Assembly of Schizosaccharomyces cryophilus chromosomes and their comparative genomic analyses revealed principles of genome evolution of the haploid fission yeasts

Abstract

The fission yeast clade, which has a distinct life history from other yeasts, can provide important clues about evolutionary changes. To reveal these changes the large S. cryophilus supercontigs were assembled into chromosomes using synteny relationships and the conserved pericentromeric, subtelomeric genes. Togetherness of the supercontigs was confirmed by PCR. Investigation of the gene order revealed localisation of the rDNA arrays, more than 300 new conserved orthologues and proved that S. cryophilus supercontigs were mosaics of collinear blocks. PFGE analysis showed that size of the S. cryophilus chromosomes differ from the S. pombe chromosomes. Comparative genomic analyses of the newly assembled chromosomes confirmed that the closest relative of S. cryophilus was S. octosporus not just in sequence similarity but also in a structural way, and revealed that preservation of the conserved regions did not arise from the lower number of chromosomal rearrangements. Translocations were more typical in the closely related species, while the number of inversions increased with the phylogenetic distances. Our data suggested that sites of the chromosomal rearrangements were not random and often associated with repetitive sequences, structural- and nucleotide evolution might correlate. Chromosomal rearrangements of the fission yeasts compared to other lineages were also discussed.

Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection

“…In spite of that, the gene content and structure are remarkably conserved among the fission yeasts species, higher than within the Saccharomyces or Kluyveromyces genera [ 2 ]. This was also supported by our previous work [ 30 ], where we assembled the large contigs of S. cryophilus to chromosome-like units using different in silico and molecular techniques. Comparison of the newly assembled genome to the genomic sequences of the related species revealed that numerous chromosomal rearrangements could have happened during the evolution of the species despite their conserved genomic structures [ 30 ].…”

“…This was also supported by our previous work [ 30 ], where we assembled the large contigs of S. cryophilus to chromosome-like units using different in silico and molecular techniques. Comparison of the newly assembled genome to the genomic sequences of the related species revealed that numerous chromosomal rearrangements could have happened during the evolution of the species despite their conserved genomic structures [ 30 ]. Thus, the question has arisen: what could the reason for their unusually stable genome structures be?…”

“…In the past few years this species has also become the subject of population genetic/genomic studies [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. The genus comprises four additional species: S. japonicus [ 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ], S. octosporus [ 26 , 27 , 28 ], S. cryophilus [ 29 , 30 ] and the recently described S. osmophilus [ 31 ]. The genus exhibits such evolutionary breadth that the idea of dividing the group into three genera has emerged several times in the past [ 32 , 33 ].…”

Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes

“…structure (Rhind et al 2011;Ács-Szabó et al 2018). Taking advantage of these opportunities, our aim was to reveal similarities and differences of mycelial growth of the different yeast species and find deviations, if there are, in the genomes of the dimorphic and non-dimorphic fission yeasts.…”

“…Synteny analyses of certain genes between S. japonicus and S. pombe were performed manually using orthology inference and the genomic coordinates of the concerning genes. Synteny information on S. octosporus and S. cryophilus was obtained from Ács-Szabó et al (2018). Small-scale collinearity and gene losses were depicted with the online tool SimpleSynteny (https:// www.…”