNAs(ncRNAs)have been discovered,of which long ncRNAs(lncRNAs)refer to a class of transcripts that are more than 200 nucleotides in length.Accumulating evidence demonstrates that lncRNAs play significant roles in a wide range of biological processes,including regulating plant growth and development as well as modulating biotic and abiotic stress responses.Although the study of lncRNAs has been a hotspot of biological research in recent years,the functional characteristics of plant lncRNAs are still in their initial phase and face great challenges.Here,we summarize the characteristics and screening methods of lncRNAs and highlight their biological functions in major vegetable crops,including tomato,Brassica genus crops,cucumber,pepper,carrot,radish,potato,and spinach,which are implicated in the interaction of lncRNAs and miRNAs.This review enhances the understanding of lncRNAs'roles and can guide crop improvement programs in the future.