Nature Plants
·
2021
·Vol. 7
·期 8
·1026-1036
·
IF 15.793
Xiong Xingyao,Gou Junbo,Liao Qinggang,Li Yanlin,Zhou Qian,Bi Guiqi,Li Chong,Du Ran,Wang Xiaotong,Sun Tianshu,Guo Lvjun,Liang Haifei,Lu Pengjun,Wu Yaoyao,Zhang Zhonghua,Ro Dae-Kyun,Shang Yi,Huang Sanwen,Yan Jianbin
The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725A s (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus .
研究领域:
植物生物学
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基因组学
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生物化学
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药理学
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PubMed
高影响因子
ACS Synthetic Biology
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2022
·
IF 5.249
Ming Zhao,Miaomiao Gao,Liangbin Xiong,Yongjun Liu,Xinyi Tao,Bei Gao,Min Liu,Feng-Qing Wang,Dong-Zhi Wei
Genome mutagenesis drives the evolution of organisms. Here, we developed a CRISPR-Cas assisted random mutation (CARM) technique for whole-genome mutagenesis. The method leverages an entirely random gRNA library and SpCas9-NG to randomly damage genomes in a controllable shotgunlike manner that then triggers diverse and abundant mutations via low-fidelity repair. As a proof of principle, CARM was applied to evolve the capacity of Saccharomyces cerevisiae BY4741 to produce β-carotene. After seven rounds of iterative evolution over two months, a β-carotene hyperproducing strain, C7-143, was isolated with a 10.5-fold increase in β-carotene production and 857 diverse genomic mutations that comprised indels, duplications, inversions, and chromosomal rearrangements. Transcriptomic analysis revealed that the expression of 2541 genes of strain C7-143 was significantly altered, suggesting that the metabolic landscape of the strain was deeply reconstructed. In addition, CARM was applied to evolve industrially relevant S. cerevisiae CEN.PK2-1C for S-adenosyl-L-methionine production, which was increased 2.28 times after just one round. Thus, CARM can contribute to increasing genetic diversity to identify new phenotypes that could further be investigated by reverse engineering.
研究领域:
遗传学
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合成生物学
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微生物学
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代谢工程
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PubMed
高影响因子
Nature Protocols
·
2020
·Vol. 16
·期 1
·431-457
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IF 10.419
Jin Shuai,Gao Qiang,Gao Caixia
Base editors can achieve targeted genomic base conversion. However, the off-target issue is one of the major concerns in their application. Whole-genome sequencing (WGS) at the individual level can provide direct information on genome-wide specificity, but it is difficult to distinguish true off-target single-nucleotide variants (SNVs) induced by base editors from background variation. Here we describe an unbiased WGS method for evaluating the specificity of base editors in rice. In this protocol, we describe the experimental design and provide details of vector construction, rice transformation and tissue culture, as well as a comprehensive WGS data analysis pipeline for overcoming two related core problems in various plant species: high background mutation rates and the heterogeneity of examined populations. Using this protocol, researchers can straightforwardly and accurately assess the genome-wide specificity of base editors and other genome editing tools in 12–15 weeks.
研究领域:
遗传学
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植物生物学
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分子生物学
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DOI
PubMed
高影响因子
BMC PLANT BIOLOGY
·
2025
·Vol. 25
·期 1
·1-20
·
IF 4.8
Sun Meiyu,Han Baocai,Xiao Jianhua,Yu Haiyan,Jia Yinli,Yuan Shuhai,Yao Juan,Xing Quan,Wu Dongqi,Sun Guofeng,Zhang Jinzheng
Background Hemerocallis middendorffii is a kind of high quality ornamental plant with strong cold resistance, pleasant aroma, and gorgeous floral color. Hemerocallis is one of the three internationally recognized perennial flowers that has huge demand in the flower market. However, little is known about the floral scent and color biosynthesis in daylily due to the large genome size. Results We reported here a high-quality chromosome-scale genome of H. middendorffii which was a native daylily in China. Using PacBio HiFi and Hi-C sequencing technologies, we assembled a chromosome-level genome of 4.10 Gb with a contig N50 of 12.81 Mb. We identified 65,536 protein-coding genes across the 11 chromosomes. We employed a combination of genomic, transcriptomic, and metabolomic approaches to investigate mechanisms behind the floral scent and color biosynthesis in daylily. The main terpenoids contributing to floral fragrance were linalool, 3-carene, nerolidol, and α-farnesene, while carotenoids and anthocyanidins were the main components of floral color. These traits could be stably inherited by their hybrid progenies, and some of them exhibited heterosis. Through Weighted Gene Co-expression Network Analysis (WGCNA) analysis, we identified two modules MEblueviolet and MEgreenyellow related to terpenoids (floral scents) and carotenoids (floral colors) biosynthesis. The 10 hub genes including DXS , MVD , MVK , DXR , LCYBs , Z-ISO , CYPs , and JAS were screened by network construction. The results of qRT-PCR analysis showed that these hub genes were significant differentially expressed in daylily samples, and these results were basically consistent with the relative transcript levels of RNA-seq. Conclusions This study not only provides new insights into the molecular mechanisms of floral scent and color, but also lays a foundation for subsequent research on key gene functions and molecular breeding in Hemerocallis .
研究领域:
植物学
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遗传学
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生物化学
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PubMed
高影响因子
Processes
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2025
·Vol. 13
·期 3
·731
·
IF 2.8
Shuanghu Fan,Zihan Feng,Meiting Xu,Zhenxia Shi,Yufeng Zhang,Peipei Zhang,Xiaoqiang Hou
Phthalic acid esters (PAEs) are mainly used as plasticizers and result in serious environmental contamination worldwide. Microbial biodegradation becomes an efficient strategy for PAE elimination. In the current study, the PAE-degrading strainGordoniasp. LUNF6 was isolated from contaminated soil. Strain LUNF6 can efficiently degrade DBP in a wide range of temperatures, pH values, and salinity levels. This strain is also capable of degrading 11 types of PAEs and displays remediation potential in wastewater. The complete genome of strain LUNF6 was sequenced to determine its efficient degradation performance. Its genome comprises a chromosome (3,971,257 bp) and a plasmid (78,813 bp). After gene function annotation, the complete PAE degradation pathway was proposed. The gene of monoalkyl PAE hydrolase MphGd2 was cloned and heterologously expressed. The protein of MphGd2 was purified by infinity chromatography, and we hydrolyzed MBP to produce PA. These results reveal the molecular mechanism of PAE degradation by strain LUNF6, which will contribute to the application of strain LUNF6 and hydrolase MphGd2 in bioremediation.
研究领域:
环境微生物学
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分子生物学
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DOI
高影响因子
Synthetic and Systems Biotechnology
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2020
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IF 0
Ruida Wang,Fanjing Kong,Haizhen Wu,Bingbing Hou,Yajing Kang,Yuan Cao,Shiwei Duan,Jiang Ye,Huizhan Zhang
The lincosamide family antibiotic lincomycin is a widely used antibacterial pharmaceutical generated by Streptomyces lincolnensis , and the high-yield strain B48 produces 2.5 g/L lincomycin, approximately 30-fold as the wild-type strain NRRL 2936. Here, the genome of S. lincolnensis B48 was completely sequenced, revealing a ~10.0 Mb single chromosome with 71.03% G + C content. Based on the genomic information, lincomycin-related primary metabolism network was constructed and the secondary metabolic potential was analyzed. In order to dissect the overproduction mechanism, a comparative genomic analysis with NRRL 2936 was performed. Three large deletions (LDI-III), one large inverted duplication (LID), one long inversion and 80 small variations (including 50 single nucleotide variations, 13 insertions and 17 deletions) were found in B48 genome. Then several crucial mutants contributing to higher production phenotype were validated. Deleting of a MarR-type regulator-encoding gene slinc377 from LDI, and the whole 24.7 kb LDII in NRRL 2936 enhanced lincomycin titer by 244% and 284%, respectively. Besides, lincomycin production of NRRL 2936 was increased to 7.7-fold when a 71 kb supercluster BGC33 from LDIII was eliminated. As for the duplication region, overexpression of the cluster situated genes lmbB2 and lmbU , as well as two novel transcriptional regulator-encoding genes ( slinc191 and slinc348 ) elevated lincomycin titer by 77%, 75%, 114% and 702%, respectively. Furthermore, three negative correlation genes ( slinc6156 , slinc4481 and slinc6011 ) on lincomycin biosynthesis, participating in regulation were found out. And surprisingly, inactivation of RNase J-encoding gene slinc6156 and TPR (tetratricopeptide repeat) domain-containing protein-encoding gene slinc4481 achieved lincomycin titer equivalent to 83% and 68% of B48, respectively, to 22.4 and 18.4-fold compared to NRRL 2936. Therefore, the comparative genomics approach combined with confirmatory experiments identified that large fragment deletion, long sequence duplication, along with several mutations of genes, especially regulator genes, are crucial for lincomycin overproduction.
研究领域:
微生物学
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基因组学
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药学
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分子生物学
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DOI
PubMed
Frontiers in Plant Science
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2023
·
IF 5.6
Chen Qingbing,Gao Kang,Xu YuRan,Sun YaHui,Pan Bo,Chen Dongliang,Luo Chang,Cheng Xi,Liu Hua,Huang Conglin
Chrysanthemums are one of the top ten most well-known traditional famous flowers in China and one of the top four cut flowers worldwide, holding a significant position in landscape gardening. The cold temperatures of winter restrict the cultivation, introduction, and application of chrysanthemum, resulting in high costs for year-round production. This severely impacts the ornamental and economic value of chrysanthemum. Therefore, research on cold tolerance is of vital importance for guiding chrysanthemum production and application. With the development of genomics, transcriptomics, metabolomics, and other omics approaches, along with high-throughput molecular marker technologies, research on chrysanthemum cold tolerance has been continuously advancing. This article provides a comprehensive overview of the progress in cold tolerance research from various aspects, including chrysanthemum phenotype, physiological mechanisms, the forward genetics, molecular mechanisms, and breeding. The aim is to offer insights into the mechanisms of cold tolerance in chrysanthemum and provide reference for in-depth research and the development of new cold tolerance chrysanthemum varieties.
研究领域:
植物学
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遗传学
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园艺学
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DOI
高影响因子
Water
·
2023
·Vol. 15
·期 4
·830
·
IF 3.4
Shuaiguo Li,Kejian Tian,Qing Qiu,Yue Yu,Han Li,Menghan Chang,Xuejian Sun,Jinming Gu,Fenglin Zhang,Yibing Wang,Hongliang Huo
As a widespread pollutant, bisphenol A (BPA) has created a serious threat to ecosystem and human health. Therefore, expanding the available microbial resources used to screen highly efficient BPA-degrading bacteria with BPA as the sole carbon source is very important for the removal of this pollutant from the environment. In this study, the BPA degradation rate ofPseudomonassp. P1 to 30 mg/L was 96.89% within 120 h. Whole genome sequencing showed that the genome of strain P1 was composed of a single circular chromosome with a full length of 6.17 Mb, which contained 5636 predicted coding genes. Comparative genomic analysis showed that strain P1 contained 210 functional genes related to BPA degradation. It was confirmed that BPA degradation genes ferredoxin (bisdA), P450 (bisdB),CotAandLacin strain P1 were highly expressed under the induction of BPA. Combined with the identification of metabolites, the route of BPA degradation byPseudomonaswas proposed. A new metabolite, 4-vinylphenol, was detected for the first time in pathway Ⅰ. In pathway Ⅱ, BPA is directly oxidized to phenol and 4-isopropenyl phenol in the presence of laccase, which is rarely reported in the process of bacterial degradation of BPA. This study confirmed that strain P1 had good tolerance to various environmental factors at the gene level and enriched the degradation mechanism of BPA.Keywords:Bisphenol A;Pseudomonas;whole genome;biodegradation
研究领域:
环境微生物学
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基因组学
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DOI
高影响因子
Plant Communications
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2022
·
IF 8.625
Meiyu Sun,Yanan Zhang,Li Zhu,Ningning Liu,Hongtong Bai,Guofeng Sun,Jinzheng Zhang,Lei Shi
Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties. However, the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes. Thymus quinquecostatus Čelak., which contains large amounts of bioactive monoterpenes such as thymol and carvacrol, is an important wild medicinal and aromatic plant in China. Monoterpenoids are abundant in glandular secretory trichomes. Here, high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T. quinquecostatus genome at the chromosome level. The 13 chromosomes of T. quinquecostatus had a total length of 528.66 Mb, a contig N50 of 8.06 Mb, and a BUSCO score of 97.34%. We found that T. quinquecostatus had experienced two whole-genome duplications, with the most recent event occurring ∼4.34 million years ago. Deep analyses of the genome, in conjunction with comparative genomic, phylogenetic, transcriptomic, and metabonomic studies, uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development. Genes encoding terpene synthase (TPS), cytochrome P450 monooxygenases (CYPs), short-chain dehydrogenase/reductase (SDR), R2R3-MYB, and homeodomain-leucine zipper (HD-ZIP) IV were among those present in the T. quinquecostatus genome. Notably, Tq02G002290.1 ( TqTPS1 ) was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product γ-terpinene from geranyl diphosphate (GPP). Our study provides significant insight into the mechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme. This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.
研究领域:
植物基因组学
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分子生物学
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次生代谢
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发育生物学
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芳香植物研究
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药用植物学
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系统进化
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DOI
PubMed
高影响因子
Frontiers in Genetics
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2025
·
IF 2.8
Peng Tian,Yangna Liu,Yingli Cheng,Bin Yang,Yuzhi Wang,Bangbang Wu
Folate plays essential role in sustaining cell activity, promoting cell growth, and participating in cell division and proliferation. The demand for colored wheat is increasing day by day due to its high content of anthocyanin, iron, zinc, selenium, and other beneficial elements. To investigate the folate content and its derivatives in colored grains wheat, in this study employed a total of 113 wheat varieties (lines) with varying grain colors. The content of four folate derivatives, tetrahydrofolate (THF), 5-methyltetrahydrofolate (5-CH3-THF), 5-formyltetrahydrofolate (5-CHO-THF), and 5,10-methylenetetrahydrofolate (5,10-CH+THF), in grains cultivated under three different growing conditions were quantified using high performance liquid chromatography (HPLC). The results revealed that the four folate derivatives were distributed among wheat varieties exhibiting varying grain colors, with a coefficient of variation (CV) ranging from 15.34% to 20.10%. Among them, Lin 4179 emerged as a high-folate variety with a total content of 76.00 μg · 100 g-1. The contents of 5-CH3-THF and 5-CHO-THF in the four folate derivatives accounted for approximately 70% of the total folate content and exhibited a significant correlation with total folate content. The mean total folate level in purple and blue grains was 61.84 and 60.95 μg · 100 g-1, respectively, which was significantly higher than that in white (41.93 μg · 100 g−1) and red grains (42.40 μg · 100 g−1). The genotypic effect is the main factor affecting total folate content, while environmental factors had less impact. Genome-wide association studies (GWAS) identified four major loci associated with folate content on the chromosomes 1B, 4D and 7A, of which QFac.4D and QFac.7A.1 were stated as novel. The results of this study provide valuable insight into the development and breeding of folate biofortified wheat varieties.
研究领域:
植物学
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营养学
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遗传学
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产品关联
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
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2025
·Vol. 75
·期 3
·006708
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IF 2
Ling Yao,Manik Prabhu Narsing Rao,Cheng-Jie Xie,Peng Gao,Shu-Qun Zhang,Guo-Hong Liu,Shun-Gui Zhou
Two facultatively aerobic, Gram-stain-positive, rod-shaped, endospore-forming, endophytic bacteria, designated SGZ-1009Tand SGZ-1014, were isolated from the plantPennisetumsp. Strain SGZ-1009Tgrew at 5–50 °C, pH 4.5–11.0 and tolerated up to 4.5% NaCl (w/v), while strain SGZ-1014 exhibited growth at a temperature range of 10–50 °C, pH range 4.5–11.0 and tolerated up to 4.5% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belong to the genusPaenibacillus, closely related to the reference type strain ofPaenibacillus wenxiniaeDSM 100576T(similarity of 97.0%). The genomic relatedness values for both strains, SGZ-1009Tand SGZ-1014, compared to their closest reference strainP. wenxiniaeDSM 100576T, were 81.6% for average nucleotide identity and 26.0% for digital DNA–DNA hybridization, suggesting strain SGZ-1009Trepresents a novel species. The genomic DNA G+C content of strain SGZ-1009Twas 46.4%. Both strains shared anteiso-C15:0(55.9%) as the predominant fatty acid, menaquinone-7 as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Based on these results, strains SGZ-1009Tand SGZ-1014 represent a novel species ofPaenibacillus, for which the namePaenibacillus campisp. nov. is proposed. The type strain is SGZ-1009T(=MCCC 1K08892T=GDMCC 1.4280T=KCTC 43677T=JCM 36670T).
研究领域:
微生物学
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植物学
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分子生物学
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DOI
PubMed
高影响因子
Antibiotics-Basel
·
2019
·Vol. 8
·期 2
·45
·
IF 2.921
Bernardo Ribeiro da Cunha,Luís P. Fonseca,Cecília R. C. Calado
Given the increase in antibiotic-resistant bacteria, alongside the alarmingly low rate of newly approved antibiotics for clinical usage, we are on the verge of not having effective treatments for many common infectious diseases. Historically, antibiotic discovery has been crucial in outpacing resistance and success is closely related to systematic procedures—platforms—that have catalyzed the antibiotic golden age, namely the Waksman platform, followed by the platforms of semi-synthesis and fully synthetic antibiotics. Said platforms resulted in the major antibiotic classes: aminoglycosides, amphenicols, ansamycins, beta-lactams, lipopeptides, diaminopyrimidines, fosfomycins, imidazoles, macrolides, oxazolidinones, streptogramins, polymyxins, sulphonamides, glycopeptides, quinolones and tetracyclines. During the genomics era came the target-based platform, mostly considered a failure due to limitations in translating drugs to the clinic. Therefore, cell-based platforms were re-instituted, and are still of the utmost importance in the fight against infectious diseases. Although the antibiotic pipeline is still lackluster, especially of new classes and novel mechanisms of action, in the post-genomic era, there is an increasingly large set of information available on microbial metabolism. The translation of such knowledge into novel platforms will hopefully result in the discovery of new and better therapeutics, which can sway the war on infectious diseases back in our favor.Keywords:antibiotic discovery platforms;drug screening;semi-synthesis;fully synthetic antibiotics;genomics;proteomics;metabolomics;lipidomics;metagenomics
研究领域:
药理学
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微生物学
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基因组学
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生物信息学
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DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）