Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus.

The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

EfGD: the Erianthus fulvus genome database.

Erianthus fulvus (TaxID: 154759) is a valuable germplasm resource in sugarcane breeding and research and has excellent agronomic traits, such as drought resistance, cold resistance, barren tolerance and high brix. With a stable chromosome number (2n = 20) and a small genome (0.9 Gb), it is an ideal candidate for research on sugarcane. Next-generation sequencing technology has enabled a growing number of studies to focus on genomics. Due to the large amount of omics data available, a centralized platform is necessary for ensuring the consistency, independence and maintainability of these large-scale datasets through storage, analysis and integration. Here, we present a comprehensive database for the E. fulvus genome, EfGD. By using the new high-quality reference genome and its annotations, the EfGD provides the largest whole-genome sequencing reference dataset for E. fulvus, which archives 27 165 protein-coding genes and 55 564 488 SNPs from 202 newly resequenced genomes. Furthermore, we created a user-friendly graphical interface for visualizing genomic diversity, population structure and evolution and provided other tools on an open platform. Database URL: https://efgenome.ynau.edu.cn.

Genome-wide identification and expression analysis of the NAC transcription factor family in Saccharum spontaneum under different stresses.

The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The NAC family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the NAC gene family in the wild species Saccharum spontaneum has not been systematically studied. In this study, 115 SsNAC genes were identified in the S. spontaneum genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the SsNAC family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The SsNAC gene has different expression patterns at different developmental stages of stems and leaves. Further qRT-PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 SsNAC genes, indicating that these genes may play a key role in the resistance of S. spontaneum to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the NAC transcription factor family, providing a reference for further functional studies of the SsNAC gene.