PT  - JOURNAL ARTICLE
AU  - Jacob L. Steenwyk
AU  - Dana A. Opulente
AU  - Jacek Kominek
AU  - Xing-Xing Shen
AU  - Xiaofan Zhou
AU  - Abigail L. Labella
AU  - Noah P. Bradley
AU  - Brandt F. Eichman
AU  - Neža Čadež
AU  - Diego Libkind
AU  - Jeremy DeVirgilio
AU  - Amanda Beth Hulfachor
AU  - Cletus P. Kurtzman
AU  - Chris Todd Hittinger
AU  - Antonis Rokas
TI  - Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
AID  - 10.1101/546366
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 546366
4099  - http://biorxiv.org/content/early/2019/02/11/546366.short
4100  - http://biorxiv.org/content/early/2019/02/11/546366.full
AB  - Cell cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low GC content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18 / 21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, the fast-evolving lineage (FEL), which began diversifying ∼87 million years ago (mya), and the slow-evolving lineage (SEL), which began diversifying ∼54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. For example, all species lost the cell cycle regulator WHI5, and the FEL lost components of the spindle checkpoint pathway (e.g., MAD1, MAD2) and DNA damage checkpoint pathway (e.g., MEC3, RAD9). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene MAG1, which is part of the base excision repair pathway, and the DNA photolyase gene PHR1, which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POL4 and POL32) and telomere-associated genes (e.g., RIF1, RFA3, CDC13, PBP2). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell cycle and genome integrity genes and pathways, and may represent a novel system for studying cellular life without them.