Molecular polymorphism and expression of MHC I α, II α, II β and II invariant chain in the critically endangered Dabry's sturgeon (Acipenser dabryanus)

Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys (Rhinopithecus bieti)

Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.

Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analysed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.

Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes)

The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.

Comprehensive transcriptome analysis reveals the effect of feeding rhythm on the immunity and metabolism of Acipenser dabryanus

Acipenser dabryanus is a species endemic to Yangtze River drainage in China and is listed as a critical endangered species on the IUCN Red List. In the present study, the liver and spleen transcriptomes were analyzed by comparing the data of A. dabryanus that experienced nine different feeding rhythms (once a day diurnal, T1; two times a day diurnal, T2; three times a day diurnal, T3; four times a day, T4; five times a day, T5; six times a day, T6; once a day nocturnal, Tn1; two times a day nocturnal, Tn2; and three times a day nocturnal, Tn3). Transcriptome sequencing generated 1,901,236,482 clean reads, encompassing 570.4 Gb of sequence data. The reads were assembled into 287,372 unigenes with an average length of 803 bp and an N50 of 1004 bp. KEGG analysis showed that 1,080, 1,030, and 1216 unigenes were annotated to lipid metabolism, amino acid metabolism and carbohydrate metabolism, respectively, and 2549 unigenes were annotated to the immune system category. Differentially expressed genes (DEGs) between different feeding frequency groups or between nighttime and daytime feeding were obtained and functionally enriched. Importantly, DEGs participating in nutrition metabolism and various immunoregulation pathways and their expression profiles in A. dabryanus were discussed. Interestingly, the majority of key genes related to lipid metabolism or in immunodependent gene families, such as antimicrobial peptides, Toll-like receptors, chemokines, NOD-like receptors, B cell receptors and the major histocompatibility complex, were all significantly upregulated in animals in the T6 group compared to the characteristics of animals in the T2 group that had a normal feeding frequency. In addition, light/dark rhythm also affected the immunity of A. dabryanus, and fish fed at night possessed an improved immune response than fish fed at daytime. Our study suggested that feeding six times a day is optimal for A. dabryanus juvenile growth as it enhances the organism's nutrition metabolism and immune function.

Functional analysis of a novel MHC-Iα genotype in orange-spotted grouper: Effects on Singapore grouper iridovirus (SGIV) replication and apoptosis

The classical major histocompatibility complex class I (MHC-Ⅰ) molecule plays a key role in vertebrate immune response for its important functions in antigen presentation and immune regulation. MHC pathway is closely related to many diseases involving autoimmunity, antigen intrusion and inflammation. However, rare literatures about the effect of MHC-I on fish cells apoptosis were reported. In this study, a novel type of MHC-Ⅰα genotype from orange-spotted grouper (named EcMHC-ⅠA*01) were cloned and characterized. It shared a 77% identity to its Epinephelus coioides MHC-Iα homology that has been uploaded to NCBI (ACZ97571.1). Molecular characterization analysis showed that EcMHC-ⅠA*01 encodes a 357-amino-acid protein, containing a signal peptide，α1，α2，α3, Cytoplasmic (Cyt) and Transmembrane (TM) domains. Tissue expression pattern showed that EcMHC-ⅠA*01 was extensively distributed in twelve selected tissues, with higher expression in the gill, intestine and skin. The expression of EcMHC-ⅠA*01 in grouper liver and spleen tissues were significantly induced by different stimuli (Zymosan A, LPS, Ploy I:C, RGNNV and SGIV). Comparing with the EcMHC-ⅠA*01 expression levels induced by Zymosan A, Ploy I:C and RGNNV, the effects induced by SGIV and LPS were more significant. Subcellular localization analysis showed that EcMHC-ⅠA*01 localizes throughout the cytoplasm appeared both diffuse and focal intracellular expression pattern. Overexpression of EcMHC-ⅠA*01 inhibited the CPE progression, the mRNA expression of the SGIV related genes (MCP, LITAF, ICP-18 and VP19) and the protein expression of MCP. Meanwhile, qRT-PCR result showed that EcMHC-ⅠA*01 overexpression upregulated the expression of interferon signaling molecules (IFN-γ, ISG56, MDA5 and MXI) and inflammatory cytokines (IL-1β, IL-6, TNF-α and TRAF6). In addition, our results showed that overexpression of EcMHC-ⅠA*01 promoted the apoptosis of normal fathead minnow (FHM) cells as well as the apoptosis of FHM cells induced by SGIV. However, there was no significant change in the activity of caspase 3 between control group and EcMHC-ⅠA*01 overexpression group, suggesting that EcMHC-ⅠA*01-induced apoptosis may not depend on the caspase 3 pathway. Taken together, these data in our study provide new insights into the role of MHC-I in antiviral immune response and apoptosis in fish.

Molecular characterization and tissue distribution of cholecystokinin and its receptor in Yangtze sturgeon (Acipenser dabryanus) and their response to different feeding conditions

Yangtze sturgeon (Acipenser dabryanus) is a species endemic to Yangtze River drainage in China and is listed as a critically endangered species on the IUCN Red List. In the present study, cholecystokinin (CCK), one of the most important neuroregulatory digestive genes, and its receptor (CCKr) were identified from the full-length transcriptome analysis of A. dabryanus. The deduced amino acid sequences of CCK and CCKr from A. dabryanus showed structural features common to those in other vertebrates. Gene expression profile analysis showed that CCK and CCKr were universally expressed in different tissues, and both had the highest expression in the brain. Starvation and refeeding significantly regulated the expression levels of CCK and CCKr in the brain, suggesting that CCK and CCKr were involved in feed intake regulation in A. dabryanus as in mammals. In addition, the expression levels of CCK and CCKr under different feeding frequencies were studied. Compared with the control group (fed two times a day), the expression levels of CCK and CCKr in the intestine and brain did not change significantly in the other groups after 8 weeks of rearing, indicating that the feeding frequency might not influence the appetite of A. dabryanus. The present work provides a basis for further investigation into the regulation of feeding in A. dabryanus.

Molecular cloning, characterization and expression analysis of major histocompatibility complex class I alpha gene of pufferfish (Takifugu obscurus)

The major histocompatibility complex (MHC) genes play a key role in immune response in vertebrates. In this study, an MHC I alpha homolog gene (PfMHC Ⅰα) from pufferfish (Takifugu obscurus) was identified and its subcellular localization and expression patterns of PfMHC Ⅰα after challenge in vivo and in vitro were analysed. The open reading frame of PfMHC Ⅰα was 1,089 bp in length, encoding 362 aa. The immunofluorescence result revealed that PfMHC Ⅰα was presented on the membrane of lymphocytes. qRT-PCR analysis indicated that PfMHC Ⅰα was expressed in all examined tissues, with the highest expression in skin, followed by the expression in gills and whole blood. After challenge of Aeromonas hydrophila or polyinosinic: polycytidylic acid (Poly I:C) in vitro, the expression levels of PfMHC Ⅰα on pufferfish kidney lymphocytes were significantly up-regulated, with the highest expression level at 48 hr post-challenge. After infection with A. hydrophila or Poly I:C in vivo, the expression levels of PfMHC Ⅰα in the skin, whole blood and kidneys were significantly up-regulated. Taken together, it is speculated that PfMHC Ⅰα associates with resistance to both intracellular and extracellular antigens and plays an important role in the host response against pathogen infection in pufferfish.

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.

Fate of MHCII in salmonids following 4WGD

Major histocompatibility complex (MHC) genes are key players in the adaptive immunity providing a defense against invading pathogens. Although the basic structures are similar when comparing mammalian and teleost MHC class II (MHCII) molecules, there are also clear-cut differences. Based on structural requirements, the teleosts non-classical MHCII molecules do not comply with a function similar to the human HLA-DM and HLA-DO, i.e., assisting in peptide loading and editing of classical MHCII molecules. We have previously studied the evolution of teleost class II genes identifying various lineages and tracing their phylogenetic occurrence back to ancient ray-finned fishes. We found no syntenic MHCII regions shared between cyprinids, salmonids, and neoteleosts, suggesting regional instabilities. Salmonids have experienced a unique whole genome duplication 94 million years ago, providing them with the opportunity to experiment with gene duplicates. Many salmonid genomes have recently become available, and here we set out to investigate how MHCII has evolved in salmonids using Northern pike as a diploid sister phyla, that split from the salmonid lineage prior to the fourth whole genome duplication (4WGD) event. We identified 120 MHCII genes in pike and salmonids, ranging from 11 to 20 genes per species analyzed where DB-group genes had the most expansions. Comparing the MHC of Northern pike with that of Atlantic salmon and other salmonids species provides a tale of gene loss, translocations, and genome rearrangements.