title: Clade- and species-specific features of genome evolution in the Saccharomycetaceae.
abstract: Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm-for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components.
authors.affiliation: UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland kenneth.wolfe@ucd.ie.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wolfe
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - INRA USC 1370, 46 allée d'Italie, 69364 Lyon cedex 07, France.
authors.forename: David
authors.initials: D
authors.lastname: Armisén
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden.
authors.forename: Estelle
authors.initials: E
authors.lastname: Proux-Wera
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Centre for the Study of Existential Risk, University of Cambridge, CRASSH, Alison Richard Building, 7 West Road, Cambridge, CB3 9DT, UK.
authors.forename: Seán S
authors.initials: SS
authors.lastname: ÓhÉigeartaigh
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Haleema
authors.initials: H
authors.lastname: Azam
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland CIRAD, UMR CMAEE, Site de Duclos, Prise d'eau, F-97170, Petit-Bourg, Guadeloupe, France.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Gordon
authors.affiliation: UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Byrne
mesh_terms: D005075:Biological Evolution; D017124:Conserved Sequence; D000072159:Dynactin Complex; D004398:Dyneins / Q000235:genetics; D019143:Evolution, Molecular; D005800:Genes, Fungal; D016681:Genome, Fungal / Q000235:genetics*; D006639:Histidine / Q000096:biosynthesis; D008869:Microtubule-Associated Proteins / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D034622:RNA Interference; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D055319:Torulaspora / Q000235:genetics*
chemical_list: D000072159:Dynactin Complex; D008869:Microtubule-Associated Proteins; D029701:Saccharomyces cerevisiae Proteins; D006639:Histidine; D004398:Dyneins
keywords: Kazachstania; Naumovozyma; Tetrapisispora; Torulaspora; comparative genomics; evolution