Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress.

BACKGROUND: GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. RESULTS: In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. CONCLUSIONS: These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

[Microbial Community Succession in Industrial Composting with Livestock Manure and Peach Branches and Relations with Environmental Factors].

This study sets out to understand the evolution of the microbial community structure in industrial composting with livestock manure and peach branches. Pig manure, peach branches, and decomposed organic fertilizer were used as materials for composting. Changes in physical and chemical indicators and the evolution in the structure of the compost microbial community, determined by high-throughput sequencing, were analyzed. The results of physical and chemical parameters show that the pile reached the high-temperature stage on day 2, and the thermophilic period lasted for 30 days. The changes in total carbon were volatile, and there was an overall decline in the amount of TOC in the whole process of composting; The final content of TN was 20.58 g·kg-1, which was 5.90% lower compared to the initial compost. Alpha analysis indicated that a different microbial community diversity existed at different times during aerobic composting periods. At the bacterial phyla level, Firmicutes and Actinobacteria were the dominant phyla, and the proportion of relative abundance were 79.31%-95.09% and 2.98%-19.70%, respectively, in the entire compost. The relative abundance of Firmicutes and Actinobacteria were 87.36% and 9.66%, respectively, and their respective relative abundances were 79.38% and 19.70% at the end of composting. At the bacterial genus level, the dominant group changed from Clostridium_sensu_stricto_1, Terrisporobacter, and Bacillus to norank_f_Bacillaceae, Bacillus, Oceanbacillus, and Pseudogracilibacillus; Regarding the fungus phyla, the Ascomycota was the dominant phylum. For the fungus genus, the relative abundance of norank_c_Sordariomycetes gradually increased during composting, and finally was predominant group. The redundancy analysis (RDA) showed that the correlation rank between environmental factors and microbial community structure was:pH > NH4+-N > T > TOC > TN, where pH had the greatest impact on the microbial community composition. norank_c_Sordariomycetes, norank_o_Sordariales, and norank_c_Agaricomycetes may be related to the volatilization of ammonium nitrogen.