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Zusammenfassung:
Auxenochlorella is a unicellular Trebouxiophyte alga with excellent properties for discovery research and biotechnology. Unlike most green algae, Auxenochlorella is vegetatively diploid and can be efficiently transformed via homologous recombination, enabling the functions of uncharacterised photosynthesis genes to be investigated using reverse genetics. We present a telomere-to-telomere, fully phased, and extensively annotated genome assembly for Auxenochlorella UTEX250, a strain with robust laboratory growth and lipid production. The 44 Mb diploid assembly is highly heterozygous, and six of the twelve chromosomes feature extensive inter-chromosomal rearrangements. Via genome sequencing of additional strains, we demonstrate that the complex genome architecture of UTEX250 is the result of allodiploid hybridisation between the described species A. protothecoides and A. symbiontica. Following hybridisation, the UTEX250 genome has likely undergone multiple mitotic recombination events, many of which are non-reciprocal and have resulted in widespread loss-of-heterozygosity. Furthermore, three chromosome pairs are entirely homozygous, likely due to duplication of one homologous chromosome and subsequent loss of the other. Finally, two chromosomes are trisomic following duplication of one homologous chromosome. We sequenced a clone of UTEX250 that has been maintained independently for several decades and demonstrate that many of the loss-of-heterozygosity events and one of the trisomies have occurred in laboratory culture. Loss-of-heterozygosity and aneuploidy may be the product of ongoing selection against genomic incompatibilities, or alternatively inadvertent artificial selection introduced by culturing techniques. The unusual genomic properties of UTEX250 mirror patterns of genome evolution in allodiploid hybrid yeast, presenting opportunities to create generalised models of evolution in vegetative diploid species.
