Structural,Expression and Interaction Analysis of Rice SKP1-Like Genes

The degradation of proteins by the 26S proteasome is initiated by protein polyubiquitination mediated by a three-step cascade. The specific ubiquitination of different target proteins is mediated by different classes of E3 ubiquitin ligases, among which the best known are Skp1-Cullin-F-box complexes. Whereas protists, fungi and some vertebrates have a single SKP1 gene, many animal and plant species possess multiple SKP1 homologues. In this paper, we report on the structure, phylogeny and expression of the complete set of rice SKP1 genes (OSKs, Oryza sativa SKP1-like genes). Our analyses indicated that OSK1 and OSK20 belong to a class of SKP1 genes that contain one intron at a conserved position and are highly expressed. In addition, our yeast two-hybrid results revealed that OSK proteins display a differing ability to interact with F-box proteins. However, OSK1 and OSK20 seemed to interact with most of the nine F-box proteins tested. We suggest that rice OSK1 and OSK20 are likely to have functions similar to the Arabidopsis ASK1 and ASK2 genes.     

Temporal and Spatial Distribution of Auxin Response Factor Genes During Tomato Flower Abscission

Abscission facilitates growth and reproduction and improves plant defenses against pathogens. This tightly regulated process is triggered by environmental cues and hormones such as ethylene and auxin. Because auxin is crucial for abscission, auxin response factors (ARFs) may play important roles in this process. Here, we examined changes in gene expression during abscission in tomato, focusing on regulation of genes encoding ARFs. Specifically, we analyzed the pattern of ARF gene expression in tomato flower pedicel explants treated with ethylene, the ethylene blocker 1-methylcyclopropene (1-MCP), or auxin to determine how auxin and ethylene affect ARF gene expression. In addition, we examined the spatial and temporal distribution of IAA during abscission by examining transgenic tomato plants expressing an IAA-inducible promoter fused to the GUS reporter gene (the P5::GUS ‘Chico III’ line). Flower removal from the explants quickly induced abscission by ethylene, which was inhibited by exogenous auxin or 1-MCP. During early abscission, auxin (or 1-MCP) regulated the expression of various ARFs, including ARF1, 2, 3, 4, 5, 7, 8-1, 9, 11, 12, 13, 13-1, 14, and 17, whereas ethylene had the opposite effect on most of these genes. Further analysis shows that during this stage, auxin may mediate the expression of ARF8-1, 9, 11, 12, 13, 13-1, and 14, whereas ethylene may mediate ARF13-1. During the later stage of abscission, ARF2, 8, 10, 11, and 19 were upregulated, and 8-1, 12, 13, and 13-1 were downregulated, compared with nonabscising parts of plants. Fluorometric GUS analysis indicated that GUS activity in the abscission zone remained stable at 4 h and sharply decreased after 8 h until abscission was complete (32 h).     

Difference Analysis of ClCYC2-Like Genes Expression and DNA Methylation Between the Two Types of Florets in Chrysanthemum lavandulifolium

DNA methylation is an important epigenetic modification, that is involved in the regulation of gene expression and cell differentiation, and plays an important regulatory role in flower development in higher plants. There are two types of florets on the capitulum in the genus Chrysanthemum, the flower symmetry factor CYCLOIDEA (CYC) 2-like genes may be important candidate genes for determining the identity of the two types of florets. In this study, the diploid plant Chrysanthemum lavandulifolium was used as the research material, and qRT-PCR and bisulfite sequencing polymerase chain reaction (BSP) were used to identify the expression and DNA methylation pattern of CYC2-like genes in the two types of florets. Gene expression analysis showed that the six ClCYC2-like genes were significantly different in the two types of florets, and the expression levels of ClCYC2c, ClCYC2d, ClCYC2e and ClCYC2f in the ray florets were significantly higher than those in the disc florets. For the DNA methylation analysis of the three genes ClCYC2c, ClCYC2d, and ClCYC2e, it was found that the DNA methylation levels of these three genes were negative correlated with their expression levels, and the ways in which the three genes were regulated by the DNA methylation were different. It is speculated that the different DNA methylation of ClCYC2-like genes in the two types of florets may affect the differentiation and development of the two types of florets. This study provides new clues about epigenetics for the analysis of capitulum formation in Asteraceae.

     

Sequence,Structural and Expression Divergence of Duplicate Genes in the Bovine Genome

Gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. In the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. A total of 3131 putative duplicated gene pairs were identified, including 712 cattle-specific duplicate gene pairs unevenly distributed across the genome, which are significantly enriched for specific biological functions including immunity, growth, digestion, reproduction, embryonic development, inflammatory response, and defense response to bacterium. Around 97.1% (87.8%) of (cattle-specific) duplicate gene pairs were found to have distinct exon-intron structures. Analysis of gene expression by RNA-Seq and sequence divergence (synonymous or non-synonymous) revealed that expression divergence is correlated with sequence divergence, as has been previously observed in other species. This analysis also led to the identification of a subset of cattle-specific duplicate gene pairs exhibiting very high expression divergence. Interestingly, further investigation revealed a significant relationship between structural and expression divergence while controlling for the effect of synonymous sequence divergence. Together these results provide further insight into duplicate gene sequence and expression divergence in cattle, and their potential contributions to phenotypic divergence.     

Male Sex Interspecies Divergence and Down Regulation of Expression of Spermatogenesis Genes in Drosophila Sterile Hybrids

Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeiotic with few exceptions, and that most misregulated genes are involved in late stages of spermatogenesis. Comparative studies of gene regulation in sterile hybrids and parental species have mainly used microarrays providing a whole genome representation of regulatory problems in sterile hybrids. Real-time PCR studies can reject or reveal differences not observed in microarray assays. Moreover, differences in gene expression between samples can be dependant on the source of RNA (e.g., whole body vs. tissue). Here we survey expression in D. simulans, D. mauritiana and both intra and interspecies hybrids using a real-time PCR approach for eight genes expressed at the four main stages of sperm development. We find that all genes show a trend toward under expression in the testes of sterile hybrids relative to parental species with only the two proliferation genes (bam and bgcn) and the two meiotic class genes (can and sa) showing significant down regulation. The observed pattern of down regulation for the genes tested can not fully explain hybrid male sterility. We discuss the down regulation of spermatogenesis genes in hybrids between closely-related species within the contest of rapid divergence experienced by the male genome, hybrid sterility and possible allometric changes due to subtle testes-specific developmental abnormalities.     

Comparative Genomics Using Microarrays Reveals Divergence and Loss of Virulence-Associated Genes in Host-Specific Strains of the Insect Pathogen Metarhizium anisopliae

Many strains of Metarhizium anisopliae have broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.It is difficult to trace and reconstruct the evolutionary processes of diversification and radiation of species. In particular, genes that contribute to ecological diversification and the nature of the evolutionary forces acting during this process are poorly understood, partly because genes directly involved in ecological attributes are hard to identify (13). This is not the case with fungi, as they have genes encoding secreted products with specific environmental adaptations, e.g., scavenging nutrients and penetrating host barriers. During its pathogenic life cycle the ubiquitous insect pathogen Metarhizium anisopliae secretes a formidable array of hydrolytic enzymes, antimicrobial compounds, and toxins. These properties, plus its experimental tractability, have made M. anisopliae a common research subject and model system for studying pathogenicity and for developing useful products for medicine, agriculture, and biotechnology (33).The phylogeny of the Metarhizium genus has been well characterized (12). It is a largely clonal organism (4), containing subtypes with wide host ranges (e.g., M. anisopliae var. anisopliae Ma2575) and subtypes that, like M. anisopliae var. acridum Ma324 (used for locust control), show specificity for certain locusts, beetles, crickets, homopterans, etc., and are unable to infect other insects (5). While some specialized lineages, such as M. anisopliae var. acridum, are phylogenetically distant from generalist strains, implying evolutionarily conserved host use patterns, closely related strains can also differ greatly in host range and requirements for germination (16, 40, 42). Evidence that most specialists arose from generalists includes the following: (i) the vast majority of isolates found in nature belong to the genetically very diverse M. anisopliae var. anisopliae and typically demonstrate wide host ranges; (ii) specialist strains are scattered among generalists in phylogenies and have independently adapted to different insects; (iii) specialization is associated with conditions that are assumed to be derived, including reduced diet breadth (2, 35, 40). Specialist and generalist strains are often closely linked in phylogenies, indicating that there are genetic mechanisms allowing rapid adaptation (40).We are using genetic variation to explore the evolutionary history and pathogenic adaptations of M. anisopliae. The goal is to provide a detailed molecular classification of multiple strains and address the origins of intraspecific differences (gene loss/gain/divergence or modulation of gene expression). Correlation of strain differences with adaptations to specific hosts will identify the underlying regulatory, metabolic, and biosynthetic differences that define host preferences. To initiate this study, we used expressed sequence tag (EST) approaches to compare gene expression patterns between Ma2575 and Ma324 (17). These are two of the most distantly related strains and essentially span the range of variation within M. anisopliae (12, 40). About 60% of the ESTs expressed by Ma2575 during growth on insect cuticle encode secreted enzymes and toxins. We speculated that the large number and diversity of these effectors may be the key to Ma2575''s ability to infect a wide variety of insects. In contrast, Ma324 ESTs revealed fewer hydrolytic enzymes and very few toxins. This relates to life-styles. Strain Ma2575 kills hosts quickly via toxins and grows saprophytically in the cadaver. In contrast, Ma324 causes a systemic infection of host tissues before the host dies. This study showed that ESTs allow different pathogenic strategies to be understood from a broad perspective.Patterns of gene duplication, divergence, and deletion can be specifically determined by heterologous hybridization of total genomic DNA to microarrays (11, 20, 27). Heterologous hybridization has provided a fast and powerful tool facilitating the merging of functional genomics with physiology, ecology, and evolution (7, 31, 38) in species of yeast (22, 27), fish (9, 24), mammals (23, 25), and plants (1, 15). We have already verified that an array of Ma2575 ESTs can be used for heterologous hybridization with cDNAs. Thus, Ma2575 arrays were used to probe the causes of sectorization (production of nonsporulating cultures) in two commercial strains of M. anisopliae var. anisopliae. Probes from both strains cross-reacted strongly with the arrays, although with different expression profiles (46). We also used Ma2575 arrays to identify hundreds of genes differentially regulated by Ma324 in response to host or nonhost cuticles (45). Although only 8% of paralogous Ma2575 genes have greater than 80% identity, we expected cross-hybridization would potentially overestimate the overlap in genes expressed by different strains. However, individual genes within gene families were distinguished, revealing processes unique to Ma324 (45). In this study we exploit the fact that heterologous cDNA can provide information on physiological processes to allow us to gain a mechanistic perspective on the different life-styles that exist in insect-fungus interactions.     

Divergence in Expression of Candidate Genes for the Smoltification Process Between Juvenile Resident Rainbow and Anadromous Steelhead Trout

Rainbow and steelhead trout (Oncorhynchus mykiss), among other salmonid fishes, exhibit tremendous life history diversity, foremost of which is variation in migratory propensity. While some individuals possess the ability to undertake an anadromous marine migration, others remain resident in freshwater throughout their life cycle. Those that will migrate undergo tremendous physiological, morphological, and behavioral transformations in a process called smoltification which transitions freshwater-adapted parr to marine-adapted smolts. While the behavior, ecology, and physiology of smoltification are well described, our understanding of the proximate genetic mechanisms that trigger the process are not well known. Quantitative genetic analyses have identified several genomic regions associated with smoltification and migration-related traits within this species. Here we investigate the divergence in gene expression of 18 functional and positional candidate genes for the smoltification process in the brain, gill, and liver tissues of migratory smolts, resident parr, and precocious mature male trout at the developmental stage of out-migration. Our analysis reveals several genes differentially expressed between life history classes and validates the candidate nature of several genes in the parr-smolt transformation including Clock1α, FSHβ, GR, GH2, GHR1, GHR2, NDK7, p53, SC6a7, Taldo1, THRα, THRβ, and Vdac2.