Chromosome-level genomes of three key Allium crops and their trait evolution.

Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.

Effects of dietary supplementation of Gracilaria lemaneiformis-derived sulfated polysaccharides on the growth, antioxidant capacity, and innate immunity of rabbitfish (Siganus canaliculatus).

The dietary supplementation of red seaweed-derived polysaccharides has been shown to be beneficial to fish and shellfish aquaculture. However, the function of red seaweed (Gracilaria lemaneiformis)-extracted polysaccharide (GLP) on the health status of rabbitfish (Siganus canaliculatus) is still unknown. This study explored the influences of GLP on growth performance, antioxidant activity, and immunity of rabbitfish. Herein, the fish were fed commercial pelleted feed incorporated with the diverse amount of GLP: 0 (control), 0.10 (GLP0.10), and 0.15 g kg-1 (GLP0.15) for 60 days. The results demonstrated that dietary GLP0.15 significantly elevated FBW and WG, while feed utilization efficiency improved (reduced feed conversion ratio and increased protein efficiency ratio) upon GLP0.10 treatment, regarding the control (P < 0.05). Also, dietary administration of GLP0.15 suggestively improved the serum acid phosphatase and lysozyme activity as well as hepatic total antioxidant capacity, catalase, and superoxide dismutase activity. In contrast, GLP0.15decreased the serum alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, and malonaldehyde activity when compared to the control (P<0.05). Moreover, the lipase (36.08 and 16.46 U/mgprot in GLP0.10 and GLP0.15, respectively) and amylase (0.43 and 0.23 U/mgprot in GLP0.10 and GLP0.15, respectively) activity recorded the maximum values than the control (8.61 and 0.13 U/mgprot, respectively).Further, the intestinal morphometry was developed (such as increased villus length, width, and area) in the fish fed with a GLP-supplemented diet compared to the control. The KEGG pathway analysis unveiled that several differentially expressed genes (DEGs) in control vs. GLP0.10 and control vs. GLP0.15 were associated with metabolic or immune-associated pathways like antigen processing and presentation, phagosome, complement and coagulation cascades, and platelet activation. The DEGs, namely C3, f5, fgb, MHC1, and cfb, were evaluated in control vs. GLP0.10 and C3 and MHC1 in control vs. GLP0.15, suggesting their possible contributions to GLP-regulated immunity. Additionally, the cumulative mortality of rabbitfish after the Vibrio parahaemolyticus challenge was lower in both GLP0.10 (8.88%) and GLP0.15 (11.11%) than in control (33.33%) (P<0.05). Thus, these findings direct the potential use of GLP as an immunostimulant and growth promoter in rabbitfish aquaculture.

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival.

BACKGROUND: Numerous microorganisms are found in aquaculture ponds, including several pathogenic bacteria. Infection of cultured animals by these pathogens results in diseases and metabolic dysregulation. However, changes in the metabolic profiles that occur at different infection stages in the same ponds and how these metabolic changes can be modulated by exogenous metabolites in Penaeus vannamei remain unknown. RESULTS: Here, we collected gastrointestinal tract (GIT) samples from healthy, diseased, and moribund P. vannamei in the same aquaculture pond for histological, metabolic, and transcriptome profiling. We found that diseased and moribund shrimp with empty GITs and atrophied hepatopancreas were mainly infected with Vibrio parahaemolyticus and Vibrio harveyi. Although significant dysregulation of crucial metabolites and their enzymes were observed in diseased and moribund shrimps, diseased shrimp expressed high levels of taurine and taurine metabolism-related enzymes, while moribund shrimp expressed high levels of hypoxanthine and related metabolism enzymes. Moreover, a strong negative correlation was observed between taurine levels and the relative abundance of V. parahaemolyticus and V. harveyi. Besides, exogenous taurine enhanced shrimp survival against V. parahaemolyticus challenge by increasing the expression of key taurine metabolism enzymes, mainly, cysteine dioxygenase (CDO) and cysteine sulfinic acid decarboxylase (CSD). CONCLUSIONS: Our study revealed that taurine metabolism could be modulated by exogenous supplementation to improve crustacean immune response against pathogenic microbes. Video Abstract.

Effects of prebiotic mixtures on growth performance, intestinal microbiota and immune response in juvenile chu's croaker, Nibea coibor.

Prebiotics has been known to be growth promoter and immunostimulant in aquatic animals. In this study, we investigated the effects of prebiotics on growth performance, intestinal microbiota, short-chain fatty acids (SCFAs) production and immune response of the marine fish, juvenile chu's croaker (Nibea coibor). The fish were fed IG (including 0.5% inulin and 0.5% GOS), GS (0.5% GOS and 0.5% D-sorbitol), IGS (0.33% inulin, 0.33% GOS and 0.33% D-sorbitol) or control diets for 8 weeks. The results showed that the growth performance of the fish was promoted by IG and GS, but not by IGS. The intestinal microbiota in NDC (non-digestible carbohydrates, NDC)-supplemented groups was clearly separated from that of the control, and the highest Shannon and Simpson diversity indices were observed in the IGS group. In the intestine of the croaker, Proteobacteria, Firmicutes, and Bacteroidetes were dominant; among them, 24 taxa revealed a significant difference among groups. Most of these bacteria are able to produce SCFAs, which were significantly increased in all NDC-supplemented groups. Moreover, NDCs were found to activate the immune system of the fish by modulating the serum complements, cytokine levels, lysozyme activities and antioxidant capacity. Furthermore, the results of this study revealed correlations among intestinal microbiota, SCFAs production, innate immunity, antioxidant capacity and digestive enzymes in the croaker fed NDCs. Taken together, our results demonstrated that NDC mixtures might promote growth performance, antioxidant capacity and immune responses of the croaker through modulating the composition of intestinal microbiota and the subsequent SCFAs production, which suggest that NDCs were efficient feed additives for marine fish.

A multi-CRD C-type lectin gene Cnlec-1 enhance the immunity response in noble scallop Chlamys nobilis with higher carotenoids contents through up-regulating under different immunostimulants.

C-type lectins have a variety of immunological functions in invertebrates. In order to investigate whether C-type lectin gene and carotenoids do have immune influences on noble scallop Chlamys nobilis under pathogen stress, acute challenges lasting 48 h to Vibrio parahaemolyticus, lipopolysaccharide (LPS), polyinosinic polycytidylic acid (Poly I: C), and PBS were conducted in noble scallop with different carotenoids content. A multi-CRD C-type lectin gene called Cnlec-1 was cloned and its transcripts under different challenges were determined. Full length cDNA of Cnlec-1 is 2267 bp with an open reading frame (ORF) of 1845 bp encoding 614 deduced amino acids, containing four carbohydrate recognition domains (CRD1, CRD2, CRD3 and CRD4). Phylogenetic tree analysis showed that CRDs of Cnlec-1 were clustered with CRDs of shellfish C-type lectins, especially closely related to Chlamys farreri and Argopecten irradians CRDs. Cnlec-1 transcripts were detected in hemocytes, mantle, gonad, kidney, intestines, gill and adductor. Compared with PBS control group, Cnlec-1 transcripts were up-regulated in V. parahaemolyticus, LPS and Poly I: C groups. Furthermore, Cnlec-1 transcript levels of Golden scallops were significantly higher than that of Brown ones at 3-48 h (P < 0.05) in V. parahemolyticus groups, at 24 h in LPS groups and at 12-24 h in Poly I: C groups. These results suggesting that Cnlec-1 is an important immune factor involved in the defense against pathogens in the noble scallop, and carotenoids can enhance the immunity of noble scallop through up-regulating Cnlec-1 to different immunostimulants.

Identification and characterization of the related immune-enhancing proteins in crab Scylla paramamosain stimulated with rhubarb polysaccharides.

Recently, considerable interest has been focused on immunostimulants to reduce diseases in crab aquaculture. However, information regarding to the related immune-enhancing proteins in crabs is not available yet. In this study, rhubarb polysaccharides were tested for enhancement of the immune activity in crab Scylla paramamosain. Compared with those in the control group, values of, phenoloxidase (PO), alkaline phosphatase (AKP) and alkaline phosphatasein (ACP) activity in the, experimental group were improved significantly 4 d after the treatment. Furthermore, 15 and 17 altered proteins from haemocytes and hepatopancreas, respectively, were found in rhubarb polysaccharide-treated crabs using 2-DE approach. Of these, hemocyanin, chymotrypsin, cryptocyanin, C-type lectin receptor, and ferritin protein were identified by mass spectrometry. In addition, RT-PCR, analysis showed that the mRNA levels of hemocyanin and chymotrypsin increased about 2.4- and 1.4-fold in the experiment group. Moreover, the hemocyanin gene in S. paramamosain (SpHMC) was, cloned and characterized. SpHMC contains one open reading frame of 2022 bp and encodes a polypeptide of 673 amino acids. It is clustered into one branch along with crab hemocyanin in a phylogenetic tree. The mRNA transcripts of SpHMC were detected mainly in the tissues of, hepatopancreas, hemocyte and intestines, and its levels were up-regulated significantly in hemocytes, of S. paramamosain treated with Vibrio parahemolyticus, Beta streptococcus or poly I:C for 6-48 h. Taken together, these studies found 5 related immune-enhancing proteins and a novel heomcyanin homologue with potential pathogen-resistant activities in crab.