Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure

Optimal codons in Tremella fuciformis end in C/G, a strong difference with known Tremella species

Tremella fuciformis is a popular edible fungus with fruiting bodies that can be produced in large quantities at low costs, while it is easy to transform and cultivate as yeast. This makes it an attractive potential bioreactor. Enhanced heterologous gene expression through codon optimization would be useful, but until now codon usage preferences in T. fuciformis remain unknown. To precisely determine the preferred codon usage of T. fuciformis we sequenced the genome of strain Tr26 resulting in a 24.2 Mb draft genome with 10,040 predicted genes. 3288 of the derived predicted proteins matched the UniProtKB/Swiss-Prot databases with 40% or more similarity. Corresponding gene models of this subset were subsequently optimized through repetitive comparison of alternative start codons and selection of best length matching gene models. For experimental confirmation of gene models, 96 random clones from an existing T. fuciformis cDNA library were sequenced, generating 80 complete CDSs. Calculated optimal codons for the 3288 predicted and the 80 cloned CDSs were highly similar, indicating sufficient accuracy of predicted gene models for codon usage analysis. T. fuciformis showed a strong preference for C and then G at the third base pair position of used codons, while average GC content of predicted genes was slightly higher than the total genome sequence average. Most optimal codons ended in C or G except for one, and an increased frequency of C ending codons was observed in genes with higher expression levels. Surprisingly, the preferred codon usage in T. fuciformis strongly differed from T. mesenterica and C. neoformans. Instead, optimal codon usage was similar to more distant related species such as Ustilago maydis and Neurospora crassa. Despite much higher overall sequence homology between T. fuciformis and T. mesenterica, only 7 out of 21 optimal codons were equal, whereas T. fuciformis shared up to 20 out of 21 optimal codons with other species. Clearly, codon usage in Tremella can differ largely and should be estimated for individual species. The precise identification of optimal and high expression related codons is therefore an important step in the development of T. fuciformis as a bioreactor system.

Identification of putative ecdysteroid and juvenile hormone pathway genes in the shrimp Neocaridina denticulata

Although the sesquiterpenoid juvenile hormone (JH) and the steroidal ecdysteroids are of vital importance to the development and reproduction of insects, our understanding of the evolution of these crucial hormonal regulators in other arthropods is limited. To better understand arthropod hormone evolution and regulation, here we describe the hormonal pathway genes (e.g. those involved in hormone biosynthesis, degradation, regulation and signal transduction) of a new decapod model, the shrimp Neocaridina denticulata. The majority of known insect sesquiterpenoid and ecdysteroid pathway genes and their regulators are contained in the N. denticulata genome. In the sesquiterpenoid pathway, these include biosynthetic pathway components: juvenile hormone acid methyltransferase (JHAMT); hormone binding protein: juvenile hormone binding protein (JHBP); and degradation pathway components: juvenile hormone esterase (JHE), juvenile hormone esterase binding protein (JHEBP) and juvenile hormone epoxide hydrolase (JHEH), with the JHBP, JHEBP and JHEH genes being discovered in a crustacean for the first time here. Ecdysteroid biosynthetic pathway genes identified include spook, phantom, disembodied, shadow and CYP18. Potential hormonal regulators and signal transducers such as allatostatins (ASTs), Methoprene-tolerant (Met), Retinoid X receptor (RXR), Ecdysone receptor (EcR), calponin-like protein Chd64, FK509-binding protein (FKBP39), Broad-complex (Br-c), and crustacean hyperglycemic hormone/molt-inhibiting hormone/gonad-inhibiting hormone (CHH/MIH/GIH) genes are all present in the shrimp N. denticulata. To our knowledge, this is the first report of these hormonal pathways and their regulatory genes together in a single decapod, providing a vital resource for further research into development, reproduction, endocrinology and evolution of crustaceans, and arthropods in general.

Analysis of the central nervous system transcriptome of the eastern rock lobster Sagmariasus verreauxi reveals its putative neuropeptidome

Neuropeptides have been discovered in many arthropod species including crustaceans. The nature of their biological function is well studied and varies from behavior modulation to physiological regulation of complex biochemical processes such as metabolism, molt and reproduction. Due to their key role in these fundamental processes, neuropeptides are often targeted for modulating these processes to align with market demands in commercially important species. We generated a comprehensive transcriptome of the eyestalk and brain of one of the few commercially important spiny lobster species in the southern Hemisphere, the Eastern rock lobster Sagmariasus verreauxi and mined it for novel neuropeptide and protein hormone-encoding transcripts. We then characterized the predicted mature hormones to verify their validity based on conserved motifs and features known from previously reported hormones. Overall, 37 transcripts which are predicted to encode mature full-length/partial peptides/proteins were identified, representing 21 peptide/protein families/subfamilies. All transcripts had high similarity to hormones that were previously characterized in other decapod crustacean species or, where absent in crustaceans, in other arthropod species. These included, in addition to other proteins previously described in crustaceans, prohormone-3 and prohormone-4 which were previously identified only in insects. A homolog of the crustacean female sex hormone (CFSH), recently found to be female-specific in brachyuran crabs was found to have the same levels of expression in both male and female eyestalks, suggesting that the CFSH female specificity is not conserved throughout decapod crustaceans. Digital gene expression showed that 24 out of the 37 transcripts presented in this study have significant changes in expression between eyestalk and brain. In some cases a trend of difference between males and females could be seen. Taken together, this study provides a comprehensive neuropeptidome of a commercially important crustacean species with novel peptides and protein hormones identified for the first time in decapods.

Identification, mRNA expression and genomic structure of TLR22 and its association with GCRV susceptibility/resistance in grass carp (Ctenopharyngodon idella)

Toll-like receptor 22 (TLR22) plays a crucial role in response to virus infection by recognizing double stranded RNA (dsRNA) in aquatic animals. In the present study, a TLR22 homologue gene was identified and characterized from grass carp (Ctenopharyngodon idella) (CiTLR22). CiTLR22 genomic sequence comprises 4754 base pairs (bp), containing one intron. The cDNA sequence consists of 3831bp, encoding a protein of 954 amino acid residues. CiTLR22 was constitutively expressed in all 15 investigated tissues, highly in gill and lowly in liver and spleen. The expression profile of CiTLR22 in spleen was rapidly and significantly up-regulated at 6h (456.13-fold, P<0.05), then rapidly recovered to normal level at 12h (P>0.05) post-injection of grass carp reovirus (GCRV). The expression levels of CiTLR22 were rapidly elevated post-poly(I:C) stimulation in dose- and time-dependent manners in CIK (C. idella kidney) cell line. After GCRV infection, CiTLR22 transcripts were inhibited at the early stage, then were up-regulated and reached a peak at 24h post-infection, latterly down-regulated in CIK cell culture. In the whole genomic sequence, six single nucleotide polymorphisms (SNPs) were detected. Five of them were sited in the coding region and all synonymous, and another located in the 5' untranslated region (UTR). The following SNP analysis revealed that 2406 C/T was just a mutation. Only 417 G/T was significantly associated with the resistance of grass carp to GCRV both in genotype (P=0.013) and allele (P=0.015). -8 A/T and 2574 C/T, 863 C/T and 1923 G/T, 863 C/T and 2574 C/T were pairwise linkage disequilibrium. None of the haplotype was associated with the resistance of grass carp to GCRV. The results indicate that CiTLR22 plays an important role in the responses to dsRNA and GCRV, and is partially inhibited by GCRV in vitro. The potential molecular marker lays foundation for the selective breeding of the GCRV-resistant grass carp.