Comparative and Population Genomics Platforms for Fungi and Oomycetes

Abstract

Fungal genomes have been extensively sequenced mainly aided by next-generation sequencing technologies. Currently, more than 300 fully-sequenced fungal genomes are available in public domain, facilitating comparative and evolutionary genomics at the kingdom-wide level. Recently, the 1,000 Fungal Genomes Project (http://1000.fungalgenomes.org/) was launched to sequence the species especially focused on taxa which are rarely sequenced, hence providing foundation for deciphering underpinnings of fungal evolution and diversity. The emerging technologies and a number of genomes from fungi, animals and plants would provide an opportunity for exhaustive comparative genomics. In order to fully take advantage of such an opportunity, comprehensive and systematic genomics solution had an immediate need. As a solution, Comparative Fungal Genomics Platform (CFGP

http://cfgp.snu.ac.kr/) was publicly open with 65 genomes belonging to 58 fungal and Oomycete species in 2007. The first release provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since then, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants, and 105 animals. In addition, the number of tools in Favorite increased to 27. As a result, CFGP 2.0 was released with the considerable update and development. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB

http://genomebrowser.snu.ac.kr/), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, gene family analysis platforms including Fungal Secretome Database (FSD

http://fsd.snu.ac.kr/) and Fungal Plant Cell Wall-degrading Enzyme Database (FPDB

http://pcwde.riceblast.snu.ac.kr/) were constructed. Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed the FSD. A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/Oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition of plant cell walls. In addition, many of PCWDEs are also utilized by biofuel and pulp industries. In order to develop a comparative genomics platform focused in fungal PCWDEs and provide a resource for evolutionary studies, FPDB was constructed (http://pcwde.riceblast.snu.ac.kr/). In order to archive genes encoding PCWDEs, 22 sequence profiles were constructed and searched on 328 genomes of fungi, Oomycetes, plants and animals. A total of 6,682 putative genes encoding PCWDEs were predicted, showing differential distribution by their life styles, host ranges and taxonomy. Genes known to be involved in fungal pathogenicity, including polygalacturonase (PG) and pectin lyase, were enriched in plant pathogens. Furthermore, crop pathogens had more PCWDEs than those of rot fungi, implying that the PCWDEs analysed in this study are more needed for invading plant hosts than wood-decaying processes. Evolutionary analysis of PGs in 34 selected genomes revealed that gene duplication and loss events were mainly driven by taxonomic divergence and partly contributed by those events in species-level, especially in plant pathogens. Understanding intra-species diversity of the rice blast fungus, Magnaporthe oryzae, is important, since the reference strain 70-15 is a lab strain. In order to set a multiple reference genomes and study genomic differences among field isolates, a world-wide collection of 37 M. oryzae genomes were sequenced. The repeat-masked genome size, the number of predicted genes and domain profile were similar to each other, but they showed differential distribution of structural variations and Zn(II)2Cys6, CCHC and C2H2 transcription factor families. The average size of assembled genomes was 36.41 Mb and the number of predicted genes was 13,403, on average. The size of core genome for M. oryzae was estimated as 8,262 genes, and the size of pan-genome was predicted to contain 20,655 genes. In order to provide a genomics platform focused on M. oryzae, a web-based system, Magnaporthe Atlas (http://www.magnaporthe.org/) was developed by implementing genome assembly, gene prediction, gene family annotation, SNUGB module and Favorite extension. Collectively, CFGP 2.0, FSD and FPDB would serve as comprehensive fungal genomics platforms which were also used for analyzing 38 M. oryzae genomes. Comparative analysis on multiple M. oryzae genomes showed genomic characteristics at population scale, thus providing a foundation for further comparative and evolutionary genomics studies.