Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

<p>Abstract</p> <p>Background</p> <p>Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.</p> <p>Results</p> <p>Analogous to the use of the genomics context in genome alignments, we test whether conserved functional context can be used to select candidate homologs from insignificant BLAST hits. We make a co-complex network alignment between complex subunits in yeast and human and find that proteins with an insignificant BLAST hit that are part of homologous complexes, are likely to be homologous themselves. Further analysis of the distant homologs we recovered using the co-complex network alignment, shows that a large majority of these distant homologs are in fact ancient paralogs.</p> <p>Conclusions</p> <p>Our results show that, even though evolution takes place at the sequence and genome level, co-complex networks can be used as circumstantial evidence to improve confidence in the homology of distantly related sequences.</p

Insights into Adaptations to a Near- Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora

Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle

Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes

Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes and probe the biological and methodological factors influencing our estimates. We have collected various datasets of protein complexes and pathways in Saccheromyces cerevisiae. We define orthologous groups on 34 eukaryotic genomes and measure the extent of cohesive evolution of sets of orthologous groups of which members constitute a known complex or pathway. Within this framework it appears that most functional modules evolve flexibly rather than cohesively. Even after correcting for uncertain module definitions and potentially problematic orthologous groups, only 46% of pathways and complexes evolve more cohesively than random modules. This flexibility seems partly coupled to the nature of the functional module because biochemical pathways are generally more cohesively evolving than complexes

Bamfiles ChIP-seq

Bamfiles resulting from mapping reads deposited in GEO (Accession GSE121283) to the genome of Fusarium oxysporum f. sp. lycopersici 4287 (Fol4287). Adapter sequences were removed and quality scores were converted to Sanger format with the MAQ sol2sanger command if needed. Quality was checked manually using FastQC. Reads were aligned to the genome of Fol4287 using `bwa aln` (bwa version 0.7.12) Duplicate reads were removed with `Picard tools` (version 1.134) (http://broadinstitute.github.io/picard, MarkDuplicates) See 10.1016/j.fgb.2015.03.006 for details on ChIP-seq experiment protocols. This dataset is described in 10.1101/465070

Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age

<p>Abstract</p> <p>Background</p> <p>The study of biological networks and how they have evolved is fundamental to our understanding of the cell. By investigating how proteins of different ages are connected in the protein interaction network, one can infer how that network has expanded in evolution, without the need for explicit reconstruction of ancestral networks. Studies that implement this approach show that proteins are often connected to proteins of a similar age, suggesting a simultaneous emergence of interacting proteins. There are several theories explaining this phenomenon, but despite the importance of gene duplication in genome evolution, none consider protein family dynamics as a contributing factor.</p> <p>Results</p> <p>In an <it>S. cerevisiae</it> protein interaction network we investigate to what extent edges that arise from duplication events contribute to the observed tendency to interact with proteins of a similar age. We find that part of this tendency is explained by interactions between paralogs. Age is usually defined on the level of protein families, rather than individual proteins, hence paralogs have the same age. The major contribution however, is from interaction partners that are shared between paralogs. These interactions have most likely been conserved after a duplication event. To investigate to what extent a nearly neutral process of network growth can explain these results, we adjust a well-studied network growth model to incorporate protein families. Our model shows that the number of edges between paralogs can be amplified by subsequent duplication events, thus explaining the overrepresentation of interparalog edges in the data. The fact that interaction partners shared by paralogs are often of the same age as the paralogs does not arise naturally from our model and needs further investigation.</p> <p>Conclusion</p> <p>We amend previous theories that explain why proteins of a similar age prefer to interact by demonstrating that this observation can be partially explained by gene duplication events. There is an ongoing debate on whether the protein interaction network is predominantly shaped by duplication and subfunctionalization or whether network rewiring is most important. Our analyses of <it>S. cerevisiae</it> protein interaction networks demonstrate that duplications have influenced at least one property of the protein interaction network: how proteins of different ages are connected.</p

Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene

Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850), flowering locus KH-domain containing protein and a DUF1639-containing protein. Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth

A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem

Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem

Patrimonio costruito e pianificazione urbanistica nel Giappone del dopoguerra

La Legge per la conservazione dei beni culturali (bunkazai) fu promulgata durante l’occupazione dello Scap in Giappone nel 1950. Il presente studio esamina il processo di emanazione di questa Legge con il fine di mettere in luce se esso sia stato influenzato dalle politiche e dalla pratica di conservazione dei beni culturali degli Stati uniti. Inoltre, attraverso l’analisi di alcuni casi emblematici, questo saggio intende riflettere sulla conservazione del costruito attuale in Giappone e cercare di definire una sua possibile direzione per il futuro. Non è facile trovare una chiara relazione fra la conservazione di bunkazai e le politiche e la pratica della ricostruzione post-bellica nelle città danneggiate durante la Seconda guerra mondiale. I beni immobili, quali gli edifici, i siti archeologici e il paesaggio, presentano valori molteplici – storico, economico, sociale. Tuttavia, a partire dalla fine della Seconda guerra mondiale, la conservazione dei bunkazai fu portata avanti sotto la guida del governo centrale che pose l’attenzione sui soli valori storico e culturale degli oggetti, sulla loro forma e materia. Invece, alcune organizzazioni e gruppi portarono avanti un tipo diverso di esperienza conservativa, che tiene in grande considerazione la fruizione e l’uso del patrimonio culturale. Di conseguenza, nonostante la guerra e l’enorme perdita di patrimonio culturale, è possibile trovare paradossalmente una relazione fra aspetti storici e d’uso di edifici e luoghi storici. The Law for the Protection of Cultural Properties (bunkazai) was legislated under the occupation of the SCAP (Supreme Commander for the Allied Powers) in Japan in 1950. This study examines the legislation process of this Law in order to understand which could have been the influence of the American policy and practice of historic heritage preservation. Moreover, through the analysis of some case-studies, this paper aims at reconsidering the present state of protection of immovable cultural heritage in Japan and seeking for its future potentiality. It is not easy to find a clear relationship between bunkazai conservation and the reconstruction policies and practices in the war-damaged cities after the Second World War. Immovable cultural heritage such as buildings, archaeological sites and landscape contains various values including historical, economic and social values. However, since the end of the Second World War, conservation of bunkazai has been taken care under the governmental leadership and strongly focused on the historical and cultural values of the cultural objects, their features and materials. On the other hand, other organizations and groups have carried out a different kind of conservation experiences, which take care of the living aspect of cultural heritage. As a result, despite of the war and the loss of so much of the cultural heritage, a close relationship can paradoxically be found between historic aspect and living aspect of buildings and sites