Erratum to: Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)

Genome-wide identification of late embryogenesis abundant protein family and their key regulatory network in Pinus tabuliformis cold acclimation

Cold acclimation is a crucial biological process that enables conifers to overwinter safely. The late embryogenesis abundant (LEA) protein family plays a pivotal role in enhancing freezing tolerance during this process. Despite its importance, the identification, molecular functions and regulatory networks of the LEA protein family have not been extensively studied in conifers or gymnosperms. Pinus tabuliformis, a conifer with high ecological and economic values and with high-quality genome sequence, is an ideal candidate for such studies. Here, a total of 104 LEA genes were identified from P. tabuliformis, and we renamed them according to their subfamily group: PtLEA1-PtLEA92 (group LEA1-LEA6), PtSMP1-PtSMP6 (group seed maturation protein) and PtDHN1-PtDHN6 (group Dehydrin). While the sequence structure of P. tabuliformis  LEA genes are conserved, their physicochemical properties exhibit unique characteristics within different subfamily groupings. Notably, the abundance of low-temperature responsive elements in PtLEA genes was observed. Using annual rhythm and temperature gradient transcriptome data, PtLEA22 was identified as a key gene that responds to low-temperature induction while conforming to the annual cycle of cold acclimation. Overexpression of PtLEA22 enhanced Arabidopsis freezing tolerance. Furthermore, several transcription factors potentially co-expressed with PtLEA22 were validated using yeast one-hybrid and dual-luciferase assays, revealing that PtDREB1 could directly bind PtLEA22 promoter to positively regulate its expression. These findings reveal the genome-wide characterization of P. tabuliformis  LEA genes and their importance in the cold acclimation, while providing a theoretical basis for studying the molecular mechanisms of cold acclimation in conifers.

Metabolite and transcriptome analyses revealed the modulation of fructo-oligosaccharide on ileum metabolism of Taiping chickens

AIM

The metabolic markers and differentially expressed genes (DEGs) related to fructo-oligosaccharide (FOS) were screened, and the response of FOS to the ileum metabolic pathway of Taiping chickens was analysed.

METHODS AND RESULTS

Prebiotic are widely used in agricultural breeding for care and maintenance of animal health, especially FOS. Metabonomics evaluation of ileum of Taiping chicken ultra-performance liquid chromatography-quadruple time of-flight high-sensitivity mass spectrometry showed that 93 differentially altered metabolites were identified and divided into eight categories, of which organic acids and derivatives was the most important one. Transcriptomic analysis showed that DEGs were mainly enriched in drug metabolism-cytochrome p450, metabolism of xenobiotics by cytochrome p450, retinol metabolism and fat digestion and absorption. Integrated analysis of metabolite profiles and gene expression revealed that the significantly up-regulated GSTT1 was significantly correlated with most of the different lipid metabolites, suggesting that GSTT1 may play an important role in FOS regulation of lipid metabolism.

CONCLUSIONS

The results of this study suggest that supplementation of FOS can have a positive effect on gut metabolites, which may contribute to the overall health with indigenous chickens.

SIGNIFICANCE AND IMPACT OF THE STUDY

Insight into the responses of intestinal prebiotics of Taiping chicken is helpful to understand the role of prebiotics in maintaining intestinal microflora balance and improving immune response and productivity of poultry from the molecular and metabolic levels.

Response of the ileum transcriptome to probiotic and fructo-oligosaccharides in Taiping chicken

Taiping chicken is indigenous chickens (Gallus gallus domesticus), which was one of China's excellent poultry species, is an excellent chicken in Gansu Province. As the problems caused by the overuse of antibiotics become more and more severe, people begin to look for ways to replace them. Among them, probiotics and fructo-oligosaccharides are the research hotspot to replace antibiotics. Probiotics and fructo-oligosaccharides can promote the absorption of nutrients, improve the ability to resist and prevent diseases, and improve the intestinal tissue morphology. In this study, we used RNA-Seq analysis to study the gene expression in ileum tissue after Taiping chicken was given probiotics and fructo-oligosaccharides. In total, 67 genes were differentially expressed in the ileum. Ten of the differently expressed genes were further validated by RT-qPCR. In addition, these differentially expressed genes were mainly enriched to tyrosine metabolism, AGE-RAGE signaling pathway in diabetic complications, phenylalanine metabolism, and pyrimidine metabolism. The results which this study provides contribute to our understanding application of probiotics and fructo-oligosaccharides in indigenous chickens production and provide a theoretical basis for the genetic development of indigenous chickens.

Response of the ileum transcriptome to fructo-oligosaccharides in Taiping chickens

The aim of this study was to investigate the effects of fructo-oligosaccharide (FOS) supplementation intake of Taiping chickens (Gallus gallus domesticus) and its stimulating effects on ileum. 120 healthy chickens were randomly divided into two groups; control group (CT) and fructo-oligosaccharides group (FOS). At the 60th day of age, ileum mucosa of three chickens per group were collected and performed transcriptome profiling of Taiping chicken ileum mucosa using the Hiseq™ 2500 sequencing platform. Compared with CT group, 50 genes were differentially expressed in the FOS group. Ten of the differently expressed genes were further validated by RT-qPCR. In addition, gene ontology and Kyoto encyclopedia of genes and genomes analyses revealed that these differentially expressed genes were mainly enriched to drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, retinol metabolism, fat digestion and absorption, herpes simplex infection and valine, leucine and isoleucine biosynthesis. The results of this study provided the help to our understanding application of fructo-oligosaccharides in indigenous chicken production and provide a theoretical basis for the genetic development of indigenous chickens.

RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic

Taiping chicken is indigenous chickens (Gallus gallus domesticus), which was one of China's excellent poultry species. As the problems caused by the overuse of antibiotics become more and more concern, people begin to look for ways to replace them. Among them, probiotics and their preparations are the research hotspot to replace antibiotics. Probiotics can promote the absorption of nutrients, improve the ratio of meat to meat, resist and prevent diseases, and improve the intestinal tissue morphology. Here, we performed transcriptome profiling of Taiping chicken ileum which was given probiotics by using the Hiseq™ 2500 sequencing platform. A total of 18 genes were differentially expressed in the ileum under control group and probiotics group. Thirteen genes were upregulated with a range of fold change from 1.02 to 8.61, and 5 were downregulated with a range of fold change from - 1.06 to - 2.29. Ten of the differently expressed genes were further validated by qRT-PCR. In addition, Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these differentially expressed genes were mainly enriched to bile secretion, alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, and arachidonic acid metabolism. This study will help us to understand the role of probiotics in indigenous chicken production and provide theoretical basis for the genetic development of indigenous chickens.