Baoying Guo

The draft genome of the large yellow croaker reveals well-developed innate immunity

The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

Identification and comparative analysis of the Pseudosciaena crocea microRNA transcriptome response to poly(I:C) infection using a deep sequencing approach.

Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfromatic analysis identified 534 miRNAs, of which, 158 miRNAs were known in miRBase 20.0 and the remaining 376 were not found homology to any known metazoan miRNAs, suggesting a possible species-specificity. We analyzed the significance of differently expressed miRNAs between two libraries using pairwise comparison. There was significant differential expression of 112 miRNAs (p < 0.001) between two libraries. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR experiments (RT-qPCR) were preformed for 6 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first comprehensive study of miRNAs in P. crocea and of expression analysis of P. crocea miRNAs in response to poly(I:C) infection, and many miRNAs were differentially regulated under normal and infection conditions. These findings deepened our understanding of the role of miRNAs in the intricate hosts immune system, and should be useful to develop new control strategies for host immune defense against various foreign infection in P. crocea.

Molecular characterization and expression analysis of a complement component C3 in large yellow croaker (Larimichthys crocea)

The complement system has been discovered in invertebrates and vertebrates, and plays a crucial role in the innate defense against common pathogens. Complement component 3 is a key molecule in the complement system, whose activation is essential for all the important functions performed by this system. In this study, the complete C3 cDNA sequence was isolated from the large yellow croaker (Larimichthys crocea), which was high similarity to other complement C3. We reported the primary sequence, tissue expression profile, polypeptide domain architecture and phylogenetic analysis of L. crocea complement component C3 (L.c-C3) gene. Its open reading frame (ORF) is 4962 bp and encodes for 1653 amino acids with a putative signal peptide of 23 amino acid residues. The deduced amino acid sequence showed that L.c-C3 has conserved residues and domains known to be crucial for C3 function. Phylogenetic analysis showed that L. crocea was closely related to Miichthys miiuy. The mRNA expressions of L.c-C3 was detectable at different tissues. L.c-C3 was expressed in a wide range of adult tissues, it showed highest expression in the liver. But the different developmental stages from fertilized egg to newborn larvae of the large yellow croaker the highest expression levels of L.c-C3 gene were not found. Bacterial challenge experiments showed that the levels of L.c-C3 mRNA expression were up-regulated in the liver, spleen and brain of adult large yellow croaker respectively. The results showed that L.c-C3 mRNA expression in the large yellow croaker is influenced by bacterial stress and L.c-C3 might play an important role in immunity mechanisms. This study will further increase our understanding of the function of L.c-C3 and molecular mechanism of innate immunity in teleosts.

Characterisation and expression analysis of two terminal complement components: C7 and C9 from large yellow croaker, Larimichthys crocea.

The large yellow croaker Larimichthys crocea, as one of the most economically important marine fish in China and East Asian countries, are facing the fatal attraction of various pathogens in recent years. Elucidation of the organism immunomodulatory mechanism of croaker response to pathogen infection is essential for the disease control. In present study, we reported for the first time the molecular characterization and expression analysis of two terminal complement components (TCCs) of croaker, Lc-C7 and Lc-C9. These two structural conserved TCCs were detected in many tissues in adult healthy fish, with highest levels detected in liver. The transcriptional expression analysis of Lc-C7 and Lc-C9 at different developmental stages showed a continuous increase towards hatch, however the two TCCs mRNA were not detected at the unfertilized stage, hinting the origination of these two TCCs after fertilization. Rapid and drastic responses to Vibrio alginolyticus challenge were observed for Lc-C7 and Lc-C9, suggesting the involvement of component C7 and C9 in innate immune responses to pathogenic invasion in teleost fish. These findings could deepen our understanding about immunomodulatory mechanisms of croaker and shed a new light to the role of component system in teleostean immunomodulation.

Complete mitochondrial genome of Paramisgurnus dabryanus

Abstract In this study, the complete mitochondrial genome of Paramisgurnus dabryanus was obtained by PCR base on 18 pairs of primers. Among the 18 primers, the 14 primers were from the previously published universal primers for Cyprinus carpio L. mitogenome amplification. The remaining 4 primers were designed on the basis of related species mtDNA sequences. The genome is 16,570 bp in length, including 2 ribosomal RNA genes. 13 proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition of Paramisgurnus dabryanus is T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence is a slight A + T bias of 55.8%, which is similar to other fishes. Mitochondrial genome is widely used in phylogenetic analysis, evolutionary genomics, species identification and related research of fish.

Complete mitochondrial genome of the spineless cuttlefish Sepiella inermis (Sepioidea, Sepiidae)

Abstract In this study, we determined the complete mitochondrial genome of the spineless cuttlefish Sepiella inermis. The genome was 16,191 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [both are control regions (CR)]. The composition and order of genes, for the mitogenome found in S. inermis were similar to most other invertebrates. The overall base composition of S. inermis is T 35.6%, C 16.4%, A 40.0% and G 8.0%, with a highly A + T bias of 75.6%. Two control regions contain both termination-associated sequences and conserved sequence blocks. Thus, mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Sepiidae.

Complete mitochondrial genome of the common cuttlefish Sepia pharaonis (Sepioidea, Sepiidae)

Abstract In this study, the complete mitochondrial genome of the common cuttlefish Sepia pharaonis was determined first. The genome was 16,208 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 main non-coding regions [both are control regions (CR)], the gene composition and order of which were similar to most other invertebrates. The overall base composition of S. pharaonis is T: 36.3%, C: 14.7%, A: 40.9% and G: 8.1%, with a hightly A + T bias of 77.2%. Two control regions all contain termination-associated sequences and conserved sequence blocks. This mitogenome sequence data would play an important role in the investigations of the phylogenetic relationships, taxonomic resolution and phylogeography of the Sepiidae.

Complete mitochondrial genome of the needle cuttlefish Sepia aculeata (Sepioidea, Sepiidae)

Abstract In this study, we determined the complete mitochondrial genome of the needle cuttlefish Sepia aculeata. The genome was 16,219 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 main non-coding regions [both are control regions (CR)]. The composition and order of genes, for the mitogenome found in S. aculeate, were similar to most other invertebrates. The overall base composition of S. aculeata is T 34.0%, C 17.0%, A 40.5% and G 8.5%, with a highly A + T bias of 74.5%. Two control regions (CR) both contain termination-associated sequences and conserved sequence blocks. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Sepiidae.

The receptor for activated C kinase 1 (RACK1) mediating immune response in thick shell mussel Mytilus coruscus

ABSTRACT The receptor for activated C kinase 1 (RACK1) is a intracellular receptor for the protein kinase C family which mediates various biological processes. Here, a novel RACK1 gene termed Mc‐RACK1 was identified from thick shell mussel, Mytilus coruscus. Mc‐RACK1 shared typical RACK1 domains containing WD repeats, PKC phosphorylation sites, N‐myristoylation sites, PKC activation sites, TK phosphorylation site and WD motifs. Mc‐RACK1 was constitutively expressed in all examined tissues, and its expression in gills, haemocytes and digestive glands were significantly up‐regulated upon LPS challenge. Mc‐RACK1 showed a significantly down‐regulated expression in gills and haemocytes at the early phase upon copper exposure. Mc‐RACK1 in haemocytes was silenced after receiving its dsRNA, meanwhile, the increases of SOD and CAT activity were investigated. Further, Mc‐RACK1 could activate the NF‐&kgr;B and ISRE reporter in HEK‐293T cells. These suggested that Mc‐RACK1 had a deeper involvement in mollusc immunity, and played an important role in antioxidant system. HighlightsA novel RACK1 gene was firstly identified from Mytilus coruscus.Mc‐RACK1 expression were significantly up‐regulated upon LPS challenge.Mc‐RACK1 expression were down‐regulated at the early phase upon copper exposure.The enhanced activities of SOD and CAT in haemocytes received Mc‐RACK1 dsRNA.Mc‐RACK1 could activate the NF‐&kgr;B and ISRE reporter in HEK‐293T cells.

Complete mitochondrial genome of Abramis brama orientalis Berg (cypriniformes, Cyprinidae, Leuciscinae).

Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Abramis brama orientalis Berg. The genome was 16,610 bp (LR) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to those reported from other fish mitochondrial genomes. The overall base composition of the heavy strand was T 26.7%, C 26.5 %, A 30.0% and G 16.8%, with a slight A + T bias of 56.7%. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Leuciscinae.