Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

Background F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the Caenorhabditis genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in Caenorhabditis. Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of Caenorhabditis genus, including C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei. Results Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in Caenorhabditis genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in Caenorhabditis species. Conclusions Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in Caenorhabditis, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. In summary, our findings outline the evolution of F-box genes in the Caenorhabditis genome and lay the foundation for future functional studies.

Genome-Wide Characterization, Evolution, Structure, and Expression Analysis of the F-box Genes in Caenorhabditis

Background: F-box proteins represent a diverse class of adaptor proteins of ubiquition proteasome system (UPS) that play critical roles in cell signaling pathway and immune response. Among closely related organisms of Caenorhabditis, tremendous divergence in F-box gene copy numbers was caused by large species-specific expansion and contraction. Although F-box gene number expansion plays an important role in shaping the genomic diversity of Caenorhabditis, the mechanisms responsible for the copy number variation of F-box genes and their functional diversification is very poorly understood. In this study, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five Caenorhabditis species: C.brenneri, C.briggsae, C.elegans, C.japonica, C.remanei).Results: Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs in the genome of C.brenneri, C.briggsae, C.elegans, C.japonica, C.remanei respectively. Our work suggested that extensive species-specific tandem duplication followed by slightly gene loss was the main mechanism responsible for F-box gene number divergence in Caenorhabditis. After F-box gene duplication events occurred, several different mechanisms have contributed to gene structural divergence including exon/intron gain/loss, mutation, exonization/pseudoexonization, insertion, deletion, and particularly ubiquitous intron sequence elongation. Based on the analysis of high-throughput RNA sequencing data, we proposed that F-box gene function have diversified by both sub- and neofunctionalization through diverged stage-specific expression patterns in Caenorhabditis.Conclusions: Species-specific tandem duplications as well as trifling gene loss have contributed to the disequilibrium evolution pattern of F-box gene family in Caenorhabditis, which lead to complex structural variation as well as diversified functions affecting growth and development within and among Caenorhabditis. Taken together, our results provide an overview of F-box genes in Caenorhabditis genome and the basis for further functional studies.

Effects of Different Laying Hen Species on Odour Emissions

Odour is one of the main environmental concerns in the laying hen industry and may also influence animal health and production performance. Previous studies showed that odours from the laying hen body are primarily produced from the microbial fermentation (breakdown) of organic materials in the caecum, and different laying hen species may have different odour production potentials. This study was conducted to evaluate the emissions of two primary odorous gases, ammonia (NH3) and hydrogen sulphide (H2S), from six different laying hen species (Hyline, Lohmann, Nongda, Jingfen, Xinghua and Zhusi). An in vitro fermentation technique was adopted in this study, which has been reported to be an appropriate method for simulating gas production from the microbial fermentation of organic materials in the caecum. The results of this study show that Jingfen produced the greatest volume of gas after 12 h of fermentation (p < 0.05). Hyline had the highest, while Lohmann had the lowest, total NH3 emissions (p < 0.05). The total H2S emissions of Zhusi and Hyline were higher than those of Lohmann, Jingfen and Xinghua (p < 0.05), while Xinghua exhibited the lowest total H2S emissions (p < 0.05). Of the six laying hen species, Xinghua was identified as the best species because it produced the lowest total amount of NH3 + H2S (39.94 µg). The results for the biochemical indicators showed that the concentration of volatile fatty acids (VFAs) from Zhusi was higher than that for the other five species, while the pH in Zhusi was lower (p < 0.01), and the concentrations of ammonium nitrogen (NH4+), uric acid and urea in Xinghua were lower than those in the other species (p < 0.01). Hyline had the highest change in SO42− concentration during the fermentation processes (p < 0.05). In addition, the results of the correlation analysis suggested that NH3 emission is positively related to urease activities but is not significantly related to the ureC gene number. Furthermore, H2S emission was observed to be significantly related to the reduction of SO42− but showed no connection with the aprA gene number. Overall, our findings provide a reference for future feeding programmes attempting to reduce odour pollution in the laying hen industry.

Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart

Three mycobacteriophages, Bipolarisk, Bread, and FudgeTart, were isolated from enriched soil samples found in Crete, NE. All three phages are lytic, belong to subcluster C1, and infect Mycobacterium smegmatis mc2155. The structures of the three genomes are similar, with slight variations in gene number and content.

A novel homology-based algorithm for the identification of physically linked clusters of paralogous genes

Highly diverse phenotypic traits are often encoded by clusters of gene paralogs that are physically linked on chromosomes. Examples include olfactory receptor gene clusters involved in the recognition of diverse odors, defensin and phospholipase gene clusters involved in snake venoms, and Hox gene clusters involved in morphological diversity. Historically, gene clusters have been identified subjectively as genomic neighborhoods containing several paralogs, however, their genomic arrangements are often highly variable with respect to gene number, intergenic distance, and synteny. For example, the prolactin gene cluster shows variation in paralogous gene number, order and intergenic distance across mammals, whereas animal Hox gene clusters are often broken into sub-clusters of different sizes. A lack of formal definition for clusters of gene paralogs does not only hamper the study of their evolutionary dynamics, but also the discovery of novel ones in the exponentially growing body of genomic data. To address this gap, we developed a novel homology-based algorithm, CGPFinder, which formalizes and automates the identification of clusters of gene paralogs (CGPs) by examining the physical distribution of individual gene members of families of paralogous genes across chromosomes. Application of CGPFinder to diverse mammalian genomes accurately identified CGPs for many well-known gene clusters in the human and mouse genomes (e.g., Hox, protocadherin, Siglec, and beta-globin gene clusters) as well as for 20 other mammalian genomes. Differences were due to the exclusion of non-homologous genes that have historically been considered parts of specific gene clusters, the inclusion or absence of one or more genes between the CGPs and their corresponding gene clusters, and the splitting of certain gene clusters into distinct CGPs. Finally, examination of human genes showing tissue-specific enhancement of their expression by CGPFinder identified members of several well-known gene clusters (e.g., cytochrome P450, aquaporins, and olfactory receptors) and revealed that they were unequally distributed across tissues. By formalizing and automating the identification of CGPs and of genes that are members of CGPs, CGPFinder will facilitate furthering our understanding of the evolutionary dynamics of genomic neighborhoods containing CGPs, their functional implications, and how they are associated with phenotypic diversity.