Xianggang Gao

The innate immune-related genes in catfish.

Catfish is one of the most important aquaculture species in America (as well as in Asia and Africa). In recent years, the production of catfish has suffered massive financial losses due to pathogen spread and breakouts. Innate immunity plays a crucial role in increasing resistance to pathogenic organisms and has generated increasing interest in the past few years. This review summarizes the current understanding of innate immune-related genes in catfish, including pattern recognition receptors, antimicrobial peptides, complements, lectins, cytokines, transferrin and gene expression profiling using microarrays and next generation sequencing technologies. This review will benefit the understanding of innate immune system in catfish and further efforts in studying the innate immune-related genes in fish.

Low microsatellite variation in spotted seal (Phoca largha) shows a decrease in population size in the Liaodong Gulf colony.

We report the first investigation of nuclear genetic variability in the colony of the spotted seal (Phoca largha) in the Liaodong Gulf, China, where the estimated population size was under 1000 individuals during the study period (2005–2008). A total of 29 microsatellite loci from five pinniped species were employed in 176 spotted seals. Only 15 were polymorphic, with a maximum of 4 alleles detected in samples, with the mean number of alleles per locus being 2.73. Estimates of expected heterozygosity He for the polymorphic loci ranged from 0.24 (± 0.05 SD) to 0.72 (± 0.02 SD), with a mean He per polymorphic locus of 0.51 (± 0.05 SD). No deviation from the Hardy-Weinberg equilibrium was detected for any of the loci. No differences were detected for either genic or genotypic frequencies of seals from the different sampling sites and years. Several statistical methods were applied to detect the population reduction and compare it with that in other seal species. The result indicated that the population of the Liaodong Gulf spotted seal has suffered a decrease in genetic variability and population reduction over the last several decades. The present study supports a notion that a decrease in population size is the main factor accounting for the low levels of variability observed. These research results provide useful data for the conservation and management of the Liaodong Gulf colony.

Characterization of 10 polymorphic microsatellite markers for Mediterranean blue mussel Mytilus galloprovincialis by EST database mining and cross-species amplification

. The lack of sufficient polymorphic molec-ular markers has limited the development of molecularphylogeny, population genetic analysis and marker-assistedbreeding in this species.Among the various currently available DNA markers thatcan be used to examine genetic diversity at the molecularlevel, the most informative and polymorphic are microsatel-lite DNA markers (Liu and Cordes 2004;Li

De novo assembly and characterization of spotted seal Phoca largha transcriptome using Illumina paired-end sequencing

Spotted seal (Phoca largha) is categorized as a critically endangered species in China. The aim of this study was to investigate spotted seal transcriptome by the approach of Illumina paired-end sequencing technology. We obtained a total of 52,146,394 reads for the mixed tissues of liver and spleen from the spotted seal. The de novo assemblies yielded 354,014 contigs and 178,466 unigenes. In the transcriptome, 193 unigenes were assigned to defense mechanisms. Three unigenes encoded MHC class I and 17 unigenes encoded MHC class II. In addition, bioinformatics analysis revealed a total of 4425 simple sequence repeats (SSRs). Fifty SSRs were randomly selected to validate amplification and determine the degree of polymorphism in the genomic DNA pools. Thirty-five primer pairs successfully amplified the expected DNA fragments and detected significant polymorphism among 28 spotted seal individuals. These results would contribute to the understanding of the genetic makeup of spotted seal transcriptome and provide useful information for functional genomic research in this species.

Genetic differentiation between natural and hatchery stocks of Japanese scallop (Mizuhopecten yessoensis) as revealed by AFLP analysis.

Japanese scallop (Mizuhopecten yessoensis) is a cold-tolerant bivalve that was introduced to China for aquaculture in 1982. In this study, amplified fragment length polymorphism (AFLP) markers were used to investigate levels of genetic diversity within M. yessoensis cultured stocks and compare them with wild populations. Six pairs of primer combinations generated 368 loci among 332 individuals, in four cultured and three wild populations. High polymorphism at AFLP markers was found within both cultured and wild M. yessoensis populations. The percentage of polymorphic loci ranged from 61.04% to 72.08%, while the mean heterozygosity ranged from 0.2116 to 0.2596. Compared with wild populations, the four hatchery populations showed significant genetic changes, such as lower expected heterozygosity and percentage of polymorphic loci, and smaller frequency of private alleles, all indicative of a reduction in genetic diversity. Some genetic structures were associated with the geographical distribution of samples; with all samples from Dalian and Japan being closely related, while the population from Russia fell into a distinct clade in the phylogenetic analysis. The genetic information derived from this study indicated that intentional or accidental release of selected Japanese scallops into natural sea areas might result in disturbance of local gene pools and loss of genetic variability. We recommend monitoring the genetic variability of selected hatchery populations to enhance conservation of natural Japanese scallop resources.

RETRACTED: Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers

Next-generation sequencing provides a powerful new approach for developing functional genomic tools for non-model species. This study aims to investigate the spotted seal (Phoca largha) transcriptome by the approach of Illumina paired-end sequencing technology. We obtained a total of 52,146,394 reads for the mixed tissues of liver and spleen from spotted seal. The de novo assemblies yielded 354,014 contigs and 178,466 unigenes. In addition, bioinformatics analysis revealed a total of 4425 simple sequence repeats (SSRs). Fifty SSRs were randomly selected to validate amplification and determine the degree of polymorphism in the genomic DNA pools. Thirty-five primer pairs successfully amplified expected DNA fragments and detected significant polymorphism among 28 spotted seal individuals. These results contribute to the understanding of the genetic makeup of spotted seal transcriptome and provide useful information for functional genomic research in this species.

Sixteen Polymorphic Simple Sequence Repeat Markers from Expressed Sequence Tags of the Chinese Mitten Crab Eriocheir sinensis

The Chinese mitten crab (Eriocheir sinensis) is an economically important aquaculture species in China. In this study, we developed and evaluated simple sequence repeat markers from expressed sequence tags of E. sinensis. Among the 40 wild E. sinensis individuals tested, 16 loci were polymorphic. The number of alleles per locus ranged from two to ten. The observed heterozygosity ranged from 0.0667 to 0.9667, whereas the expected heterozygosity ranged from 0.0661 to 0.9051. These markers have the potential for use in genetic studies of population structure and intraspecific variation in E. sinensis.

Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri).

In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.

Development and characterization of 13 polymorphic microsatellite markers for the Chinese surf clam (Mactra chinensis) through Illumina paired-end sequencing

Chinese surf clam (Mactra chinensis) is a commercially important bivalve in China. The high-throughout transcriptome sequencing of M. chinensis provided a valuable resource for mining large number of microsatellite markers. In this study, we developed and characterized 13 novel polymorphic microsatellite markers for M. chinensis. The number of alleles varied from 4 to 7, with an average of 5.2 per locus. The observed and expected heterozygosity ranged from 0.1667 to 0.7368 and 0.6434 to 0.8056, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. These novel informative microsatellite markers will be useful for further genetic diversity analysis, linkage mapping, evolutionary studies and marker-assisted breeding.

The polymorphisms of chemokine gene in channel catfish (Ictalurus punctatus) and the associations with susceptibility/resistance to Edwardsiella ictaluri

Abstract Chemokines play a crucial role in the recruitment, activation and adhesion of immune effector cells to the foci of infection and injury under both homeostatic and inflammatory conditions. Identification of markers of chemokine