Gui Jian-Fang

Genetic basis and breeding application of clonal diversity and dual reproduction modes in polyploid Carassius auratus gibelio

A unisexual species is generally associated with polyploidy, and reproduced by a unisexual reproduction mode, such as gynogenesis, hybridogenesis or parthenogenesis. Compared with other unisexual and polyploid species, gibel carp (Carassius auratus gibelio) has a higher ploidy level of hexaploid. It has undergone several successive rounds of genome polyploidy, and experienced an additional, more recent genome duplication event. More significantly, the dual reproduction modes, including gynogenesis and sexual reproduction, have been demonstrated to coexist in the polyploid gibel carp. This article reviews the genetic basis concerning polyploidy origin, clonal diversity and dual reproduction modes, and outlines the progress in new variety breeding and gene identification involved in the reproduction and early development. The data suggests that gibel carp are under an evolutionary trajectory of diploidization. As a novel evolutionary developmental (Evo-Devo) biology model, this work highlights future perspectives about the functional divergence of duplicated genes and the sexual origin of vertebrate animals.

Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish

Aquaculture has made an enormous contribution to the world food production, especially to the sustainable supply of animal proteins. The utility of diverse reproduction strategies in fish, such as the exploiting use of unisexual gynogenesis, has created a typical case of fish genetic breeding. A number of fish species show substantial sexual dimorphism that is closely linked to multiple economic traits including growth rate and body size, and the efficient development of sex-linked genetic markers and sex control biotechnologies has provided significant approaches to increase the production and value for commercial purposes. Along with the rapid development of genomics and molecular genetic techniques, the genetic basis of sexual dimorphism has been gradually deciphered, and great progress has been made in the mechanisms of fish sex determination and identification of sex-determining genes. This review summarizes the progress to provide some directive and objective thinking for further research in this field.

Virus genomes and virus-host interactions in aquaculture animals

Over the last 30 years, aquaculture has become the fastest growing form of agriculture production in the world, but its development has been hampered by a diverse range of pathogenic viruses. During the last decade, a large number of viruses from aquatic animals have been identified, and more than 100 viral genomes have been sequenced and genetically characterized. These advances are leading to better understanding about antiviral mechanisms and the types of interaction occurring between aquatic viruses and their hosts. Here, based on our research experience of more than 20 years, we review the wealth of genetic and genomic information from studies on a diverse range of aquatic viruses, including iridoviruses, herpesviruses, reoviruses, and rhabdoviruses, and outline some major advances in our understanding of virus-host interactions in animals used in aquaculture.

Scientific frontiers and hot issues in hydrobiology

Fish genetics and fish immunity are two central topics in hydrobiology. As some fish species including zebrafish and medaka are able to use models for genetics, development, immunity, and other life-related fundamental issues, zebrafish and other model fishes have become the leading players in many important findings of life sciences, especially in evolutionary developmental genomics of vertebrates. Along with complete genome analysis of several important fishes and other aquaculture animals, some special and aquaculture-related biological phenomena have been thoroughly resolved from molecular mechanisms for evolutionary adaption, and two modern breeding biotechnologies, such as molecular module-based designer breeding system and genome-wide genotyping-based selective breeding approach, have been developed and applied in aquaculture animals. Additionally, a series of significant breakthroughs in immune mechanisms and protective strategies of aquaculture fishes and animals have promoted the climax coming of developmental and comparative immunology in vertebrates, and provided new technological approaches for disease-resistant breeding and disease control. Altogether, these studies and advances will be the sources for sustainable aquaculture, as fishes and aquatic animals have been believed to be one of the most important sources of animal proteins for human.

斑马鱼 IRF 11基因的鉴定、亚细胞定位及表达特征

早期的研究表明 IRF 11是鱼类特有的IRF家族成员。查询最近解析的斑马鱼第九版基因组时，发现斑马鱼 IRF 1和 IRF 11命名出现了混乱。通过对脊椎动物 IRF 1和 IRF 11基因位点进行同线型分析表明， IRF 11与 IRF 1是两个不同的基因，不宜命名为 IRF1b 和 IRF1a 。系统进化树分析发现，在脊椎动物中 IRF 11基因比 IRF 1起源更早；两栖类以后的脊椎动物基因组只有 IRF 1，没有 IRF 11，其中原因可能是因为基因丢失。斑马鱼 IRF 11与脊椎动物 IRF 1一样，其表达蛋白定位在细胞核中。缺失分析揭示斑马鱼IRF11的DBD有一个能引导蛋白定位进入细胞核的序列。表达分析发现poly（I：C）能诱导斑马鱼 IRF 11的表达，但其表达水平低于 IRF 1。

How do fins and limbs develop and evolve

How do fish fins come into being and how do fins evolve into terrestrial tetrapod limbs? To answer this scientific question is substantially to understand how the genes that determine these traits are subject to natural and sexual selection, and how they thereby involve the innovation mechanics and evolution mechanisms with respect to development. Increasing evidence in recent 10 years suggests that fins might be as single fin-fold in early jawless fish, and then get makeable changes on the evolution roads from jawless fish to jaw fish and tetrapods, in which sequence divergence, expression pattern change, cooperative interaction, and even deletion of some required genes for fin development might play critical roles. The origin of fish fins and tetrapod limbs has been debated for more than three centuries from early natural philosophers and anatomists to modern developmental geneticists. In the recent 10 years, extensive and valuable data have been revealed from a lot of studies on paleontology, comparative anatomy and developmental genetics, and these complementary results have made us to understand the origin and underlying mechanisms behind the formation of the fish fin and tetrapod limb skeletons. It has been certified that fish has evolved to tetrapods and the multiple-basal bones of ancestral fish fins have been reduced to evolve into a single bone of tetrapod limb with fossil records. Similarly, during early embryogenesis, fish fins and tetrapod limbs share similar development mechanism, even though significant differences in histological, developmental and structural patterns exist between them. Many functional genes, such as Hox , And , Gli3 , Hand2 , play key roles in this transition or transformation. Natural selection and sex selection have led to sexual dimorphism of fish fins and morphological differences of tetrapod limbs. Along with the rapid development of genomics, genome editing and biotechnological manipulation techniques, the genetic basis of sexual dimorphism has been explored. Some gene families and signal pathways, such as Tbx gene family, Hox gene family, Ptch1 and its regulation elements, have been identified to involve in the morphological evolution. Significantly, it has been demonstrated that the differential expression of some sex-biased genes and its affected genes which are related with growth and gender differentiation may ultimately lead to sexual dimorphism of the fins. In this article, we have reviewed origin, evolutionary history and development patterns of fins, and elaborated molecule mechanisms on fin-to-limb evolution, sexual dimorphism of fish fins and morphological evolution of limbs. It is expected that a new era is coming for studies on developmental mechanisms and genetic basis of fin origin and fin-to-limb evolution, and some novel sights will be further provided.

EST ANALYSIS AND IMMUNE-RELATED GENE IDENTIFICATION OF GRASS CARP THYMUS IN RESPONSE TO VIRUS INFECTION

The thymus is the primary tissues for production of functional T lymphocytes in vertebrate and is directly involved in defense mechanism. The grass carp ( Ctenopharyngodon idellus) is an integral part of fish culture and forms an important source of protein for human consumption in China. Histological studies showed that grass carp display thymus tissue, which is important for cellular immunity and humoral immunity and similar to mammals, becoming degenerated with fish ages. While the research from molecular level on grass carp thymus is rare. The underlying molecular mechanisms involved in the immune responses of fish thymus are poorly understood and its value as an indicator of immune competence is unknown. In order to obtain more molecular evidence for the physiological function of grass carp thymus, a cDNA library was constructed by using the SMART eDNA synthesis method with mRNAs derived from thymus of grass carp infected with grass carp hemorrhage virus (GCHV), and then EST ( expressed sequence tags) analysis was performed. SMART-prepared cDNA was full-length-enriched and well suitable for generation of cDNA libraries for various applications. Expressed sequence tags ( EST) were an efficient approach to characterize the transcripts of genes expressed in tissues exposed to a given set of environmental conditions. In this study, a total of 1933 ESTs longer than 220bp were yielded and sequenced. BLASTX analysis showed that 583 ESTs represent grass carp genes which were homologous to known genes in mammals (E-value = 30%), while the other 1350 ESTs shared low or no similarity by search of public protein databases in NCBI. Further analyses revealed that these genes, based on the functions of the homologous mammalian genes, could be classified into 6 categories, including immune-related, transcription and translation, metabolism, cell structure, signal transduction, cell proliferation, differentiation and apoptosis. Most of them encode proteins involved in biological processes, cell structure maintaining and immune response. Relatively few teleost genes involved in immune functions have been sequenced, compared to those from higher vertebrates. This study obtained a large number of immune-related genes that had not been previously reported for C. idellus, and which might represent key molecules for the understanding of the immune response to infection in fish thymus. 100 ESTs representing 59 different immune-related genes had been identified from the cDNA library. These genes encoding proteins involved in antigen processing and presentation, cell recognition, adhesion and activation, innate immune and so on. Many of these immune related genes had various immune functions. This study revealed from molecular level that grass carp thymus was the important immune tissue and might play an important role in the immune response to virus infection. In addition, this result also showed that grass carp thymus expressed many novel genes that were functionally unknown so far. Further investigations are needed to determine the function of these genes, as well as their role in the immune response. The generation of a collection of ESTs clones from grass carp thymus will provide the basis for functional genomics studies in this important organ.

MOLECULAR CLONING AND EXPRESSION ANALYSIS OF FRUCTOSE-1,6-BISPHOSPHATASE IN GIBEL CARP

Fructose-1,6-bisphosphatase is one of the key rate-limiting enzymes in gluconeogenesis,which plays important roles in carbohydrate metabolism.Mammals have two isoforms,liver and muscle fructose-1,6-bisphosphatase encoded by Fbp1 and Fbp2 respectively.Gibel carp is widely cultured as an economic fish in China.However,the fructose-1,6-bisphosphatase gene has not been elucidated in teleosts,especially its tissue distribution in adult fish and spatiotemporal expression in embryogenesis.In this study,we cloned the full-length cDNA of gibel carp Fbp1 by RACE polymerase chain reaction from the gastrula embryo SMART cDNA library,and we also examined its expression pattern in the tissues of adult fish and the developmental process of embryos in this fish by gene specific primers.The full length sequence of CagFbp1 consists of 1170 base pairs which encodes 337 amino acids.Multiple alignment and phylogenetic analysis showed that the cloned gene was liver Fbp of gibel carp.The tissue expression pattern analysis by RT-PCR with specific primers showed that CagFbp1 was expressed in the liver,brain,heart,spleen,kidney,intestine,muscle and ovary,and the expression in the liver was obviously higher than others.At the same times,there were two protein bands in liver by western blot analysis,one was common in the detected tissue except muscle,and the other was specific for liver.However,only one band emerged in the muscle,which was specific for muscle tissues.Mature eggs and ontogenic analysis by RT-PCR and western blotting with specific primers showed that both the transcripts and proteins of CagFbp1 were maternal.The transcripts were increased from gastrula and reached a higher level in neurula till hatching.Interestingly,there was a new band with smaller molecular weight other than the maternal proteins after tail bud stage,which was similar to the liver specific band.These results indicated that the fructose-1,6-bisphosphatase gene cloned in gibel carp was liver isoform,and there might be at least two isoenzymes,the liver fructose-1,6-bisphosphatase and muscle one in teleost.