Data_Sheet_3_Full-Length Genome of a Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions.ZIP

BackgroundCurrently, methylotrophic yeasts (e.g., Pichia pastoris, Ogataea polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains-CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, the O. polymorpha strain CBS4732 ura3Δ (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion.
ResultsIn the present study, we have assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat retrotransposons (LTR-rts), rDNA, 5′ and 3′ telomeric, subtelomeric, low complexity and other repeat regions were exactly determined to improve the genome quality. In brief, the main findings include complete rDNAs, complete LTR-rts, three large duplicated segments in subtelomeric regions and three structural variations between the HU-11/CBS4732 and NCYC495 genomes. These findings are very important for the assembly of full-length genomes of yeast and the correction of assembly errors in the published genomes of Ogataea spp. HU-11/CBS4732 is so phylogenetically close to NCYC495 that the syntenic regions cover nearly 100% of their genomes. Moreover, HU-11/CBS4732 and NCYC495 share a nucleotide identity of 99.5% through their whole genomes. CBS4732 and NCYC495 can be regarded as the same strain in basic research and industrial applications.
ConclusionThe present study preliminarily revealed the relationship between CBS4732, NCYC495, and DL-1. Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of O. polymorpha HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies of Ogataea spp.

研究背景
当前，甲基营养型酵母（methylotrophic yeasts）（如巴斯德毕赤酵母Pichia pastoris、多形汉逊酵母Ogataea polymorpha与博伊丁念珠菌Candida boindii）是基础研究与工业应用领域中基因组学研究的热点对象。在汉逊酵母属（Ogataea）中，多数研究聚焦于三株经典的多形汉逊酵母菌株：CBS4732、NCYC495与DL-1。然而，由于缺乏这三株菌株的高质量完整基因组序列，其基因组差异尚未被精准解析，因此CBS4732、NCYC495与DL-1三者间的亲缘关系仍不明确。
作为源自CBS4732的营养缺陷型突变株，多形汉逊酵母CBS4732 ura3Δ（命名为HU-11）已被用于多种重要蛋白质或肽类的高产量生产。HU-11与CBS4732拥有相同的参考基因组（标注为HU-11/CBS4732），因为二者仅存在一个5 bp的插入片段差异。

研究结果
本研究利用高深度PacBio与Illumina测序数据，完成了多形汉逊酵母HU-11/CBS4732的全长基因组组装。通过精准解析长末端重复序列反转录转座子（Long terminal repeat retrotransposons, LTR-rts）、核糖体DNA（rDNA）、5'与3'端端粒、亚端粒、低复杂度及其他重复序列区域，进一步提升了基因组组装质量。简言之，本研究的核心发现包括：完整的核糖体DNA序列、完整的长末端重复序列反转录转座子、亚端粒区域的三处大片段重复序列，以及HU-11/CBS4732与NCYC495基因组间的三处结构变异。
上述发现对于酵母全长基因组组装以及修正已发表的汉逊酵母属（Ogataea spp.）基因组组装错误具有重要参考价值。HU-11/CBS4732与NCYC495的系统发育关系极为接近，二者的共线性区域覆盖了几乎全部基因组；此外，二者全基因组的核苷酸一致性高达99.5%。据此，CBS4732与NCYC495在基础研究与工业应用中可视为同一菌株。

研究结论
本研究初步阐明了CBS4732、NCYC495与DL-1三者间的亲缘关系。研究结果为深入理解甲基营养型酵母的基因组演化提供了新契机，同时为多形汉逊酵母CBS4732、NCYC495、DL-1及其衍生菌株的工业应用奠定了坚实基础。建议将多形汉逊酵母HU-11/CBS4732的全长基因组序列纳入NCBI RefSeq数据库，以支撑后续汉逊酵母属的相关研究。