The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina

Abstract

BackgroundXanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota.ResultsThe genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned.ConclusionsThe current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1380-0) contains supplementary material, which is available to authorized users.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

“…For comparative purposes, we also re-analyzed the recently published genome sequence of the Holarctic strain CBS 6938 [20] using the same bioinformatic framework. Further information on the strains is depicted in Table 1 and will be discussed in the following sections.…”

“…The lower number of common genes and the higher dissimilarity detected in the Patagonian strain is probably related to the fact that it belongs to a genetically divergent lineage. In order to retrieve putative Phaffia orphan genes, we worked with the common set of predicted genes of the three strains ( n  = 5463) and kept genes with expression evidence from Sharma et al [20] (RNA-seq of CBS 6938) that were not present in any of the other tremellomycetous yeasts and lacked hits in the NCBI nr database (see methods). This resulted in a set of 283 orphan genes that is shared among the three strains of P. rhodozyma , is transcribed, and contains putative CDSs that do not have known relatives in any other branch of the tree of life (Additional file 1: Table S1).…”

“…Thus, we consider the Holarctic strain CBS 7918 T to be the valid type strain for the species. Here we selected it for genome sequencing to compare it to the previously published genome sequence of another Holarctic isolate, CBS 6938 [20]. We also sought to obtain and analyze the draft genome sequence of a representative P. rhodozyma strain from the Southern Hemisphere (CRUB 1149) to compare it to its counterparts from the Northern Hemisphere.…”

FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing

“…Due to these advantages, NGS technologies have quickly been implemented in various fields of life sciences (Metzker 2010), including de novo sequencing of whole genomes Sharma et al 2015), genome re-sequencing (Stratton 2008), cDNA sequencing (Martin and Wang 2011;Ozsolak and Milos 2011;Wang et al 2009), genotyping (Davey et al 2011;Sharma et al 2014;Yoshida et al 2013), and community genomics analyses (Qin et al 2010). Also, several filamentous organisms, including fungi and oomycetes have been sequenced over the last decade (Raffaele and Kamoun 2012).…”

Dr. Robert Bauer (1950-2014) in memoriam: botanist, mycologist, and electron microscopist

“…The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provided insights into the organization of its acetyl-CoA derived pathways (Sharma et al 2015).…”