Diversified Phenotypes Research Articles

DNA barcoding, identification, and validation of the pufferfish (Order: Tetraodontiformes) in China coastal waters.

The order Tetraodontiformes are one of the most unique groups of teleostean fish, exhibiting highly derived and greatly diversified phenotypes. It is a difficult task for both professionals and nonprofessionals to accurately identify these species only according to morphological characteristics. DNA barcoding can identify species at the molecular level to overcome the limitations of morphological classification. In this study, we collected 616 specimens of pufferfish from the coastal waters of China. According to the morphological characteristics, they were preliminarily identified as 50 species. Further analysis using DNA barcodes identified these specimens as 46 species, belonging to 23 genera, 6 families. According to the species classification results of DNA barcoding, the three species identified by morphology as Takifugu pseudommus, Takifugu chinensis, and Takifugu rubripes should be the same species. Similarly, Lagocephalus wheeleri is the synonym of Lagocephalus spadiceus. Another important discovery of DNA barcoding analysis is that there are closer interspecific genetic distances within the genus Takifugu. If T. rubripes, T. pseudommus, and T. chinensis are taken as one species, the average interspecific to intraspecific genetic distance ratio of Takifugu is only 6.21 times, which does not reach the DNA barcoding threshold of more than 10 times proposed previously. Although the interspecific genetic distance in the genus Takifugu is relatively small, each species can be clustered into independent clades in the NJ tree. In conclusion, this study not only found that there are synonymous phenomena in the order Tetraodontiformes but also provided molecular evidence for the valid species names of Takifugu rubripes and Lagocephalus Spadiceus. The results can provide reliable DNA barcoding information for the identification of pufferfish species, help solve the problem of classification confusion in this order, and provide technical support for the identification of the original components of related commodities on the aquatic product market.

Asymmetric and uncertain interactions within mutualisms

Abstract Although understanding mutualism stability has advanced over the last few decades, two fundamental problems still remain in explaining how mutualisms maintain stable. (i) How does resolve conflict between mutualists over resources? (ii) In the presence of less cooperative and/or uncooperative symbionts, how does prevent symbiont populations from becoming dominated by uncooperative individuals? Many past explanations of mutualism stability have assumed that interactions between mutualists are symmetrical. However, in most mutualisms, interactions between hosts and symbionts show varying degrees of asymmetry at different levels. Here, we review three major types of asymmetric interactions within obligate mutualisms: (i) asymmetric payoffs, which is also defined as individual power differences, (ii) asymmetric potential rates of evolutionary change, and (iii) asymmetric information states between hosts and symbionts. We suggest that these asymmetries between mutualists help explain why cooperation and conflict are inherent in the evolution of mutualisms, and why both hosts and symbionts present diversified phenotypes while cooperation predominates.

Copy number variants impact phenotype-genotype relationships for adaptation of industrial yeast Saccharomyces cerevisiae.

The industrial yeast Saccharomyces cerevisiae possesses a plastic genome enabling its adaptation to varied environment conditions. A more robust ethanologenic industrial yeast strain NRRL Y-50049 was obtained through laboratory adaptation that is resistant to 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF), a major class of toxic chemicals associated with lignocellulose-to-biofuel conversion. A significant amount of knowledge has been achieved in characterizing its tolerant phenotypes and molecular mechanisms of the resistance. Recent findings on a limited number of nonsynonymous SNP (single nucleotide polymorphism) detected in NRRL Y-50049 compared with its progenitor NRRL Y-12632 raised doubt of SNP roles in the tolerance adaptation. The genotype-phenotype relationship for yeast adaptation to the toxic chemicals is yet unclear. Here, we examine copy number variant (CNV) of the adapted strain NRRL Y-50049 to address phenotype-genotype relationships. As a background information, CNV of model strain S288C of the reference genome was also examined versus the industrial-type strain NRRL Y-12632. More than 200 CNVs, mostly duplication events, were detected in NRRL Y-12632 compared with the laboratory model strain S288C. Such enriched genetic background supports its more diversified phenotype response for the industrial yeastthan the laboratory strainS288C. Comparing the two industrial strains, we found extra nine CNVs in the mitochondrial genome and 28 CNVs in the nuclear genome of NRRL Y-50049 versus its progenitor NRRL Y-12632. Continued DNA recombination event and high rate of CNV observed in NRRL Y-50049 versus its progenitor suggests that CNV is more impactful than SNP in association with phenotype-genotype relationships of yeast adaptation to the toxic chemical stress. COX1 and COB loci were defined as DNA recombination hotspots in the mitochondrial genome for the industrial yeast based on the high frequency of CNVs observed in these loci. KEY POINTS: • COX1 and COB loci are identified as DNA recombination hotspots for the industrial yeast. • The industrial yeast type strain NRRL Y-12632 possesses more CNVs vs the reference genome S288C. • CNV is more important than SNP on phenotype-genotype relationships for yeast adaptation.

Role of Epigenetics in the Pathogenesis, Treatment, Prediction, and Cellular Transformation of Asthma.

Asthma is a mysterious disease with heterogeneity in etiology, pathogenesis, and clinical phenotypes. Although ongoing studies have provided a better understanding of asthma, its natural history, progression, pathogenesis, diversified phenotypes, and even the exact epigenetic linkage between childhood asthma and adult-onset/old age asthma remain elusive in many aspects. Asthma heritability has been established through genetic studies, but genetics is not the only influencing factor in asthma. The increasing incidence and some unsolved queries suggest that there may be other elements related to asthma heredity. Epigenetic mechanisms link genetic and environmental factors with developmental trajectories in asthma. This review provides an overview of asthma epigenetics and its components, including several epigenetic studies on asthma, and discusses the epigenetic linkage between childhood asthma and adult-onset/old age asthma. Studies involving asthma epigenetics present valuable novel approaches to solve issues related to asthma. Asthma epigenetic research guides us towards gene therapy and personalized T cell therapy, directs the discovery of new therapeutic agents, predicts long-term outcomes in severe cases, and is also involved in the cellular transformation of childhood asthma to adult-onset/old age asthma.

The Genetic Basis of Morphological Diversity in Domesticated Goldfish

Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.

Diversified phenotype of antigen specific CD8+ T cells responding to the immunodominant epitopes of IE and pp65 antigens of human cytomegalovirus

To study the cytomegalovirus (CMV)-specific CD8+ T cells in individuals with HLA A∗1101, A∗0201 and A∗2402, our findings showed that peptide SK-10-2, KI-10 and KV-10 of CMV IE and pp65 antigens were immunodominant in 198 individuals with HLA A∗1101, A∗0201 and A∗2402, the most frequent genotypes in Chinese. Interestingly, SK-10-2 induced the strongest T cell response to produce IFN-γ whereas the others did not induce prominent IFN-γ production despite they all induced remarkable T cell proliferation. The peptides induced different phenotypes including IFN-γhighTNF-αlow and TNF-αlowFoxp3low. It suggests that only some of CMV-reactive CD8+ T cells are real protective IFN-γhigh cytotoxic T cells.

Molecular Polymorphism and Phenotypic Diversity in the Eutypa Dieback Pathogen Eutypa lata.

Pathogen adaptation to different hosts can lead to specialization and, when coupled with reproductive isolation, genome-wide differentiation and ecological speciation. We tested the hypothesis of host specialization among California populations of Eutypa lata (causal fungus of Eutypa dieback of grapevine and apricot), which is reported from >90 species. Genetic analyses of nine microsatellite loci in 182 isolates from three hosts (grapevine, apricot, and willow) at three locations were complemented by cross-inoculations on cultivated hosts grapevine and apricot to reveal patterns of host specialization. The cultivated hosts are likely more important sources of inoculum than the wild host willow, based on our findings of higher pathogen prevalence and allelic richness in grapevine and apricot. High levels of gene flow among all three hosts and locations, and no grouping by clustering analyses, suggest neither host nor geographic differentiation. Cross-inoculations revealed diversified phenotypes harboring various performance levels in grapevine and apricot, with no apparent correlation with their host of origin. Such phenotypic diversity may enable this pathogen to persist and reproduce as a generalist. Regular genetic reshuffling through sexual recombination, frequent immigration among hosts, and the lack of habitat choice in this passively dispersed fungus may prevent fixation of alleles controlling host specialization.

Mosaic physiology from developmental noise: within-organism physiological diversity as an alternative to phenotypic plasticity and phenotypic flexibility

A key problem in organismal biology is to explain the origins of functional diversity. In the context of organismal biology, functional diversity describes the set of phenotypes, across scales of biological organization and through time, that a single genotype, or genome, or organism, can produce. Functional diversity encompasses many phenomena: differences in cell types within organisms; physiological and morphological differences among tissues and organs; differences in performance; morphological shifts in external phenotype; and changes in behavior. How can single genomes produce so many different phenotypes? Modern biology proposes two general mechanisms. The first is developmental programs, by which single cells and their single genomes diversify, via relatively deterministic processes, into the sets of cell types, tissues and organs that we see in most multicellular organisms. The second general mechanism is phenotypic modification stemming from interactions between organisms and their environments - modifications known either as phenotypic plasticity or as phenotypic flexibility, depending on the time scale of the response and the degree of reversibility. These two diversity-generating mechanisms are related because phenotypic modifications may sometimes arise as a consequence of environments influencing developmental programs. Here, I propose that functional diversity also arises via a third fundamental mechanism: stochastic developmental events giving rise to mosaics of physiological diversity within individual organisms. In biological systems, stochasticity stems from the inherently random actions of small numbers of molecules interacting with one another. Although stochastic effects occur in many biological contexts, available evidence suggests that they can be especially important in gene networks, specifically as a consequence of low transcript numbers in individual cells. I briefly review known mechanisms by which organisms control such stochasticity, and how they may use it to create adaptive functional diversity. I then fold this idea into modern thinking on phenotypic plasticity and flexibility, proposing that multicellular organisms exhibit 'mosaic physiology'. Mosaic physiology refers to sets of diversified phenotypes, within individual organisms, that carry out related functions at the same time, but that are distributed in space. Mosaic physiology arises from stochasticity-driven differentiation of cells, early during cell diversification, which is then amplified by cell division and growth into macroscopic phenotypic modules (cells, tissues, organs) making up the physiological systems of later life stages. Mosaic physiology provides a set of standing, diversified phenotypes, within single organisms, that raise the likelihood of the organism coping well with novel environmental challenges. These diversified phenotypes can be distinct, akin to polyphenisms at the organismal level; or they can be continuously distributed, creating a kind of standing, simultaneously expressed reaction norm of physiological capacities.

Stress: from cells to ecosystems

If there is something that we all know about in the 21st century it is stress, whether it's the stress of work, financial stress or the stress of getting the next grant funded; we are all familiar with that heart-pounding, race-against-time feeling. But this is a very modern perspective on stress.

Local specialists among endangered populations of medaka, Oryzias latipes, harboring in fragmented patches

Habitat fragmentation seriously damages local biodiversity of widespread organisms, or so-called common species, in agricultural habitats. We hypothesized that specialists adaptive to local particular conditions makes a population of generalists vulnerable to habitat fragmentation. To evaluate the extinction-proneness of common rural species, we determined the extent of phenotypic divergence using paddy fish, medaka, Oryzias latipes. Despite its wide geographical range, a rapid population decline threatens its persistence, and remnants persist in fragmented patches. We studied niche profiling of populations from different habitats for a factor that possibly lies behind the species being abundant within particular areas. Measurements of behavioral and morphological characteristics provided comparable variables between populations. Principal component analysis summarized these variables into compounded elements relevant to foraging and predator avoidance. Detection of association between behavioral and morphological traits showed a limited number of phenotypes specific to a local habitat, through which individuals adapted to specific narrow niches. Medaka maintains its status by accumulating a variety of local specialists. Because of the limited-dispersal ability, specialized individuals are vulnerable to isolation in less suitable patches that are caused by the destruction of the habitat-network. From a conservation point of view, the results suggest that preservation of habitats that also serve as corridors is recommended for enhancing the richness of common species that are composed of adaptively diversified phenotypes.

Altered tissue-specific expression at the Wx gene of the opaque mutants in rice

Amylose content is a major determinant of the eating quality in rice. To elucidate the allelic diversity at the Waxy (Wx) gene which controls the amylose synthesis, two cultivated strains having opaque endosperms were studied. The gene responsible for opaque endosperms was introduced into the genetic background of the Japonica type of rice by successive backcrosses, and the two near-isogenic lines (NILs) were selected from the B5 generation. The genetic experiments revealed that an allele, Wxop, controls opaque endosperms which show chalky as wx endosperms in spite of the production of amylose. Immunoblotting analysis was carried out to compare the gene expression by using the NILs with 4 different alleles (Wxa, Wxb, Wxop and wx). The level of the gene product bound to starch granules was slightly lower in the NILs with Wxop than that with Wxb, showing a positive correlation with amylose content in the endosperm. Extracts from mature anthers indicated that the gene product was markedly reduced in the NILs with Wxop as well as that with wx, showing an altered expression in the tissue specificity in the Wxop lines. Sequence analysis suggested that the Wxop had been derived from Wxa, independently of the origin of Wxb. The importance of the gene regulation was discussed in relation to diversified phenotypes established during the domestication process.

Diversification of Cardiomyogenic Cell Lineages in Vitro

The ability of undifferentiated cardiogenic mesoderm to generate diversified myogenic phenotypes was assayed in a minimal culture system. During cardiogenesis in vivo, the anterior and posterior segments of the avian heart have distinct patterns of contractile protein gene expression when they first differentiate. To assess the potential of undifferentiated cardiogenic tissue to diversify into distinct anterior and posterior lineages prior to heart formation, cardiogenic mesoderm and endoderm were removed together from the embryo at Hamburger and Hamilton stages 4-8. Explants from each of these stages differentiated in defined medium as indicated by the expression of muscle-specific genes. However, the ability to express the atrial-specific myosin heavy chain (AMHC1) mRNA was confined to posterior cardiac progenitors. Diversification was not dependent on anterior endoderm, suggesting that inductive interactions between the mesoderm and endoderm are not necessary to maintain diversified cardiac lineages after stage 4. The diversified potential of explanted cardiogenic tissue was altered with retinoic acid treatment, resulting in the activation of AMHC1 gene expression in the anterior progenitors. Anterior cardiogenic cells removed from the embryo at stage 8, when the heart begins to differentiate in vivo, are not susceptible to the alteration of diversified phenotype by retinoic acid treatment. Therefore, the potential to form distinct cardiomyogenic cell lineages is present in the anterior lateral plate mesoderm soon after gastrulation and the maturation of these lineages in a positionally dependent manner is maintained in a simple defined culture system in vitro.