Identification, expression and molecular polymorphism of T-cell receptors α and β from the glacial relict Hucho bleekeri

The T-cell receptor (TCR) is a specific molecule on the surface of all T cells that mediates cellular adaptive immune responses to antigens. Hucho bleekeri is a critically endangered species and is regarded as a glacial relict that has the lowest-latitude distribution compared with any Eurasian salmonid. In the present study, two TCR genes, namely, TCR α and β, were identified and characterized in H. bleekeri. Both TCR α and TCR β have typical TCR structures, including the IgV domain, IgC domain, connecting peptide, transmembrane and cytoplasmic domains. The two TCR genes were constitutionally expressed in various tissues, with the highest expression found in the spleen for TCR α and in the trunk kidney for TCR β. Challenge of H. bleekeri with LPS or poly(I:C) resulted in significant upregulation of both TCR α and β expression in headkidney and spleen primary cells, indicating their potential roles in the immune response. Molecular polymorphism analysis of the whole ORF regions of TCR α and β in different individuals revealed high diversity of IgV domains of these two genes, especially in complementarity-determining region (CDR) 3. The ratio of nonsynonymous substitution occurred at a significantly higher frequency than synonymous substitution in the CDR of TCR α and β, demonstrating the existence of positive selection. The results obtained in the present study enhance our understanding of TCR roles in regulating immune mechanisms and provide new information for the study of TCR lineage diversity in fish.

Full-length transcriptome sequencing and identification of immune-related genes in the critically endangered Hucho bleekeri

Hucho bleekeri is a glacial relict and critically endangered fish restricted to the Yangtze River drainage in China. The lack of basic genomic information and immune characteristics will hinder the way toward protecting this species. In the present study, we conducted the first transcriptome analysis of H. bleekeri using the combination of SMRT and Illumina sequencing technology. Transcriptome sequencing generated a total of 93,330 non-redundant full-length unigenes with a mean length of 3072 bp. A total of 92,472 (99.08%) unigenes were annotated in at least one of the Nr protein, Swiss-Prot, KEGG, KOG, GO, Nt and Pfam databases. KEGG analysis showed that a total of 7240 unigenes belonging to 28 immune pathways were annotated to the immune system category. Meanwhile, differentially expressed genes between mucosa-associated tissues (skin, gill and hindgut) and systemic-immune tissues (spleen, head kidney and liver) were obtained. Importantly, genes participating in diverse immune signalling pathways and their expression profiles in H. bleekeri were discussed. In addition, a large number of long non-coding RNAs (lncRNAs) and simple sequence repeats (SSRs) were obtained in the H. bleekeri transcriptome. The present study will provide basic genomic information for H. bleekeri and for further research on analysing the characteristics of both the innate and adaptive immune systems of this critically endangered species.

Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho Bleekeri) using genome-wide SNP markers

Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen with 43 yearling individuals from three locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome-wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (2.6 × 10-3 ± 0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < .001), and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic-relatedness-guided breeding and conservation strategy for wild fish species without pedigree information records.

[Protocol optimization of eDNA analysis workflow for detecting Hucho bleekeri.]

Environmental DNA (eDNA) analysis in water, consisting of water sample collection, DNA extraction and analysis, is increasingly important in detecting rare aquatic species and determining their distribution. Optimization of protocols used in an eDNA molecular workflow is critical to reduce its uncertainty in detecting target species, especially rare species. In this study, 250 mL, 500 mL, 1 L and 2 L water samples were collected by filtering method from a pond for Sichuan taimen (Hucho bleekeri) culture, followed by extraction and purification of eDNA using DNeasy Tissue and Blood DNA extraction kit or MoBio Power Water DNA extraction kit. A PCR procedure was then applied using specific primers from the D-loop region of mtDNA in Sichuan taimen. To explore an appropriate eDNA analysis protocol, the effect of filtering method, sample size and extraction protocols on the detection rate of target gene in water eDNA was studied. The results showed that the target gene was 100% detected from the water sample by using DNeasy Tissue and Blood DNA extraction kit, which was much better that the MoBio Power Water DNA extraction kit with a detection rate of 0%. Larger volume of water samples yielded better PCR products, with 2 L being the most appropriate volume. Sequence alignment results showed that target sequence from the D-loop region of mtDNA in Sichuan taimen was successfully amplified. The results indicated that DNA extracting method and water sample volume could strongly affect the detection rate. The protocol combining filtration, 2 L water sample, DNeasy Tissue and Blood DNA extraction kit was appropriate for eDNA analysis, and mtDNA D-loop region was recommended for detecting DNA of Sichuan taimen from water samples.