Ericaceae is a diverse family of flowering plants distributed nearly worldwide, and it includes 126 genera and more than 4,000 species. In the present study, we developed The Ericaceae Genome Resource (TEGR, http://www.tegr.com.cn) as a comprehensive, user-friendly, web-based functional genomic database that is based on 16 published genomes from 16 Ericaceae species. The TEGR database contains information on many important functional genes, including 763 auxin genes, 2,407 flowering genes, 20,432 resistance genes, 617 anthocyanin-related genes, and 470 N⁶-methyladenosine (m⁶A) modification genes. We identified a total of 599,174 specific guide sequences for CRISPR in the TEGR database. The gene duplication events, synteny analysis, and orthologous analysis of the 16 Ericaceae species were performed using the TEGR database. The TEGR database contains 614,821 functional genes annotated through the GO, Nr, Pfam, TrEMBL, and Swiss-Prot databases. The TEGR database provides the Primer Design, Hmmsearch, Synteny, BLAST, and JBrowse tools for helping users perform comprehensive comparative genome analyses. All the high-quality reference genome sequences, genomic features, gene annotations, and bioinformatics results can be downloaded from the TEGR database. In the future, we will continue to improve the TEGR database with the latest data sets when they become available and to provide a useful resource that facilitates comparative genomic studies.

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

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 42 641 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 1 210 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.

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.