Phylogenetic relationships among Octopodidae species in coastal waters of China inferred from two mitochondrial DNA gene sequences

Octopus in the family Octopodidae (Mollusca: Cephalopoda) has been generally recognized as a "catch-all" genus. The monophyly of octopus species in China's coastal waters has not yet been studied. In this paper, we inferred the phylogeny of 11 octopus species (family Octopodidae) in China's coastal waters using nucleotide sequences of two mitochondrial DNA genes: cytochrome c oxidase subunit I (COI) and 16S rRNA. Sequence analysis of both genes revealed that the 11 species of Octopodidae fell into four distinct groups, which were genetically distant from one another and exhibited identical phylogenetic resolution. The phylogenies indicated strongly that the genus Octopus in China's coastal waters is also not monophyletic, and it is therefore clear that the Octopodidae systematics in this area requires major revision. It is demonstrated that partial sequence information of both the mitochondrial genes 16S rRNA and COI could be used as diagnostic molecular markers in the identification and resolution of the taxonomic ambiguity of Octopodidae species.

Horizontal gene transfer does not occur between sFat-1 transgenic pigs and nontransgenic pigs

We previously generated and characterized synthesized fatty acid desaturase-1 (sFat-1) transgenic pigs that had increased concentrations of ω-3 unsaturated fatty acid in their meat. The objective was to assess whether the inserted foreign gene in sFat-1 transgenic pigs was able to transfer and integrate into the genome of nontransgenic pigs by suckling or mating. Tests for suckling-mediated horizontal gene transfer (HGT) included sFat-1 transgenic sows nursing nontransgenic piglets and sFat-1 transgenic piglets suckling nontransgenic sows. Tests for mating-mediated HGT were performed by male sFat-1 transgenic pigs mated with nontransgenic females and female sFat-1 transgenic pigs mated with nontransgenic males. Polymerase chain reaction was used to detect the sFat-1 gene fragment in various tissues sampled from nontransgenic pigs. The foreign target gene sFat-1 was not detected in the genomic DNA of various tissues and organs sampled from nontransgenic pigs. Therefore, we concluded that HGT from transgenic pigs to wild type pigs via suckling or mating was unlikely.

Expression and SNP association analysis of porcine FBXL4 gene

As a kind of E3 ligase, the product of FBXL4 gene belongs to a member of FBLs which is the biggest eukaryotic subfamily of F-BOX proteins, it can recognize some substrate through particular protein-protein interaction domains. To investigate its functions, the polymorphism and association analysis was analyzed. The partial cDNA of porcine FBXL4 with 2384 bp long was first cloned; the deduced protein comprises a conserved F-BOX domain at position from the 277th to 332nd amino acid. The phylogenetic tree indicated porcine FBXL4 has the closest genetic relationship with bovine FBXL4 than other selected animal species. Ten tissue expression level of porcine FBXL4 mRNA fluctuated remarkably in a large range by quantitative RT-PCR analysis. For two identified SNPs, the genotyping analysis of Tail showed TT genotype owned dominance in introduced Landrace pig and miniature Guizhou and Wuzhishan breeds, but CC genotype was more than two other genotypes in miniature Laiwu breed. While in another genotyping analysis of BsaJI, CC genotype was obviously more than other genotypes in two kinds of Chinese miniature pig breeds and introduced Landrace pig breeds. Furthermore, the association analysis with immune traits and blood parameters revealed that SNP Tail was significantly associated with the lymphocyte percentage (P = 0.0166) and the antibody levels for pseudorabies virus vaccination (P = 0.0001) of neonate piglets at 0 day. Meanwhile, SNP BsaJI was significantly associated with lymphocyte percentage of individuals at 32 days (P = 0.0351), neutrophil percentage (P = 0.0005), the absolute lymphocyte count (P = 0.0458), and the mixed cells (P = 0.0010) of neonate piglets at 0 day.

The chromosomal localization, expression pattern and polymorphism analysis of porcine FSCN1 gene differently expressed from LongSAGE library

Fascin homologue 1 (FSCN1) has established roles in cell adhesion, motility, and cell-cell interactions. Our LongSAGE analysis suggested that FSCN1 was potentially differentially expressed in prenatal pig skeletal muscle. We have cloned the genomic DNA and mRNA sequence of FSCN1 gene and mapped it to SSC3p16-p17. The FSCN1 gene was differently expressed during prenatal skeletal muscle development and exhibited different expression pattern between Tongcheng and Landrace pigs. In Tongcheng pigs, FSCN1 expression was similar at 33 and 65 days post conception (dpc), and then sharply increased to a peak at 90 dpc. In Landrace pigs, however, expression increased between 33 and 65 dpc, peaked at 65 dpc, and was down-regulated thereafter. Significantly different expression levels between Tongcheng and Landrace were observed at 65 and 90 dpc. In postnatal pigs, it was strongly expressed only in the brain, but weakly in skeletal muscle and other tissues. We initially identified 32 SNPs through genomic DNA of FSCN1 gene. Association analysis suggested that the 6840(C/T) mutation was significantly associated with the age at market weight (AGE) (p = 0.0004), average day gain from birth to market (ADG1) (p = 0.0002), and average day gain at testing period (ADG2) (p < 0.0001). Our study suggested that FSCN1 gene plays an in prenatal skeletal muscle development and was a candidate gene for meat production trait.

Partial molecular characterization, expression pattern, polymorphism and association analysis of porcine SKP2 gene

As a component of E3 ubiquitin protein ligases called SCFs, SKP2 protein belongs to a member of FBLs protein which is the biggest eukaryotic subfamily of F-BOX proteins with 12 members. In this study, we cloned and sequenced partial cDNA, intron 1 and intron 6 of porcine SKP2 gene. The partial cDNA is 1,402 bp long and has an open reading frame of 1,272 bp which encodes 424 putative amino acids. The deduced protein comprises a conserved F-BOX domain at position from the 90th to 140th amino acid. The phylogenetic tree indicated that porcine SKP2 has the closest genetic relationship with bovine SKP2 than other selected animal species. Quantitative RT-PCR analysis displayed that the tissue expression level of porcine SKP2 fluctuated remarkably in a large range, and it expressed in thymus with the highest level and in longissimus dorsi muscle with the lowest level. Two SNPs were identified, meanwhile, further polymorphism analysis with Cfr42I showed that AA genotype was in dominance absolutely among four kinds of unrelated Chinese indigenous miniature and one introduced Landrace pig breeds. In addition, association analysis with immune traits and blood parameters revealed that the SNP Cfr42I in intron 1 was significantly associated with red cell distribution width of neonate piglets at 0 day (P = 0.027).