Salix matsudana , a member of Salicaceae , is an important ornamental tree in China. Because of its capability to tolerate high salt conditions, S . matsudana also plays an important ecological role when grown along Chinese coastal beaches, where the salinity content is high. Here, we aimed to elucidate the mechanism of higher salt tolerance in S . matsudana variety ‘9901’ by identifying the associated genes through RNA sequencing and comparing differential gene expression between the S . matsudana salt-tolerant and salt-sensitive samples treated with 150 mM NaCl. Transcriptomic comparison of the roots of the two samples revealed 2174 and 3159 genes responsive to salt stress in salt-sensitive and salt-tolerant sample, respectively. Real-time polymerase chain reaction analysis of 9 of the responsive genes revealed a strong, positive correlation with RNA sequencing data. The genes were enriched in several pathways, including carbon metabolism pathway, plant-pathogen interaction pathway, and plant hormone signal transduction pathway. Differentially expressed genes (DEGs) encoding transcription factors associated with abiotic stress responses and salt stress response network were identified; their expression levels differed between the two samples in response to salt stress. Hub genes were also revealed by weighted gene co-expression network (WGCNA) analysis. For functional analysis of the DEG encoding sedoheptulose-1,7-bisphosphatase (SBPase), the gene was overexpressed in transgenic Arabidopsis , resulting in increased photosynthetic rates, sucrose and starch accumulation, and enhanced salt tolerance. Further functional characterization of other hub DEGs will reveal the molecular mechanism of salt tolerance in S . matsudana and allow the application of S . matsudana in coastal afforestation.

Background Geranylgeranyl pyrophosphate synthase (GGPS) is a structural enzyme of the terpene biosynthesis pathway that is involved in regulating plant photosynthesis, growth and development, but this gene family has not been systematically studied in cotton. Results In the current research, genome-wide identification was performed, and a total of 75 GGPS family members were found in four cotton species, Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii. The GGPS genes were divided into three subgroups by evolutionary analysis. Subcellular localization prediction showed that they were mainly located in chloroplasts and plastids. The closely related GGPS contains a similar gene structure and conserved motif, but some genes are quite different, resulting in functional differentiation. Chromosome location analysis, collinearity and selection pressure analysis showed that many fragment duplication events occurred in GGPS genes. Three-dimensional structure analysis and conservative sequence analysis showed that the members of the GGPS family contained a large number of α-helices and random crimps, and all contained two aspartic acid-rich domains, DDxxxxD and DDxxD (x is an arbitrary amino acid), suggesting its key role in function. Cis-regulatory element analysis showed that cotton GGPS may be involved in light response, abiotic stress and other processes. A GGPS gene was silenced successfully by virus-induced gene silencing (VIGS), and it was found that the chlorophyll content in cotton leaves decreased significantly, suggesting that the gene plays an important role in plant photosynthesis. Conclusions In total, 75 genes were identified in four Gossypium species by a series of bioinformatics analysis. Gene silencing from GGPS members of G. hirsutum revealed that GGPS plays an important regulatory role in photosynthesis. This study provides a theoretical basis for the biological function of GGPS in cotton growth and development.

Background: AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species, including model plants, horticulture plants, crops, and trees. Many AP2/ERF TFs from various species have been functionally characterized. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered a species that can improve the soil salinity of coastal beaches. The recently produced whole genome sequencing data of Salix matsudana allowed us to conduct an evolutionary analysis on the AP2/ERF genes during polyploidization and study the genome-wide expression profiles of AP2/ERF genes in Salix matsudana under salt stress. Results: In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified and renamed according to the chromosomal location of the SmAP2/ERF genes. After phylogenetic analysis with known categories of genes from other species, the AP2/ERF genes were divided into three subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members). Two Soloist genes were also identified. Gene structure and conserved motifs were analyzed in AP2/ERF genes, and introns were not found in most genes of the ERF subfamily, although some unique motifs were found to be important for the function of AP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from other species were also investigated to elucidate their evolutionary relationships during polyploidization. Moreover, analyses on the expression profiles under salt stress were also conducted.Conclusion: The progenitors of Salix matsudana underwent whole genome duplication not more than 10 Mya. Synteny analysis with other species showed macrosynteny between willow and poplar AP2/ERF genes and that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Further investigation of the AP2/ERF TFs demonstrated that differential expression patterns during salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.