Database Resources of the BIG Data Center in 2018

Xu, Xiwei; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Li, Lan; Wang, Yanqing; Sang, Jian; Fang, Liang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Du, Zhenglin; Ni, Yuan; Zeng, Jingyao; Zhang, Zhe-Wen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Zou, Dong; Song, Shuhui; Xia, Lin; Wang, Zhennan; Li, Man; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Li, Mengwei; Sun, Shixiang; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Yin, Hongyan; Ma, Lina; Chen, Huanxin; Sun, Yuan; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Bào, Yīmíng

doi:10.1093/nar/gkx897

Cited by 117 publications

(54 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive at the Beijing Institute of Genomics, Chinese Academy of Sciences, under accession number CRA000801 and are publicly accessible at http://bigd.big.ac.cn/gsa ( Wang et al, 2017 ; Big Data Center Members, 2018 ). Unique read numbers for each expressed gene were calculated using FPKM and are shown in Supplementary Data Sheet S1 .…”

Section: Resultsmentioning

confidence: 99%

Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG

Liu¹,

Qi²,

Shu³

et al. 2018

Front. Microbiol.

View full text Add to dashboard Cite

Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis. Notably, RNA levels of the conserved and essential 3-ketoacyl carrier protein reductase in this pathway (gene FabG) were elevated in all of the four bacteria after tachyplesin treatment. In vitro tests including surface plasmon resonance and enzyme activity assays showed that tachyplesin could bind and inhibit 3-ketoacyl carrier protein reductase, which was consistent with molecular docking prediction results. As unsaturated fatty acids are important for membrane fluidity, our results provided one possible mechanism to explain how tachyplesin kills bacteria and causes cytotoxicity by targeting membranes, which may be helpful for designing more specific and safer antibiotics based on the function of tachyplesin.

show abstract

Section: Resultsmentioning

confidence: 99%

Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG

Liu¹,

Qi²,

Shu³

et al. 2018

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Data accessibility. The 67 complete ancient mitogenomes reported in this paper have been deposited in the Genome Sequence Archive [30] in BIG Data Center [31], Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession no. HRA000117 that can be accessed at https://bigd.big.ac.cn/gsa-human.…”

Section: Discussionmentioning

confidence: 99%

Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans

Ding

Wang

et al. 2020

Proc. R. Soc. B.

View full text Add to dashboard Cite

The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.

show abstract

“…The raw sequence data have been deposited in the Genome Sequence Archive (Wang et al 2017) in the BIG Data Center (Xu et al 2018), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number CRA001418 and are publicly accessible at http://bigd.big.ac.cn/gsa. The supplemental files contain the following data; Table S1 contains qRT-PCR primers for the validation of RNAseq data.…”

Section: Data Availabilitymentioning

confidence: 99%

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Duan

Armstrong

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.

show abstract

Database Resources of the BIG Data Center in 2018

Cited by 117 publications

References 32 publications

Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG

Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG

Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Contact Info

Product

Resources

About