The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats

Abstract

Point centromeres, found in some ascomycete yeasts such Saccharomyces cerevisiae, are very different in structure from the centromeres of other eukaryotes. They are tiny and nonrepetitive and contain only two short conserved sequence motifs. Until recently, point centromeres were thought to have a single evolutionary origin, in the budding yeast family Saccharomycetaceae. Most yeasts outside this family have centromeres that are many kilobases in size. Some have centromeres consisting of a large inverted repeat sequence, others have centromeric clusters of retrotransposons, and a third group including Candida albicans has centromeres with no conserved sequence features. It was recently reported that Scheffersomyces stipitis has point centromeres with a strongly conserved 125-bp core sequence, which is unexpected because S. stipitis is only distantly related to the known point-centromere species.We show here that the 125-bp core sequence is actually part of the long terminal repeat (LTR) of the Ty5-like retrotransposon Tps5, which forms a cluster in the centromeric region of each S. stipitis chromosome. Thus, the LTR of a centromereassociated retrotransposon confers centromere-like mitotic stability when cloned into a plasmid. The centromeric regions of S. stipitis contain three types of Tps5 element (Tps5a, Tps5b, and Tps5c) and a noncoding nonautonomous large retrotransposon derivative.

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium

“…Strikingly, we observed that a single degenerated LTR retrotransposon, VdLTRE9 , is strongly associated with centromeres in some Verticillium species, while it is absent from LS regions in V. dahliae . The association of specific retrotransposons with centromeres has also been observed in the yeasts Ogataea polymorpha ( 69 ), Debaryomyces hansenii ( 68 ), and Scheffersomyces stipitis ( 70 ), where a retrotransposon related to Ty5 is enriched at centromeres. Similarly, centromeres in Cryptococcus contain six retrotransposons ( Tcn1 to - 6 ) that occur nearly exclusively at centromeres ( 16 ).…”

“…Centromeres are often enriched for a variety of different retrotransposons and other repetitive elements ( 15 , 16 , 25 , 29 , 30 , 68 – 70 ). We similarly observed that centromeres in all Verticillium species are repeat rich.…”

The genome of the CTG(Ser1) yeast Scheffersomyces stipitisis plastic

“…Following assembly, BUSCO v3 was run to assess gene space (9), identifying the presence of 1683 conserved genes from the Saccharomycetales_odb9 gene database. Assembly size and contiguity statistics were assessed using QUAST v4.5 (10) The final assembly in contigs was further corrected and assembled to chromosome level by identification of centromeric sequences and overlapping regions between the contigs (11).…”

“…Although several S. stipitis natural isolates are used for the optimisation of second-generation biofuels production, the genome of only one strain (Y-11545) has been sequenced and assembled to the chromosomal level (60). The Y-11545 strain has a genome organised in 8 chromosomes containing transposon-rich regional centromeres (11, 60, 61).…”

“…Although several S. stipitis natural isolates are used for the optimisation of second-generation biofuels production, the genome of only one strain (Y-11545) has been sequenced and assembled to the chromosomal level (31). The Y-11545 genome has a size of 15.4 Million base pair (Mbp) organised in 8 chromosomes and containing ~6000 protein-coding genes (31–33). S. stipitis chromosomes are marked by regional centromeres composed of full-lenghts LTR retrotrasposons (Tps5a, Tps5b and Tps5c) and non-coding, non-autonomous LARD (large retrotransposon derivative) elements (31, 33).…”