Chromosome Genome Assembly of Cromileptes altivelis Reveals Loss of Genome Fragment in Cromileptes Compared with Epinephelus Species

The humpback grouper (Cromileptes altivelis), an Epinephelidae species, is patchily distributed in the reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rate compared with closely related grouper species. For promoting further research of the grouper, in the present study, a high-quality chromosome-level genome of humpback grouper was assembled using PacBio sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The assembled genome was 1.013 Gb in size with 283 contigs, of which, a total of 143 contigs with 1.011 Gb in size were correctly anchored into 24 chromosomes. Moreover, a total of 26,037 protein-coding genes were predicted, of them, 25,243 (96.95%) genes could be functionally annotated. The high-quality chromosome-level genome assembly will provide pivotal genomic information for future research of the speciation, evolution and molecular-assisted breeding in humpback groupers. In addition, phylogenetic analysis based on shared single-copy orthologues of the grouper species showed that the humpback grouper is included in the Epinephelus genus and clustered with the giant grouper in one clade with a divergence time of 9.86 Myr. In addition, based on the results of collinearity analysis, a gap in chromosome 6 of the humpback grouper was detected; the missed genes were mainly associated with immunity, substance metabolism and the MAPK signal pathway. The loss of the parts of genes involved in these biological processes might affect the disease resistance, stress tolerance and growth traits in humpback groupers. The present research will provide new insight into the evolution and origin of the humpback grouper.

Screening of Salt Stress Responsive Genes in Brachypodium distachyon (L.) Beauv. by Transcriptome Analysis

As one of the most common abiotic stresses, salt stress seriously impairs crop yield. Brachypodium distachyon (L.) Beauv. is a model species for studying wheat and other grasses. In the present investigation, the physiological responses of B. distachyon treated with different concentrations of NaCl for 24 h were measured. Therefore, the control and the seedlings of B. distachyon treated with 200 mM NaCl for 24 h were selected for transcriptome analysis. Transcriptome differential analysis showed that a total of 4116 differentially expressed genes (DEGs) were recognized, including 3120 upregulated and 996 downregulated ones. GO enrichment assay indicated that some subsets of genes related to the active oxygen scavenging system, osmoregulatory substance metabolism, and abscisic-acid (ABA)-induced stomatal closure were significantly upregulated under salt stress. The MapMan analysis revealed that the upregulated genes were dramatically enriched in wax metabolic pathways. The expressions of transcription factor (TF) family members such as MYB, bHLH, and AP2/ERF were increased under salt stress, regulating the response of plants to salt stress. Collectively, these findings provided valuable insights into the mechanisms underlying the responses of grass crops to salt stress.

Breed Differences in the Expression Levels of gga-miR-222a in Laying Hens Influenced H2S Production by Regulating Methionine Synthase Genes in Gut Bacteria

Background: The microbiota in the cecum of laying hens is critical for substance metabolism and odor gas production. Recent studies have suggested that host miRNAs can regulate gene expression in the gut microbiota. The expression profiles of host-derived miRNAs in the cecal content of two laying hen breeds, Hy-line Gray and Lohmann Pink, which have dissimilar H2S production, were characterized, and their possible effects on H2S production by regulating the expression of related genes in the microbiota were demonstrated. Results: The differential expression of microbial serine O-acetyltransferase, methionine synthase, aspartate aminotransferase, methionine-gamma-lyase and adenylylsulfate kinase between the two breeds resulted in lower H2S production in the Hy-line hens. The results also demonstrated miRNA microvesicles in the cecal content of laying hens and found potential miRNA-target relationships between 9 differentially expressed miRNAs and 9 differentially expressed microbial genes related to H2S production, among which gga-miR-222a targeted two methionine synthase genes, Odosp_3416 and BF9343_2953. An in vitro fermentation experiment showed that gga-miR-222a upregulated the expression of these genes, which increased methionine concentrations but decreased H2S production and soluble sulfide concentrations, indicating the potential of host-derived gga-miR-222a to reduce H2S emission in laying hens. Conclusion: These findings identify both a physiologic role by which miRNA shapes the cecal microbiota of laying hens and a strategy to use host miRNAs to manipulate the microbiome and actively expressed key microbial genes to reduce H2S emission and breed environmentally friendly laying hens.

SPECTRAL PROPERTIES OF LIGHT CONDUCTED IN STEMS OF WOODY PLANTS SHOW MARKED SEASONAL DIFFERENCES SUGGESTING A CLOSE RELATIONSHIP WITH PHOTOMORPHOGENESIS

Optical properties of stems in woody plants were investigated in the winter–spring period, and compared with those in the summer–autumn period. In both periods light could enter the interior of the stems and was conducted efficiently along the axial direction. Vessels, fibers and tracheids were all involved in this axial light conduction. However, spectral properties of the light conducted by stems differed in different periods. The light conducted in stems of the winter–spring period showed higher relative intensity ratios at wavelengths around 825 nm and 920 nm than that in stems of the summer–autumn period. Furthermore, in the winter– spring period, stems of deciduous species conducted light at a wavelength around 825 nm at a higher relative intensity ratio than those of evergreen species. These seasonal variations and inter-specific differences in spectral properties of woody stems suggest a close relationship with rhythms of growth, substance metabolism and photomorphogenesis in plants.