Transcription factors (TFs) are proteins that regulate the transcription of genes, by binding to specific DNA sequences. Based on literature (Shelest, 2008; Weirauch and Hughes,2011) collected and manually curated list of DBD Pfam domains (in total 62 DBD domains) We looked for distribution of TFs in 395 fungal genomes plus additionally in plant genomes (Phytozome), prokaryotes(IMG), some animals/metazoans and protists genomes

The photoresponsive zygomycete Phycomyces blakesleeanus is an experimentally tractable model system for elucidating the signalling pathways underlying photoregulation. Our recent sequencing, assembly, and annotation of the P. blakesleeanus genome allows us to complement classical molecular biological studies with genome-wide analyses of gene expression. We sequenced cDNAs from mycelia grown with and without light. The resulting 23410 'light' ESTs and 24437 'dark' ESTs were aligned with the genome and used to identify which of the 14792 genes could be described as transcriptionally active under either condition. We tagged 1538 genes (10%) as potentially light-specific, 1558 genes (11%) as potentially dark-specific, and 2431 genes (16%) as transcribed under both light and dark. In addition to its value as a model organism, P. blakesleeanus is one of only 2 zygomycetes with a sequenced genome, providing an opportunity to discover genes that are specific to or missing from zygomycetes, and gene families that are expanded or contracted in zygomycetes relative to the much better-sampled ascomycetes and basidiomycetes. We clustered P. blakesleeanus proteins with those of 13 other fungi and so far find 2 zygomycete-specific families of Zn-finger proteins, and a zygomycete-specific expansion of protein kinases. We also confirm the existence of a Phycomyces-specific family of F-box domain proteins.

Here we are trying to answer the question why one of the smallest genome Sporobolomyces roseus has one of the most introns of all fungal genomes in the context of fungal intron evolution. In this study we used a statistical comparative genomics approach toward intron number evolution among 16 fungal genomes.

Gene modeling has always been a challenge for computational biologists, but it becomes trivial when informed by expressed sequence tags (ESTs). New sequencing technologies such as 454 and Solexa can generate huge number of ESTs, but algorithms used in our production pipeline such as Newbler and PASA are inadequate in generating quality gene models from EST sequences. We developed a new algorithm COMBEST to generate partial or complete gene models from EST and genomic sequences. When applied to three genomes - Chamydomonas reinhardtii, Agaricus bisporus, and Aspergillus carbonarius- with coverage of 1.7 (2.7x), 22.5 (6.1x), and 51.9 (24.3x) ESTs per kb genomic sequence, we found different fractions of genes with alternative spliced forms of 6percent, 16percent, and 29percent for three genomes respectively. These numbers are 11percent, 25percent, and 49percent respectively if normalized to multi exon genes. The fraction of alternatively spliced genes is an inherent feature of a particular genome and the living condition of the organism; however, deep EST coverage is essential to reveal alternative splicing to the fullest extent. Since our algorithm also calculates the relative expression level for each splicing isoform, the results from COMBEST can be a useful resource for studying intron splicing and evolution in addition to being a tool for gene modeling in the high-throughput sequencing era. One of the interesting results from our analysis is that minor alternative forms with much shorter protein sequences occur at much lower frequencies as compared to the dominant isoform

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

We used comparative gene modeling to reannotate 21 Aspergillus genomes. Initial automatic annotation of individual genomes may contain some errors of different nature, e.g. missing genes, incorrect exon-intron structures, 'chimeras', which fuse 2 or more real genes or alternatively splitting some real genes into 2 or more models. The main premise behind the comparative modeling approach is that for closely related genomes most orthologous families have the same conserved gene structure. The algorithm maps all gene models predicted in each individual Aspergillus genome to the other genomes and, for each locus, selects from potentially many competing models, the one which most closely resembles the orthologous genes from other genomes. This procedure is iterated until no further change in gene models is observed. For Aspergillus genomes we predicted in total 4503 new gene models ( ~;2percent per genome), supported by comparative analysis, additionally correcting ~;18percent of old gene models. This resulted in a total of 4065 more genes with annotated PFAM domains (~;3percent increase per genome). Analysis of a few genomes with EST/transcriptomics data shows that the new annotation sets also have a higher number of EST-supported splice sites at exon-intron boundaries.

Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.