Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves with more refined tools and expanded taxon sampling. We investigated mitochondrial origins with the benefit of new, deeply branching genome sequences from the ancient and prolific SAR11 clade of Alphaproteobacteria and publicly available alphaproteobacterial and mitochondrial genome sequences. Using the automated phylogenomic pipeline Hal, we systematically studied the effect of taxon sampling and missing data to accommodate small mitochondrial genomes. The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life.

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of Wallemia sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. Wallemia sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic. January 2012Dear Dr. Galagan, Thank you for giving us the opportunity to revise our manuscript "The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction" for publication in Fungal Genetics and Biology.We appreciate the points raised by the reviewers and hope that we have addressed their comments satisfactorily in our response to reviews.Thank you for your time and your consideration. Sincerely, MahajabeenCover Letter Response to reviewers' commentsReviewer #1: Suggestions for major improvements:1) Conduct phylogenetic analysis to study the evolutionary origin of the duplicated genes. In a recently published Verticillium comparative genomics paper (Klosterman SJ. 2011 PlosPathogen), a duplication of Hog1 is also reported. The phylogenetic analysis from that study rejected recent duplication within the genome as the source of that additional Hog1 gene. It would be interesting to compare these two duplicates in the background of other orthologous copies from different fungal lineages.Sequences of the two WsHog1 homologs were used in BLASTp searches to extract orthologous Hog1 sequences from all the taxa used in the phylogenetic and CAFE analyses. We conducted a maximum likelihood search using a WAG+G+I model to examine the evolutionary origin of the two WsHog1. The results of the phylogenetic analyses to examine the origin of the dupli...

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