The β-model—maximum likelihood, Cramér–Rao bounds, and hypothesis testing

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordWe study the maximum-likelihood estimator in a setting where the dependent variable is a random graph and covariates are available on a graph level. The model generalizes the well-known β-model for random graphs by replacing the constant model parameters with regression functions. Cramer-Rao bounds are derived for special cases of the undirected β-model, the directed β-model, and the covariate-based β-model. The corresponding maximum-likelihood estimators are compared with the bounds by means of simulations. Moreover, examples are given on how to use the presented maximum-likelihood estimators to test for directionality and significance. Finally, the applicability of the model is demonstrated using temporal social network data describing communication among healthcare workers

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Additional file 2: Additional information on selected gene groups of Trichoderma , methods used for genome sequencing, and legends for the figures in Additional file 3. Chapter 1: Carbohydrate-Active enzymes (CAZymes). Chapter 2: Aegerolysins and other toxins. Chapter 3: Small secreted cysteine rich proteins (SSCPs). Chapter 4: EST sequencing and analysis. Chapter 5: Legends to figures. (DOCX 38 KB

MOESM1 of Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Additional file 1: Comparative properties and gene inventory of T. reesei, T. virens and T. atroviride. This file contains additional information on genomic properties and selected gene families from the three Trichoderma species comprising 19 tables. Table S1 summarizes the satellite sequences identified in the Trichoderma genomes and four other fungal genomes. Table S2 summarizes manually curated sequence alignments of transposable element families from the Trichoderma genomes. Table S3 lists the total number of CAZy families in Trichoderma and other fungi. Table S4 lists the glycoside hydrolase (GH) families in Trichoderma and other fungi. Table S5 lists the glycosyltransferase (GT) families in Trichoderma and other fungi. Table S6 lists the polysaccharide lyase (PL) families in Trichoderma and other fungi. Table S7 lists the carbohydrate esterase (CE) families in Trichoderma and other fungi. Table S8 lists the carbohydrate-binding module (CBM) families in Trichoderma and other fungi. Table S9 lists the NRPS, PKS and NRPS-PKS proteins in T. atroviride. Table S10 lists NRPS, PKS and NRPS-PKS proteins in T. virens. Table S11 lists the putative insecticidal toxins in Trichoderma. Table S12 lists the cytochrome P450 CYP4/CYP19/CYP26 class E proteins in Trichoderma. Table S13 lists the small-cysteine rich secreted protein from Trichoderma spp. Table S14 lists the most abundant PFAM domains in those genes that are unique to T. atroviride and T. virens and not present in T. reesei. Table S15 surveys the assembly statistics. Table S16 provides gene model support. Table S17 summarizes gene model statistics. Table S18 provides numbers of genes with functional annotation according to KOG, Gene Ontology, and KEGG classifications. Table S19 lists the largest KOG families responsible for metabolism. (XLSX 57 KB

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Abstract Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Results Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. Conclusions The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants

of Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

of Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderm

of Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

of Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderm

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Authors’ original file for figure

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Authors’ original file for figure