Domestic Strains Research Articles

Characterization of complete genome sequences of human coronavirus NL63 strains derived from Chinese patients

Objective To sequence and analyze the complete genome of two human coronavirus NL63 （HCoV-NL63） strains collected from Beijing Children Hospital .Methods Eighteen pairs of primers were designed according to the gene sequences of HCoV-NL63 reference strain （ HCoV-NL63_Amsterdam 1） and used to amplify the target fragments covering the complete genome of HCoV-NL63 strains.Rapid amplification of cDNA ends （ RACE） and RT-PCR assays were used to amplify the full length genome of HCoV-NL63 strains.Phylogenetic analysis was conducted by using Mega 5.0 software.Results The complete genome sequences of the two HCoV-NL63 strains were 27 538 bp in length, showing a homology of 99.1%in nucleotide sequences .There were 15 consecutive bases deleted from 1a region.The systematic phylogenetic analysis demonstrated that four genotypes of NL 63 virus including A , B, C and D have been identified , and two domestic strains were belonged to the new genotype D .Conclusion The complete genome sequences of two domestic HCoV-NL63 isolates were identified for the first time .This study provided evidence for further investigation on molecular epidemiology of HCoV-NL63 in China . Key words: Complete genome sequence; Phylogenetic analysis

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks.

Rivers are fascinating ecosystems in which the eco‐evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta‐analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that—in the studied river systems—stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity–ecosystem function relationships, and the setting of reliable conservation plans.

Genetic parameters for growth and survival traits in a base population of Pacific white shrimp (Litopenaeus vannamei) developed from domesticated strains in China

A base population containing broad genetic variation provides a fundamental resource for a successful genetic improvement program. Here, we assess quantitative data on growth traits taken from the base population of Pacific white shrimp. Body weight was scored at two ages (BW1 and BW2) from 2752 and 2452 individuals, representing 89 full-sib families. Estimated heritabilities (h2 ± SE) for BW1, BW2 and survival (S) were 0.52 ± 0.09, 0.44 ± 0.07, and 0.01 ± 0.02, respectively. The genetic correlation between growth traits (BW1 and BW2) was 0.95, a result significantly different from zero. Genetic correlations between survival and body weight were low however, 0.26 (S vs BW1) and 0.18 (S vs BW2), respectively. The SA_1 strain from South Asia showed the best performance for both growth rate and survival in the test tank systems. High heritability estimates for growth traits confirm that a substantial component of additive genetic variance is available for growth in our L. vannamei culture line families in China prior to imposing genetic selection to improve relative productivity.

Genetic evolution analysis of novel recombinant pseudorabies virus strain in Sichuan, China

Pseudorabies is a disease that seriously endangers the pig industry in China. Recently, we successfully isolated a pseudorabies virus from the brain tissue of piglets at a farm in Sichuan, China, and named it the FJ62 strain. In order to understand the molecular biological characteristics of the strain, primers were designed for glycoproteins gB, gC, gD and gE, which were amplified by a polymerase chain reaction (PCR) and sequenced. After comparing the sequence with the GenBank 22 pseudorabies virus reference strains and establishing the genetic evolutionary tree, it was found that the gB gene of pseudorabies virus was highly homologous (up to 100%) with the MY-1 strain which is isolated from a wild boar in Japan (AP018925) but that homology with other strains in China was low. The gC gene was in the same branch as most of the representative strains in China, with 99.5% homology. The gD gene is in the same branch as the domestic strain LA in China (KU552118), and the homology was 99.9%. The gE gene was in the same branch as the domestic BJ/YT strain in China (KC981239), with 99.9% homology. The results showed that the FJ62 strain of the pseudorabies virus isolated here may be a variant strain of FJ62 isolated from a domestic pig after natural recombination of pseudorabies virus genotype I from wild boar and genotype II from pigs in China. There have been no similar reports in Sichuan. The discovery of the recombinant virus strain provides a reference basis for the prevention and control of pseudorabies and a design strategy for a vaccine in Sichuan, China, in the future.

Japan in 2019

In 2019, Japanese Prime Minister Abe grappled with domestic dilemmas and diplomatic strains, highlighted by inflamed relations with South Korea. The economy continued to grow slowly, the depopulation bomb continued ticking, and demands for gender equality grew louder. The year also brought the enthronement of a new emperor and genesis of a new imperial era.

Life history and genetic characterisation of sea troutSalmo truttain the Adriatic Sea

AbstractThe brown troutSalmo truttais characterised by both anadromous (sea trout) and resident populations, naturally occurring in Atlantic and Ponto‐Caspian rivers. Sea trout are currently considered absent from rivers of the Mediterranean area, probably because of the non‐optimal chemical–physical characteristics of the Mediterranean Sea. However, the occasional bycatch of smoltifiedS. truttain the Adriatic Sea is well known among fishermen and the biological explanation of this phenomenon is still controversial. The aim of this study was to compare the genetic diversity of freshwater and marine brown trout to try to understand the factors underlying the presence of putative anadromous brown trout in the Adriatic Sea.In this study, we analysed the genetic diversity of: (1) wild brown trout collected from the Esino River (central Italy); (2) a domestic strain of brown trout used for stocking the study area; and (3) a sample of Adriatic sea trout collected near the outlet of the Esino River. Together with genetic analysis, we carried out scale analysis in order to track the freshwater/marine stages of the life cycle in the sea trout samples. The genetic characterisation was carried out by polymerase chain reaction–restriction fragment length polymorphism analysis of the mtDNA fragmentND‐5/6and the nuclear locusLDH‐C1*and by genotyping 15 microsatellite loci. The genetic polymorphism obtained was used to investigate intra‐ and inter‐population genetic diversity, rates of genetic introgression between wild and domestic samples and the origin of sea trout specimens by using assignment tests.Our genetic analyses demonstrated that the sea trout analysed in this study are from the domestic strain of Atlantic origin used in central Italy for stocking activities. The level of genetic introgression between native and domestic samples is high in the Esino River. The populations more resilient to introgressive hybridisation appeared to be those living in the portion of the river network dominated by carbonate rocks. Assignment tests (GeneClass) suggest the existence of a link between stocking efforts and the freshwater origin of the sea trout. In addition, data obtained from the analysis of scales, size measurement, and sex determination showed a pattern of smolt age, size, and sex ratio very similar to those observed in other anadromous populations.In conclusion, the present study highlighted that sea trout from the central Adriatic Sea originated from brown trout of Atlantic origin inhabiting the Esino River. Their seaward migratory behaviour could represent a consequence of an active migration instead of a passive displacement by water flow. Our results also showed that traditional stocking practices represent a negative activity for the conservation of the last Mediterranean nativeS. truttapopulations.

Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States

Spillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.

In vitro Propagation of Arbuscular Mycorrhizal Fungi May Drive Fungal Evolution.

Transformed root cultures (TRC) are used to mass produce arbuscular mycorrhizal (AM) fungal propagules in vitro. These propagules are then used in research, agriculture, and ecological restoration. There are many examples from other microbial systems that long-term in vitro propagation leads to domesticated strains that differ genetically and functionally. Here, we discuss potential consequences of in TRC propagation on AM fungal traits, and how this may affect their functionality. We examine weather domestication of AM fungi has already happened and finally, we explore whether it is possible to overcome TRC-induced domestication.

The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented brook charr populations.

Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early- and late-generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2-Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post-hybridization evolutionary outcomes.

Brucella microti-like prevalence in French farms producing frogs.

In the last 10years, many atypical novel members of Brucella species have been reported, including several Brucella inopinata-like strains in wild-caught and "exotic" amphibians from various continents. In 2017, a strain of Brucella was isolated for the first time in animals from a French farm producing frogs-Pelophylax ridibundus-for human consumption and identified as B. microti-like. Following this first isolation, investigations were performed in this farm as well as in the farm of the research unit that provided the domestic frog strain to estimate the prevalence of B. microti-like infection and its presence in the surrounding environment. Farming practices were investigated and samples including frogs at different development stages, surface tank swabs, water, feed and soil were analysed by real-time PCR and bacteriological methods. High B. microti-like prevalence values (higher than 90%) were obtained in frog samples in the commercial farm, and its presence was highlighted in the environmental samples except feed. In the research unit farm, B. microti-like species was also isolated and detected in frog and environmental samples. These results show that B. microti-like organisms are able to colonize amphibians and persist in their environment. Its presence could constitute a possible risk for consumers and workers proving the importance of assessing the zoonotic and pathogenic potentials of these new and atypical Brucella species.

Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese.

Fermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here, we show that during adaptation to cheese, phenotypic and metabolomic traits of wild Penicillium molds rapidly change to produce domesticated phenotypes with properties similar to those of the industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wild Penicillium strains serially passaged on cheese had reduced pigment, spore, and mycotoxin production. Domesticated strains also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g., geosmin) to fatty and cheesy volatiles (e.g., 2-nonanone, 2-undecanone). RNA sequencing demonstrated a significant decrease in expression of 356 genes in domesticated strains, with an enrichment of many secondary metabolite production pathways in these downregulated genes. By manipulating the presence of neighboring microbial species and overall resource availability, we demonstrate that the limited competition and high nutrient availability of the cheese environment promote rapid trait evolution of Penicillium molds.IMPORTANCE Industrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culture Penicillium camemberti can readily lose traits and quickly shift toward producing desirable aroma compounds. In addition to experimentally demonstrating a putative domestication pathway for P. camemberti, our work suggests that wild Penicillium isolates could be rapidly domesticated to produce new flavors and aesthetics in fermented foods.

Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus.

Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes.

Comparison of chemical constituents of wild silkworm cocoon and domestic silkworm cocoon by UHPLC-MS technology

Identifying and comparing the chemical constituents of wild silkworm cocoon and silkworm cocoon is of great significance for understanding the domestication of silkworm. In this study, we used high temperature and high pressure and methanol-water system to extract cocoon chemical constituents. We used UHPLC-MS to identify and compare cocoon chemical constituents of wild silkworm and domestic silkworm Dazao and Haoyue strains. The cocoon metabolic fingerprints of wild silkworm and domestic silkworm Dazao and Haoyue strains were obtained by using the UHPLC-MS in the positive ion mode and negative ion mode. By annotation, we found that cocoon chemical compounds with high abundances contained amino acids, flavonoids, alkaloids, terpenes, organic acids, and lignans. PLS-DA showed that the cocoon components were significantly different among the wild silkworm and two domestic silkworm strains Dazao and Haoyue. Proline, leucine/isoleucine and phenylalanine showed significantly higher abundances in the cocoon of domestic silkworm Dazao strain than in those of wild silkworm and domestic silkworm Haoyue strain. The flavonoid secondary metabolites are abundant in the Dazao cocoon, including quercetin, isoquercetin, quercetin 3-O-sophoroside, quercetin-3-O-α-L-rhamnoside, quercetin-3-O- rutinoside, and kaempferol. The other secondary metabolites, alkaloids, terpenes and lignans, showed higher abundances in the wild silkworm cocoon than in the domestic silkworm cocoon, including neurine, candicine, pilocarpidine, artemisiifolin, eupassopin, and eudesobovatol. By exposing cocoons to UV light and observing the green fluorescence of flavonoids, we found that Dazao cocoon had the most flavonoids, and Haoyue cocoon had least flavonoids and wild silkworm cocoon had mediate flavonoids. Alkaloids and organic acids are good anti-insect and antimicrobial agents, which have high abundance in the wild silkworm cocoon and could enhance the defense ability of wild silkworm cocoon. Flavonoids are abundant in the cocoon of domestic silkworm Dazao strain, which the main factors are leading to the yellow-green cocoon of Dazao.

Biotechnology method of salmon protection against vibriosis

Our country has all potential for development of an aquaculture as one of sectors of agriculture, due to a huge number of fresh water areas and the extended line of the seas. Vibriosis is a bacterial salmon disease, it is one of the reasons of the volumes of the fish which is grown up in a mariculture constraining increase. Modern trends on refusal of use in agriculture of antibiotic drugs, to creation of eco-friendly productions and decrease in economic expenses in fish breeding set a world task of use of biotechnology methods of protection of fishes against infectious diseases, in particular from vibriosis. In the present article results of designing of vaccine from domestic strains of vibrioes are provided. It is shown that immunization of fish antigens of the tested strains of vibrioes (Listonella anguillarum) in an inoculative dose 7x108 m.c. with adjuvant ensures safety of a livestock to 97%, does not cause allergic reactions, the host defense remains not less than 12 months.

Transcriptome Sequencing on Six Agaricus bisporus Strains at Four Developmental Stages

Objective Transcriptome analysis was conducted on Agaricus bisporus at 4 developmental stages to identify the genes associated with and decipher the molecular mechanism involving the fungal development. Method From 6 representative strains of A. bisporus including main cultivar As2796, its parents 02 and 8213, its backcrossing offspring W192, foreign wild strain ARP159, and domestic wild strain AgLH830, at primordium, young, harvesting, and opening stages, 24 fruiting body specimens were collected for transcriptome sequence analysis. By aligning them against the reference genome sequence of A. bisporus, the genes that were differentially expressed were identified. Both unique and common differentially expressed genes (DEGs) were clearly exposed to be annotated using the databases to determine their specific functions. Result Among the 10 660 transcripts obtained, 677 genes were unique with 237 functionally annotated. The tested A. bisporus shared 49 common DEGs between primordium and young stages, 82 between primordium and harvest stages, and 73 between primordium and pileus opening stages. And, 13 genes were found commonly present in the various strains. Conclusion Both unique and common DEGs in A. bisporus at the 4 developmental stages were identified and annotated in the study.

A comparative phylogenomic analysis of peste des petits ruminants virus isolated from wild and unusual hosts.

Peste des petits ruminants virus (PPRV) infects a wide range of domestic and wild ruminants, and occasionally unusual hosts such as camel, cattle and pig. Given their broad host-spectrum and disease endemicity in several developing countries, it is imperative to elucidate the viral evolutionary insights for their dynamic pathobiology and differential host-selection. For this purpose, a dataset of all available (n = 37) PPRV sequences originating from wild and unusual hosts was composed and in silico analysed. Compared to domestic small ruminant strains of same geographical region, phylogenomic and residue analysis of PPRV sequences originating from wild and unusual hosts revealed a close relationship between strains. A lack of obvious difference among the studied sequences and deduced residues suggests that these are the host factors that may play a role in their susceptibility to PPRV infection, immune response, pathogenesis, excretion patterns and potential clinical signs or resistance to clinical disease. Summarizing together, the comparative analysis enhances our understanding towards molecular epidemiology of the PPRV in wild and unusual hosts for appropriate intervention strategies particularly at livestock-wildlife interface.

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

BackgroundThe brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites.ResultsA high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation.ConclusionsThe novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations.

Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast.

Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone–protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding non-client proteins when controlling for their number of protein–protein interactions. We also find that genes encoding client proteins have accumulated more intraspecific genetic diversity than those encoding non-client proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype–phenotype maps, have a considerable accelerating effect on protein evolution.

Evolutionary drivers of kype size in Atlantic salmon (Salmo salar): domestication, age and genetics.

The diversity of reproduction and associated mating patterns in Atlantic salmon (Salmo salar) has long captivated evolutionary biologists. Salmo salar exhibit strategies involving migration, bold mating behaviours and radical morphological and physiological change. One such radical change is the elongation and curvature of the lower jaw in sexually mature males into a hook-like appendage called the kype. The kype is a secondary sexual characteristic used in mating hierarchies and a prime candidate for sexual selection. As one of the core global aquaculture fish species, however, mate choice, and thus sexual selection, has been replaced by industrial artificial fertilization seeking to develop more commercially viable strains. Removal of mate choice provides a unique opportunity to examine the kype over successive generations in the absence of sexual selection. Here we use a large-scale common-garden experiment, incorporating six experimental strains (wild, farmed and wild × farmed hybrids), experiencing one to three sea winters, to assess the impact of age and genetic background. After controlling for allometry, fork length-adjusted kype height (AKH) was significantly reduced in the domesticated strain in comparison to two wild strains. Furthermore, genetic variation at a locus on linkage group SSA1 was associated with kype height, and a locus on linkage group SSA23 was associated with fork length-adjusted kype length (AKL). The reduction in fork length-AKH in domesticated salmon suggests that the kype is of importance in mate choice and that it has decreased due to relaxation of sexual selection. Fork length-AKL showed an increase in domesticated individuals, highlighting that it may not be an important cue in mate choice. These results give us insight into the evolutionary significance of the kype, as well as implications of genetic induced phenotypic change caused by domesticated individuals escaping into the natural environment.

Re-emergence of a genotype VIII virulent Newcastle disease virus isolated from Chinese game fowl after 13years.

Circulation of dominant genotypes VI and VII of Newcastle disease virus (NDV) is causing significant economic losses to the poultry industry in China. However, reports of Newcastle disease (ND) outbreaks caused by genotype VIII strains of NDV are rare. In this study, a virulent genotype VIII strain of NDV, designated GXGB2011, was isolated from a vaccinated game fowl flock showing clinic signs of infection in Pinxiang county, Guangxi, China. The whole genome of the isolate was completely sequenced and was found to be comprised of 15,192 nucleotides (nt), encoding the six structural proteins in the order of 3'-NP-P-M-F-HN-L-5'. The pattern of cleavage site 112 RRQKR↓F117 in the fusion (F) protein and the intracerebral pathogenicity index (ICPI) value of 1.5 showed that the strain GXGB2011 was a velogenic NDV. The results of the challenge experiment with the 5-week-old SPF chickens showed that the strain was highly pathogenic with 100% morbidity and mortality of the challenged birds. Based on the detection of virus in different organs of the infected birds, the highest viral load in caecal tonsils was observed and viral levels in immune organs were higher than those in the respiratory organs. Bayesian reconstruction of complete genomes based on the sequences of 66 NDV reference strains showed that the strain belonged to the genotype VIII of NDV. Phylogenetic analysis showed that the strain was more closely related to the foreign strains gamefowl/U.S.(CA)/24225/98, 1ITTY94060 and IT-147/94 rather than to the first domestic strains of the emergence genotype VIII in Qinghai, China during 1979-1985. In summary, the results of the study demonstrated the re-emergence of a highly pathogenic virulent isolate of genotype VIII of NDV. These results indicate the risk that this genotype VIII of NDV may spread to commercial chickens from game fowl.