文献类型： 外文期刊

作者： Chang, Jia ¹ ; Bei, Jinlong ² ; Shao, Qi ¹ ; Wang, Hemu ⁴ ; Fan, Huan ⁵ ; Yau, Tung On ⁶ ; Bu, Wenjun ¹ ; Ruan, Jishou ⁸ ; Wei, Dongsheng ¹ ; Gao, Shan ¹ ;

作者机构： 1.Nankai Univ, Coll Life Sci, Key Lab Mol Microbiol & Technol, Minist Educ, Tianjin, Peoples R China

2.Guangdong Acad Agr Sci, Agrobiol Gene Res Ctr, Guangdong Prov Key Lab Crop Germplasm Resources Pr, Guangzhou, Peoples R China

3.Guangdong Lab Lingnan Modern Agr, Guangzhou, Peoples R China

4.Tianjin Hemu Hlth Biotechnol Co Ltd, Tianjin, Peoples R China

5.Tianjin Inst Anim Husb & Vet Res, Tianjin, Peoples R China

6.Nottingham Trent Univ, John Van Geest CancerResearch Ctr, Sch Sci & Technol, Nottingham, Nottinghamshire, England

7.Scotlands Rural Coll, Dept Rural Land Use, Aberdeen, Aberdeenshire, Scotland

8.Nankai Univ, Sch Math Sci, Tianjin, Peoples R China

关键词： methylotrophic yeast; Hansenula polymorpha; rDNA quadruple; genome expansion; long terminal repeat

期刊名称：FRONTIERS IN MICROBIOLOGY （ 影响因子：6.064； 五年影响因子：6.843 ）

ISSN：

年卷期： 2022 年 13 卷

页码：

收录情况： SCI

摘要： 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 ura3 Delta (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.