APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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2024
·Vol. 91
·期 1
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IF 3.9
Yuan-Ru Xiong,Yuan-Chun Fang,Min He,Ke-Jing Li,Lei Qi,Yang Sui,Ke Zhang,Xue-Chang Wu,Liang Meng,Ou Li,Dao-Qiong Zheng
This study explored the genomic alterations in Yarrowia lipolytica, a key yeast in industrial biotechnology, under both spontaneous and mutagen-induced conditions. Our findings reveal that spontaneous mutations occur at a rate of approximately 4 × 10−10 events per base pair per cell division, primarily manifesting as single-nucleotide variations (SNVs) and small insertions and deletions (InDels). Notably, C-to-T/G-to-A transitions and C-to-A/G-to-T transversions dominate the spontaneous SNVs, while 1 bp deletions, likely resulting from template slippage, are the most frequent InDels. Furthermore, chromosomal aneuploidy and rearrangements occur, albeit at a lower frequency. Exposure to ultraviolet (UV) light, methylmethane sulfonate (MMS), and Zeocin significantly enhances the rates of SNVs and alters their mutational spectra in distinct patterns. Notably, Zeocin-induced SNVs are predominantly T-to-A and T-to-G substitutions, often occurring within the 5′-TGT*−3′ motif (* denotes the mutated base). Additionally, Zeocin exhibits a higher potency in stimulating InDels compared to UV and MMS. Translesion DNA synthesis is implicated as the primary mechanism behind most Zeocin-induced SNVs and some InDels, whereas non-homologous end joining serves as the main pathway for Zeocin-mediated InDels. Intriguingly, the study identifies the gene YALI1_E21053g, encoding a protein kinase, as negatively associated with Zeocin resistance. Overall, our results not only deepened our knowledge about the genome evolution in Y. lipolytica but also provided reference to develop innovative strategies to harness its genetic potential.
研究领域:
微生物学
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遗传学
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分子生物学
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DOI
高影响因子
Diversity-Basel
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2023
·Vol. 15
·期 6
·701
·
IF 2.4
Meile Sun,Xiangrong Ren,Ya Liu,Jing Yang,Jingtao Hui,Yukun Zhang,Yanhua Cui,Jun Zhang,Guocang Lin,Yan Li
Roses are important plants, and they are cultivated worldwide for their beautiful flowers, remarkable scent, and nutritious hips. In this study, we re-sequenced the whole genomes of 57 rose cultivars and one wild species that originated from different regions around the world and had different scents, aiming to evaluate their genetic structure and to detect the potential signature of the selective sweep between different scent groups with single-nucleotide polymorphism (SNP) and indel markers. The roses were sequenced at an average depth of 6× to the reference genome ofRosa‘Old blush’. A total of 2,375,949 SNPs were obtained. The SNP numbers varied among the 58 samples, with an average of 1,271,906 per sample. The phylogeny and population structure revealed that the roses could be divided into three main clusters; however, the groups were not consistent in terms of geographic origin or scent classification. These indicated that rose cultivars have a complex genetic background due to the extensive hybridization between cultivated roses or wildrosaspecies worldwide. A selective sweep analysis was conducted to detect the selection signatures in rose scent traits. A total of 2430 candidate genes were identified in the strong scent groups, and were at the top 5% FSTcompared to the moderate group. These genes were significantly enriched in the KEGG pathways of tyrosine metabolism, cyanoamino acid metabolism, alpha-linolenic acid metabolism (13 genes), and phenylpropanoid biosynthesis (30 genes). When the low-scent group was used as the control, 2604 candidate genes were identified at the top 5% FSTthat were significantly enriched in the KEGG pathways of alpha-linolenic acid metabolism (15 genes), and glutathione metabolism (23 genes). We also observed genes enriched in pathways including the linoleic acid metabolism (five genes), diterpenoid biosynthesis (six genes), and monoterpenoid biosynthesis (seven genes), although they were not significant. These implied a positive selection of rose cultivars with a strong fragrance in terms of fatty acid derivatives, terpenoids and benzenoids/phenylpropanoids during rose breeding. Our study establishes a foundation for the further large-scale characterization of rose germplasm, improving the genetic knowledge of the background of roses.Keywords:single-nucleotide polymorphism (SNP);indel;genome variation;selection sweep;KEGG pathway
研究领域:
植物学
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遗传学
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分子生物学
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DOI
高影响因子
Forensic Sciences Research
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2022
·
IF 0
Qi Yang,Huan Yu,Yiling Qu,Xiaochun Zhang,Ruocheng Xia,Ziwei Wang,Rui Tan,Lei Xiong,Shihan Xi,Jun Wu,Yuzhen Gao,Suhua Zhang,Chengtao Li
Insertion/deletion polymorphisms (InDels) have been treated as a prospective and helpful genetic marker in the fields of forensic human identification, anthropology and population genetics for the past few years. In this study, we developed a six-dye multiplex typing system consisting of 34 autosomal InDels and Amelogenin for forensic application. The contained InDels were specifically selected for Chinese population with the MAF ≥ 0.25 in East Asia, which do not overlap with the markers of Investigator® DIPplex kit. The typing system was named as GoldeneyeTM DNA ID System 35InDel Kit, and a series of developmental validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics were conducted on this kit. We confirmed that the 35InDel kit is precise, sensitive, species specific and robust for forensic practice. Moreover, the 35InDel kit is capable of typing DNA extracted from forensic routine case-type samples as well as degraded samples and mixture samples. All markers are proved to be highly polymorphic with an average observed heterozygosity (He) of 0.4582. The combined power of discrimination (CPD) is 0.999 999 999 999 978 and the combined power of exclusion in duos (CPED) and trios (CPET) are 0.978 837 and 0.999573, respectively, which are higher than those of the Investigator® DIPplex kit. Thus, the GoldeneyeTM DNA ID System 35InDel kit is suitable for forensic human identification and could serve as a supplementary typing system for paternity testing.Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1945723 .
研究领域:
法医学
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群体遗传学
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人类学
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产品关联
DOI
PubMed
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