دانلود رایگان مقاله انگلیسی خصوصیات ژنتیکی و اصلاح یک سویه تولید مخمر تولید بیواتانول - اشپرینگر 2018

Abstract

Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.

Discussion

This study disclosed the genetic characteristics of a bioethanol-producing S. cerevisiae strain, NY1308. Using a PFGE and aCGH array, we confirmed that no chromosomal aneuploidy (loss or amplification of whole chromosome) events occurred on the diploid genome of NY1308. One cause of the heterogeneity in length between the pair of homologous chr1 and chr6 (Fig. 1a) is the insertion of DNA (Fig. 3). Whole genome sequencing identified that the nucleotide polymorphisms between NY1308 and S288c were 0.71%, which was very similar to the level separating S288c and ZTW1 (another industrial strain used for bioethanol production in China) (Zhang et al. 2015). NY1308 has a closer genetic relationship with sake strains (Fig. 2), which is consistent with the fact that these strains were isolated from East Asia. The frequency of InDels (0.02%) is much less than that of SNVs, but this type of mutation resulted in the functional deactivation of a considerable number of ORFs. A higher ratio of point mutations (up to 40% of the SNVs and 88% of the InDels) was observed in intergenic sequences, which were previously suggested as the main cause of the cis regulation of gene expression among yeast populations (Zheng et al. 2010). Among the 71,186 SNVs listed in Online Dataset S1, 63% were detected in both homologs (the ratio of variation frequency was above 80%; Online Dataset S1). Interestingly, these homologous SNVs were not evenly distributed across the NY1308 genome and were clustered within certain chromosomal segments (Online Fig. S4). For example, it can be clearly seen that the SNVs within the 277 to 348 kb regions of chr5, 202 to 551 kb of chr8, and 1 to 360 kb of chr11 were homologous for the pairs of chromosomes (Online Fig. S4).