Baoming Ge

Characterization of immune-related genes in the yellow catfish Pelteobagrus fulvidraco in response to LPS challenge

Fish are considered an excellent model for studies in comparative immunology as they are a representative population of lower vertebrates linked to invertebrate evolution. To gain a better understanding of the immune response in fish, we constructed a subtractive cDNA library from the head kidney of lipopolysaccharide-stimulated yellow catfish (Pelteobagrus fulvidraco) using suppression subtractive hybridization (SSH). A total of 300 putative EST clones were identified which contained 95 genes, including 27 immune-related genes, 7 cytoskeleton-related genes, 3 genes involved in the cell cycle and apoptosis, 9 respiration and energy metabolism-related genes, 7 genes related to transport, 24 metabolism-related genes, 10 genes involved in stress responses, seven genes involved in regulation of transcription and translation and 59 unknown genes. Using real-time quantitative reverse transcription PCR, a subset of randomly selected genes involved in the immune response to lipopolysaccharide challenge were investigated to verify the reliability of the SSH data which identified 16 up-regulated genes. The genes identified in this study provide novel insight into the immune response in fish.

The complete mitochondrial genome of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae)

Abstract The complete mitochondrial genome (mitogenome) of Tribolium castaneum (Coleoptera: Tenebrionidae) was determined to be 15,883 bp (GenBank accession No. KM009121), which contains 22 tRNA genes, 13 protein-coding genes (PCGs), 2 rRNA genes and a major non-coding A + T-rich region. It has the typical gene organization and order of mitogenomes from ancestral insects. The nucleotide composition was also biased toward A + T nucleotides (71.72%) and the AT skew of this mitogenome was slightly positive. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by AAT. Eight of the 13 PCGs harbor the incomplete termination codon by T or TA. The A + T-rich region of the mitogenome was 1237 bp in length and the A + T content was 82.30%.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp (Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

A small heat shock protein 21 (sHSP21) mediates immune responses in Chinese oak silkworm Antheraea pernyi

Small heat shock proteins (sHSPs) are conserved among insects and play an important role in the regulation of many biological processes, including temperature stress, abiotic stress, immune responses, metamorphosis, and embryo development. Antheraea pernyi is an economically valuable silk-producing moth and source of insect food containing high-quality protein. The aim of this study was to quantify expression of the ApsHSP21 gene in response to pathogen-associated molecular patterns (PAMPs) and nucleopolyhedrovirus (NPV) challenge. The deduced ApsHSP21 protein sequence consists of 186 residues with a calculated molecular mass of 21.0 kDa and an isoelectronic point (pI) of 6.63. The protein contains a conserved α-crystallin domain (ACD), and includes two casein kinase II phosphorylation sites, a protein kinase C phosphorylation site, two tyrosine kinase phosphorylation sites, and various polypeptide binding sites. Phylogenetic analysis revealed that ApsHSP21 is closely related to homologs from other insects. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis revealed that expression of ApsHSP21 was significantly up-regulated at different timepoints following simulated pathogen challenge with lipopolysaccharide (LPS), peptidoglycan (PGN), glucan, and NPV. The results suggest sHSP21 is involved in innate immune responses in A. pernyi.

Development and characterization of microsatellite loci of Oratosquilla oratoria (Crustacea: Squillidae)

Oratosquilla oratoria (Crustacea: Squillidae) is the most dominant species in the indo-pacific ocean, which has been regarded as the marine lives for its good taste and rich nutrition in fishery. In the current study, eleven polymorphic microsatellite loci were isolated from total genome of O. oratoria, and tested their polymorphism in 30 individuals collected from the sea areas of the indo-pacific ocean in Huludao, Qingdao and Yantai. The numbers of observed alleles were from two to eleven. Moreover, the observed heterozygosity from 0.278 to 0.734 was comparable to the expected heterozygosity from 0.555 to 0.776. The microsatellite markers obtained in this study were suitable for further assessing the genetic diversity and population structure of O. oratoria.

Comparative transcriptome analysis of Eriocheir japonica sinensis response to environmental salinity

Chinese mitten crabs (Eriocheir japonica sinensis) are catadromous, spending most of their lives in fresh water, but moving to a mixed salt-fresh water environment for reproduction. The characteristics of this life history might imply a rapidly evolutionary transition model for adaptation to marine from freshwater habitats. In this study, transcriptome-wide identification and differential expression on Chinese mitten crab groups were analysed. Results showed: clean reads that were obtained totalled 93,833,096 (47,440,998 in Group EF, the reference, and 46,392,098 in Group ES, the experimental) and 14.08G (7.12G in Group EF 6.96G in Group ES); there were 11,667 unigenes (15.29%) annotated, and they were located to 230 known KEGG pathways in five major categories; in differential expression analysis, most of the top 20 up-regulated pathways were connected to the immune system, disease, and signal transduction, while most of the top 20 down-regulated pathways were related to the metabolism system; meanwhile, 8 representative osmoregulation-related genes (14-3-3 epsilon, Cu2+ transport ATPase, Na+/K+ ATPase, Ca2+ transporting ATPase, V-ATPase subunit A, Putative arsenite-translocating ATPase, and Cation transport ATPase, Na+/K+ symporter) showed up-regulation, and 1 osmoregulation-related gene (V-ATPase subunit H) showed down-regulation. V-ATPase subunit H was very sensitive to the transition of habitats. These results were consistent with the tests of qRT-PCR. The present study has provided a foundation to further understand the molecular mechanism in response to salinity changing in water.

Molecular evolution of mitochondrial coding genes in the oxidative phosphorylation pathway in malacostraca: purifying selection or accelerated evolution?

Abstract The mitochondrion is the energy-producing factory of eukaryotic cells, in which oxidative phosphorylation (OXPHOS) is the main pathway for the production of adenosine triphosphate (ATP) by cellular respiration. Because of their vital role in metabolism, mitochondrial proteins are predicted to evolve primarily under constant purifying selection. However, all mitochondrial coding genes of malacostraca had a significantly higher synonymous nt divergence (Ks) in this study. Complex I (NADH dehydrogenase) and complex V (ATP synthase) had a much higher ratio of non-synonymous to synonymous nt divergence (Ka/Ks) and non-synonymous diversity (πNS), whereas complex III (cytochrome bc1 complex) and complex IV (cytochrome c oxidase) had a significantly lower Ka/Ks and non-synonymous diversity (πNS). The Ka/Ks, πNS, πS, and Ka results revealed that two types of mitochondrial genes, NADH dehydrogenase and ATP synthase, in malacostraca were consistent with accelerated evolution. Furthermore, two other types of mitochondrial genes, cytochrome bc1 complex and cytochrome c oxidase, were consistent with purifying selection. Generally, the evolutionary pattern of all mitochondrial proteins of the OXPHOS pathway in malacostraca was not entirely consistent with purifying selection.