Comparative genome analysis with the human genome reveals chicken genes associated with fatness and body weight

The selection of meat-type chickens (broilers) for rapid growth has been accompanied by excessive fat deposition. In this study, we analysed 53 candidate genes that are associated with obesity and obesity-related traits in humans, for which we found chicken orthologues by BLAST searches. We have identified single nucleotide polymorphisms (SNPs) with significant differences in allele frequencies between broilers and layers in each of the following six candidate genes: adrenergic, beta-2-, receptor, surface (ADRB2); melanocortin 5 receptor (MC5R); leptin receptor (LEPR), McKusick-Kaufman syndrome (MKKS), milk fat globule-EGF factor 8 protein (MFGE8) and adenylate kinase 1 (AK1). To examine associations with fatness and/or body weight, we used birds of extreme phenotypes in F(2) and backcross populations with varying levels of abdominal fat weight per cent (%AFW) and body weight. We then assessed the level of gene expression by real-time PCR. In two genes, ADRB2 and MFGE8, we found significant association with %AFW. The ADRB2 gene was found to have a significantly higher expression in the liver of lean chickens compared with those of the fat individuals. We believe that this approach can be applied for the identification of other quantitative genes.     

Independent subtilases expansions in fungi associated with animals

Many socially important fungi encode an elevated number of subtilisin-like serine proteases, which have been shown to be involved in fungal mutualisms with grasses and in parasitism of insects, nematodes, plants, other fungi, and mammalian skin. These proteins have endopeptidase activities and constitute a significant part of fungal secretomes. Here, we use comparative genomics to investigate the relationship between the quality and quantity of serine proteases and the ability of fungi to cause disease in invertebrate and vertebrate animals. Our screen of previously unexamined fungi allowed us to annotate and identify nearly 1000 subtilisin-containing proteins and to describe six new categories of serine proteases. Architectures of predicted proteases reveal novel combinations of subtilisin domains with other, co-occurring domains. Phylogenetic analysis of the most common clade of fungal proteases, proteinase K, showed that gene family size changed independently in fungi, pathogenic to invertebrates (Hypocreales) and vertebrates (Onygenales). Interestingly, simultaneous expansions in the S8 and S53 families of subtilases in a single fungal species are rare. Our analysis finds that closely related systemic human pathogens may not show the same gene family expansions, and that related pathogens and nonpathogens may show the same type of gene family expansion. Therefore, the number of proteases does not appear to relate to pathogenicity. Instead, we hypothesize that the number of fungal serine proteases in a species is related to the use of the animal as a food source, whether it is dead or alive.     

Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers

Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures.     

Analysis of Arabidopsis genome sequence reveals a large new gene family in plants

A detailed analysis of the currently available Arabidopsis thaliana genomic sequence has revealed the presence of a large number of open reading frames with homology to the stigmatic self-incompatibility (S) genes of Papaver rhoeas. The products of these potential genes are all predicted to be relatively small, basic, secreted proteins with similar predicted secondary structures. We have named these potential genes SPH (S-protein homologues). Their presence appears to have been largely missed by the prediction methods currently used on the genomic sequence. Equivalent homologues could not be detected in the human, microbial, Drosophila or C. elegans genomic databases, suggesting a function specific to plants. Preliminary RT-PCR analysis indicates that at least two members of the family (SPH1, SPH8) are expressed, with expression being greatest in floral tissues. The gene family may total more than 100 members, and its discovery not only illustrates the importance of the genome sequencing efforts, but also indicates the extent of information which remains hidden after the initial trawl for potential genes.     

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages

Background

Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology.

Results

We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments.We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100–10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree.

Conclusions

Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1570-9) contains supplementary material, which is available to authorized users.     

Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella

Genome colinearity has been studied for two closely related diploid species of the Brassicaceae family, Arabidopsis thaliana and Capsella rubella. Markers mapping to chromosome 4 of A. thaliana were found on two linkage groups in Capsella and colinear segments spanning more than 10 cM were revealed. Detailed analysis of a 60 kbp region in A. thaliana and its counterpart in C. rubella showed virtually complete conservation of gene repertoire, order and orientation. The comparison of orthologous genes revealed very similar exon-intron structures and sequence identities of 90% or more were found for exon sequences. This extensive genome colinearity at the genetic and molecular level allows the efficient transfer of data from the well-studied A. thaliana genome to other species in the Brassicaceae family, substantially facilitating genome analysis studies for species of this family.     

The development of gene expression systems for filamentous fungi

Filamentous fungi have been used for decades in the commercial production of enzymes, antibiotics, and specialty chemicals. Traditionally, improving the yields of these products has involved either mutagenesis and screening or modification of fermentation conditions. Generally, selective breeding of strains has not been successful, because most of the commercially important fungal species lack a sexual cycle. For a few species, strain improvements have been made possible by employing the parasexual cycle for genetic crosses (30). The recent development of DNA-mediated transformation systems for several industrially important fungal species has spawned a flurry of research activity directed toward the development of gene expression systems for these microorganisms. This technology is now a viable means for novel and more directed approaches to improving existing fungal strains which produce enzymes or antibiotics. In addition, fungal expression systems are now being tested for the production of heterologous gene products such as mammalian pharmaceutical proteins. The goal of this review is to present a summary of the gene expression systems which have recently been developed for some filamentous fungi of commercial importance. To insure that the most recent developments are presented we have included data from not only scientific papers, but also from personal communications, abstracts, symposia, and our own laboratory.     

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.     

Variability of non-mutualistic filamentous fungi associated withAtta sexdens rubropilosa nests

A survey of the filamentous fungi other than the symbiotic one found in association with Atta sexdens rubropilosa colonies was carried out. Different fungal species (27 taxa) were isolated a few days after treating the workers with toxic baits (sulfluramid; Mirex-S), from 40 laboratory and 20 field nests. Syncephalastrum racemosum (54%) and Escovopsis weberi (21%), Trichoderma harzianum (38%) and Fusarium oxysporum (23%) were the prevalent species in laboratory and field nests, respectively. Acremonium kiliense, Acremonium strictum, E. weberi, F. oxysporum, Fusarium solani, Moniliella suaveolens and T. harzianum were found in both nests' groups. We revealed that many filamentous fungi can co-exist in a dormant state inside the nests of these insects and some of them appear to be tightly associated with this environment.     

Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys

Background

The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other producing the less-toxic atranones. To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. Two of these strains produce atranones and two produce satratoxins.

Results

Comparative analysis of these four 35-Mbp genomes revealed several chemotype-specific gene clusters that are predicted to make secondary metabolites. The largest, which was named the core atranone cluster, encodes 14 proteins that may suffice to produce all observed atranone compounds via reactions that include an unusual Baeyer-Villiger oxidation. Satratoxins are suggested to be made by products of multiple gene clusters that encode 21 proteins in all, including polyketide synthases, acetyltransferases, and other enzymes expected to modify the trichothecene skeleton. One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase.

Conclusions

The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys. A unified biochemical model for Stachybotrys toxin production is presented. Overall, the four genomes described here will be useful for ongoing studies of this mold’s diverse toxicity mechanisms.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-590) contains supplementary material, which is available to authorized users.     

Distribution of a novel enzyme of sialidase family among native filamentous fungi

Sialidases (neuraminidases, EC 3.2.1.18) are widely distributed in biological systems but there are only scarce data on its production by filamentous fungi. The aim of this study was to obtain information about sialidase distribution in filamentous fungi from non-clinical isolates, to determine availability of sialidase gene, and to select a perspective producer. A total of 113 fungal strains belonging to Ascomycota and Zygomycota compassing 21 genera and 51 species were screened. Among them, 77 strains (11 orders, 14 families and 16 genera) were able to synthesize sialidase. Present data showed a habitat-dependent variation of sialidase activity between species and within species, depending on location. Sialidase gene was identified in sialidase-positive and sialidase-negative strains. .Among three perspective strains, the best producer was chosen based on their sialidase production depending on type of cultivation, medium composition, and growth temperature. The selected P. griseofulvum Р29 was cultivated in 3L bioreactor at 20 °C on medium supplemented with 0.5% milk whey. The results demonstrated better growth and 2.3-fold higher maximum enzyme activity compared to the shaken flask cultures. Moreover, the early occurring maximum (48 h) is an important prerequisite for future up scaling of the process.     

Comprehensive gene expression analysis reveals multiple signal pathways associated with prostate cancer

Prostate cancer (PC) depends on androgenic signaling for growth and survival. To data, the exact molecular mechanism of hormone controlling proliferation and tumorigenesis in the PC remains unclear. Therefore, in this study, we explored the differentially expressed genes (DEGs) and identified featured genes related to hormone stimulus from PC. Two sets of gene expression data, including PC and normal control sample, were downloaded from Gene Expression Omnibus (GEO) database. The t-test was used to identify DEGs between PC and controls. Gene ontology (GO) functional annotation was applied to analyze the function of DEGs and screen hormone-related DEGs. Then these hormone-related DEGs were further analyzed in constructed cancer network and Human Protein Reference Database to screen important signaling pathways they participated in. A total of 912 DEGs were obtained which included 326 up-regulated genes and 586 down-regulated genes. GO functional enrichment analysis identified 50 hormone-related DEGs associated with PC. After pathway and PPI network analysis, we found these hormone-related DEGs participated in several important signaling pathways including TGF-β (TGFB2, TGFB3 and TGFBR2), MAPK (TGFB2, TGFB3 and TGFBR2), insulin (PIK3R3, SHC1 and EIF4EBP1), and p53 signaling pathways (CCND2 and CDKN1A). In addition, a total of five hormone-related DEGs (SHC1, CAV1, RXRA, CDKN1A and SRF) were located in the center of PPI network and 12 hormone-related DEGs formed six protein modules. These important signal pathways and hormone-related DEGs may provide potential therapeutic targets for PC.     

Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution

The two fungal pathogens Blumeria graminis f. sp. tritici (B.g. tritici) and hordei (B.g. hordei) cause powdery mildew specifically in wheat or barley. They have the same life cycle, but their growth is restricted to the respective host. Here, we compared the sequences of two loci in both cereal mildews to determine their divergence time and their relationship with the evolution of their hosts. We sequenced a total of 273.3kb derived from B.g. tritici BAC sequences and compared them with the orthologous regions in the B.g. hordei genome. Protein-coding genes were colinear and well conserved. In contrast, the intergenic regions showed very low conservation mostly due to different integration patterns of transposable elements. To estimate the divergence time of B.g. tritici and B.g. hordei, we used conserved intergenic sequences including orthologous transposable elements. This revealed that B.g. tritici and B.g. hordei have diverged about 10 million years ago (MYA), two million years after wheat and barley (12 MYA). These data suggest that B.g. tritici and B.g. hordei have co-evolved with their hosts during most of their evolutionary history after host divergence, possibly after a short phase of host expansion when the same pathogen could still grow on the two diverged hosts.