Aromolaran O, Oyelade J, Adebiyi E. 2021. Performance
evaluation of features for gene essentiality prediction. Earth and Environmental Science, 655, 012019.
Azhagesan K, Ravindran B, Raman K. 2018. Network-based
features enable prediction of essential genes across diverse organisms. PLoS ONE, 13, e0208722.
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M.
2006. Construction of Escherichia coli K-12 in-frame, single-gene
knockout mutants: The Keio collection. Molecular Systems Biology, 2, 2006.0008.
Benson T E, Marquardt J L, Marquardt A C, Etzkorn F A,
Walsh C T. 1993. Overexpression, purification, and mechanistic study of
UDP-N-acetylenolpyruvylglucosamine reductase. Biochemistry, 32,
2024–2030.
Boinett C J, Cain A K, Hawkey J, Do Hoang N T, Khanh N N
T, Thanh D P. 2019. Clinical and laboratory-induced colistin-resistance
mechanisms in Acinetobacter baumannii. Microbial Genomics, 5, e000246.
Boulanger A, Boureau T, Carrere S, Cesbron S, Chen N W,
Cociancich S. 2016. Using ecology, physiology, and genomics to understand host
specificity in Xanthomonas. Annual Review of Phytopathology, 54, 163–187.
Brötz-Oesterhelt H, Beyer D, Kroll H P, Endermann R,
Ladel C, Schroeder W. 2005. Dysregulation of bacterial proteolytic machinery by
a new class of antibiotics. Nature Medicine, 11,
1082–1087.
Cain A K, Barquist L, Goodman A L, Paulsen I T, Parkhill
J, van Opijnen T. 2020. A decade of advances in transposon-insertion
sequencing. Nature Reviews Genetics, 21, 526–540.
Choudhery S, Brown A J, Akusobi C, Rubin E J, Sassetti C
M, Ioerger T R. 2021. Modeling site-specific nucleotide biases affecting himar1
transposon insertion frequencies in TnSeq data sets. Msystems, 6,
e00876.
Christen B, Abeliuk E, Collier J M, Kalogeraki V S,
Passarelli B, Coller J A. 2011. The essential genome of a bacterium. Molecular Systems Biology, 7, 528.
Coe K A, Lee W, Stone M C, Komazin-Meredith G, Meredith
T C, Grad Y H. 2019. Multi-strain Tn-Seq reveals common daptomycin resistance
determinants in Staphylococcus aureus. PLoS Pathogens, 15, e1007862.
Cooksey D A. 1990. Genetics of bactericide resistance in
plant pathogenic bacteria. Annual Review of Phytopathology, 28, 201–219.
DeJesus M A, Ambadipudi C, Baker R, Sassetti C, Ioerger
T R. 2015. TRANSIT-a software tool for Himar1 TnSeq analysis. Plos Computational Biology, 11, e1004401.
DeJesus M A, Zhang Y J, Sassetti C M, Rubin E J,
Sacchettini J C, Ioerger T R. 2013. Bayesian analysis of gene essentiality
based on sequencing of transposon insertion libraries. Bioinformatics, 29,
695–703.
Deutschbauer A, Price M N, Wetmore K M, Tarjan D R, Xu
Z, Shao W. 2014. Towards an informative mutant phenotype for every bacterial
gene. Journal of Bacteriology, 196, 3643–3655.
Fabian B K, Tetu S G, Paulsen I T. 2020. Application of
transposon insertion sequencing to agricultural science. Frontiers in Plant Science, 11, 291.
Fields P I, Swanson R V, Haidaris C G, Heffron F. 1986.
Mutants of Salmonella typhimurium that cannot survive within the
macrophage are avirulent. Proceedings of the National Academy of Sciences of the United States of America, 83, 5189–5193.
Freed N E. 2017. Creation of a dense transposon
insertion library using bacterial conjugation in enterobacterial strains such
as Escherichia coli or Shigella flexneri. Journal of Visualized Experiments, 127, e56216.
Gawronski J D, Wong S M, Giannoukos G, Ward D V, Akerley
B J. 2009. Tracking insertion mutants within libraries by deep sequencing and a
genome-wide screen for Haemophilus genes required in the lung. Proceedings of the National Academy of Sciences of
the United States of America, 106, 16422–16427.
Gil R, Silva FJ, Peretó J, Moya A. 2004.Determination of
the core of a minimal bacterial gene set. Microbiology and Molecular Biology Reviews, 68, 518–537.
Gong J, Yang G, Yu W, Huang M, Li F, Jin M. 2018. The
development and validation of a liquid chromatography–tandem mass spectrometry
procedure for the determination of dioctyldiethylenetriamine acetate residues
in soil, green and cured tobacco leaves using a modified QuEChERS Approach. Chromatographia, 81, 1035–1041.
Goodman A L, McNulty N P, Zhao Y, Leip D, Mitra R D,
Lozupone C A. 2009. Identifying genetic determinants needed to establish a
human gut symbiont in its habitat. Cell Host & Microbe, 6, 279–289.
Hancock S J, Phan M D, Peters K M, Forde B M, Chong T M,
Yin W F. 2017. Identification of IncA/C plasmid replication and maintenance
genes and development of a plasmid multilocus sequence typing scheme. Antimicrobial Agents and Chemotherapy, 61, e01740-16.
Hensel M, Shea J E, Gleeson C, Jones M D, Dalton E,
Holden D W. 1995. Simultaneous identification of bacterial virulence genes by
negative selection. Science, 269, 400–403.
Jana B, Cain A K, Doerrler W T, Boinett C J, Fookes M C,
Parkhill J. 2017. The secondary resistome of multidrug-resistant Klebsiella pneumoniae. Scientific Reports, 7, 1–10.
Juhas M, Eberl L, Glass J I. 2011. Essence of life:
Essential genes of minimal genomes. Trends in Cell Biology, 21, 562–568.
Kobayashi K, Ehrlich S D, Albertini A, Amati G, Andersen
K, Arnaud M. 2003. Essential Bacillus subtilis genes. Proceedings of the National Academy of Sciences of
the United States of America, 100, 4678–4683.
Lamichhane J R, Osdaghi E, Behlau F, Köhl J, Jones J B,
Aubertot J N. 2018. Thirteen decades of antimicrobial copper compounds applied
in agriculture. A review. Agronomy for Sustainable Development, 38, 1–18.
Langridge G C, Phan M D, Turner D J, Perkins T T, Parts
L, Haase J. 2009. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Research, 19,
2308–2316.
Lee B G, Park E Y, Lee K E, Jeon H, Sung K H, Paulsen H.
2010. Structures of ClpP in complex with acyldepsipeptide antibiotics reveal
its activation mechanism. Nature Structural & Molecular Biology, 17, 471–478.
Lee H H, Ostrov N, Wong B G, Gold M A, Khalil A S,
Church G M. 2019. Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nature Microbiology, 4,
1105–1113.
Lein W, Bornke F, Reindl A, Ehrhardt T, Stitt M,
Sonnewald U. 2004. Target-based discovery of novel herbicides. Current Opinion in Plant Biology, 7, 219–225.
Levitan A, Gale A N, Dallon E K, Kozan D W, Cunningham K
W, Sharan R. 2020. Comparing the utility of in vivo transposon
mutagenesis approaches in yeast species to infer gene essentiality. Current Genetics, 66, 1117–1134.
Li S, Li X, Zhang H, Wang Z, Xu H. 2021. The research
progress in and perspective of potential fungicides: Succinate dehydrogenase
inhibitors. Bioorganic & Medicinal Chemistry, 50,
116476.
Li Y, Mi X, Zhao S, Zhu J, Guo R, Xia X. 2020.
Comprehensive profiling of alternative splicing landscape during cold
acclimation in tea plant. BMC Genomics, 21, 1–16.
Lim H C, Sher J W, Rodriguez-Rivera F P, Fumeaux C,
Bertozzi C R, Bernhardt T G. 2019. Identification of new components of the
RipC-FtsEX cell separation pathway of Corynebacterineae. PLoS Genetics, 15, e1008284.
Liu S, Mi X, Zhang R, An Y, Zhou Q, Yang T. 2019.
Integrated analysis of miRNAs and their targets reveals that miR319c/TCP2
regulates apical bud burst in tea plant (Camellia sinensis). Planta, 250, 1111–1129.
Liu W, Liu J, Triplett L, Leach J E, Wang G L. 2014.
Novel insights into rice innate immunity against bacterial and fungal
pathogens. Annual Review of Phytopathology, 52,
213–241.
Liu Y, Gao Y, Liu X, Liu Q, Zhang Y, Wang Q. 2017.
Transposon insertion sequencing reveals T4SS as the major genetic trait for
conjugation transfer of multi-drug resistance pEIB202 from Edwardsiella. BMC Microbiology, 17, 1–15.
Livak K J, Schmittgen T D. 2001. Analysis of relative
gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.
Loman N J, Constantinidou C, Chan J Z, Halachev M,
Sergeant M, Penn C W. 2012. High-throughput bacterial genome sequencing: An
embarrassment of choice, a world of opportunity. Nature Reviews Microbiology, 10, 599–606.
Luo H, Lin Y, Gao F, Zhang C T, Zhang R. 2014. DEG 10,
an update of the database of essential genes that includes both protein-coding
genes and noncoding genomic elements. Nucleic Acids Research, 42, D574–D580.
Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum
M, Ronald P. 2012. Top 10 plant pathogenic bacteria in molecular plant
pathology. Molecular Plant Pathology, 13, 614–629.
Morinière L, Lecomte S, Gueguen E, Bertolla F. 2021. In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to
discriminate between core and contextual essential genes. Microbial Genomics, 7, 000546.
Müller C, Strengert M, Ertl T. 2007. Adaptive load
balancing for raycasting of non-uniformly bricked volumes. Parallel Computing, 33, 406–419.
Mushegian A R, Koonin E V. 1996. A minimal gene set for
cellular life derived by comparison of complete bacterial genomes. Proceedings of the National Academy of Sciences of
the United States of America, 93, 10268–10273.
Nandi S, Subramanian A, Sarkar R R. 2017. An integrative
machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features. Molecular BioSystems, 13, 1584–1596.
Van Opijnen T, Bodi K L, Camilli A. 2009. Tn-seq:
High-throughput parallel sequencing for fitness and genetic interaction studies
in microorganisms. Nature Methods, 6, 767–772.
Van Opijnen T, Camilli A. 2013. Transposon insertion
sequencing: A new tool for systems-level analysis of microorganisms. Nature Reviews Microbiology, 11, 435–442.
Pennisi E. 2010. Armed and dangerous. Science, 327,
804–805.
Poulin L, Raveloson H, Sester M, Raboin L, Silué D,
Koebnik R, Szurek B. 2014. Confirmation of bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola on rice in Madagascar. Plant Disease, 98, 1423.
Poulsen B E, Yang R, Clatworthy A E, White T, Osmulski S
J, Li L. 2019. Defining the core essential genome of Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 116, 10072–10080.
Price M N, Zane G M, Kuehl J V, Melnyk R A, Wall J D,
Deutschbauer A M. 2018. Filling gaps in bacterial amino acid biosynthesis
pathways with high-throughput genetics. PLoS Genetics, 14,
e1007147.
Qian X H, Lee P W, Cao S. 2010. China: Forward to the
green pesticides via a basic research program. Journal of Agricultural and Food Chemistry, 58, 2613–2623.
Qian Z H, Li T, Guan Y B. 2021. The preliminary study of
sensitivity and resistance risk of Pythium aphanidermatum to
Xinjunan. Modern Agrochemicals, 20, 61–65. (in Chinese)
Ryan R P, Vorhölter F J, Potnis N, Jones J B, Van Sluys
M A, Bogdanove A J. 2011. Pathogenomics of Xanthomonas: Understanding
bacterium–plant interactions. Nature Reviews Microbiology, 9, 344–355.
Sanner M F. 1999. Python: A programming language for
software integration and development. Journal of Molecular Graphics & Modelling, 17, 57–61.
Shen W, Le S, Li Y, Hu F. 2016. SeqKit: A cross-platform
and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE, 11, e0163962.
Sundin G W, Castiblanco L F, Yuan X, Zeng Q, Yang C H.
2016. Bacterial disease management: Challenges, experience, innovation and
future prospects: Challenges in bacterial molecular plant pathology. Molecular Plant Pathology, 17, 1506–1518.
Su Y, Xu Y, Li Q, Yuan G, Zheng D. 2020. The essential
genome of Ralstonia solanacearum. Microbiological Research, 238, 126500.
Wang S, Lin Z, Su K, Zhang J, Zhang L, Gao Z. 2018.
Effect of curcumin and pirfenidone on toxicokinetics of paraquat in rat by
UPLC–MS/MS. Acta Chromatographica, 30, 26–30.
Wetmore K M, Price M N, Waters R J, Lamson J S, He J,
Hoover C A. 2015. Rapid quantification of mutant fitness in diverse bacteria by
sequencing randomly bar-coded transposons. MBio, 6, e00306–00315.
Wu Y, Jiang X, Zhang S, Dai X, Liu Y, Tan H. 2016.
Quantification of flavonol glycosides in Camellia sinensis by MRM mode of
UPLC-QQQ-MS/MS. Journal of Chromatography B, 1017,
10–17.
Xu S, Zhao X, Liu F, Cao Y, Wang B, Wang X. 2018.
Crucial role of oxidative stress in bactericidal effect of parthenolide against Xanthomonas oryzae pv. oryzae. Pest Management Science, 74, 2716–2723.
Yasir M, Turner A K, Bastkowski S, Page A J, Telatin A,
Phan M D. 2019. A new massively-parallel transposon mutagenesis approach
comparing multiple datasets identifies novel mechanisms of action and
resistance to triclosan. BioRxiv, doi.org/10.1101/596833.
Yu G, Wang L G, Han Y, He Q Y. 2012. clusterProfiler: An
R package for comparing biological themes among gene clusters. Omics: A Journal of Integrative Biology, 16, 284–287.
Zhou Q, Li L, Liu F, Hu J, Cao Y, Qiao S. 2022. Mining
and characterization of oxidative stress-related binding proteins of
parthenolide in Xanthomonas oryzae pv. oryzae. Pest Management Science, 78, 3345–3355.
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