0_NewToolsThesis.tex

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%Acronyms
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%Organism Names
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\DeclareAcronym{Fo}{
  short = \textit{Fo},
  long  = \textit{Fusarium oxysporum},
}

\DeclareAcronym{Focub}{
  short = \textit{Focub},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{cubense}}

\DeclareAcronym{Focub4}{
  short = \textit{Focub} TR4,
  long  = \textit{Fusarium oxysporum} f. sp. \textit{cubense} Tropical Race 4}

\DeclareAcronym{Focub1}{
  short = \textit{Focub} R1,
  long  = \textit{Fusarium oxysporum} f. sp. \textit{cubense} Race 1,
}

\DeclareAcronym{Foly}{
  short = \textit{Foly},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{lycopersici},
}

\DeclareAcronym{Fon}{
  short = \textit{Foni},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{niveum},
}

\DeclareAcronym{Fona}{
  short = \textit{Fona},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{narcissi},
}

\DeclareAcronym{Fola}{
  short = \textit{Fola},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{lactucae},
}

\DeclareAcronym{Foci}{
  short = \textit{Foci},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{coriandrii},
}

\DeclareAcronym{Foma}{
  short = \textit{Foma},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{matthiolae},
}

\DeclareAcronym{Foa}{
  short = \textit{Foap},
  long  = \textit{Fusarium oxysporum} f. sp. \textit{apii},
}

\DeclareAcronym{Fs}{
  short = \textit{Fs},
  long  = \textit{Fusarium sacchari},
}

\DeclareAcronym{Fm}{
  short = \textit{Fm},
  long  = \textit{Fusarium mindanaoense},
  mark-as-used=first
}

\DeclareAcronym{Ff}{
  short = \textit{Ff},
  long  = \textit{Fusarium fujikuroi},
}

\DeclareAcronym{Fg}{
  short = \textit{F. graminearum},
  long  = \textit{Fusarium graminearum},
}

\DeclareAcronym{r1}{
  short = R1,
  long  = Race 1,
}

\DeclareAcronym{r2}{
  short = R2,
  long  = Race 2,
}  

\DeclareAcronym{r3}{
  short = R3,
  long  = Race 3,
}  

\DeclareAcronym{r4}{
  short = R4,
  long  = Race 4,
}

\DeclareAcronym{tr4}{
  short = TR4,
  long  = Tropical Race 4,
}

\DeclareAcronym{str4}{
  short = STR4,
  long  = Sub-Tropical Race 4,
}

\DeclareAcronym{fsp}{
  short = f. sp.,
  short-plural-form = f. spp.,
  long = \textit{forma specialis},
  long-plural-form  = \textit{formae speciales},
}

\DeclareAcronym{FFSC}{
  short = FFSC,
  long  = \textit{Fusarium fujikuroi} species complex,
}  

\DeclareAcronym{FOSC}{
  short = FOSC,
  long  = \textit{Fusarium oxysporum} species complex,
} 

\DeclareAcronym{FGSC}{
  short = FGSC,
  long  = \textit{Fusarium graminearum} species complex,
} 

\DeclareAcronym{vcg}{
  short = VCG,
  long  = Vegetative Compatibility Group,
} 

\DeclareAcronym{xvm}{
  short = \textit{Xvm},
  long  = \textit{Xanthomonas vasicola} pv. \textit{musacearum},
} 

\DeclareAcronym{fwb}{
  short = FWB,
  long  = Fusarium wilt of banana} 

  \DeclareAcronym{xwb}{
  short = XWB,
  long  = Xanthomonas wilt of banana,
} 

%Genes, Proteins etc
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\DeclareAcronym{tef}{
  short = TEF-1\textalpha,
  long  = translation elongation factor-1\textalpha ,
}

\DeclareAcronym{rbp2}{
  short = RPB\textit{ii},
  long  = RNA polymerase subunit 2,
}

\DeclareAcronym{mites}{
  short = MITEs,
  long  = Miniature inverted-repeat transposable elements,
}

\DeclareAcronym{te}{
  short = TE,
  long  = transposable element,
}

\DeclareAcronym{mimp}{
  short = \textit{mimp},
  long  = \textit{\underline{m}iniature \underline{imp}ala},
}

\DeclareAcronym{sixg}{
  short = \textit{SIX} gene,
  long  = \textit{Secreted In Xylem} gene,
}

\DeclareAcronym{sixp}{
  short = SIX protein,
  long  = Secreted In Xylem protein,
}

\DeclareAcronym{vic}{
  short = \textit{Vic},
  long  = \textit{Vegetative Incompatibility}}

\DeclareAcronym{rga2}{
  short = \textit{RGA2},
  long  = \textit{Resistance Gene Analog 2}}



%Biologial Processes & General Terms
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\DeclareAcronym{AVR}{
short = AVR,
long = avirulence,
}

\DeclareAcronym{cec}{
short = CEC,
long = candidate effector cluster}

\DeclareAcronym{ce}{
short = CE,
long = candidate effector,
}

\DeclareAcronym{mimpce}{
short = MACE,
long = \textit{mimp}-associated candidate effector,
}

\DeclareAcronym{ac}{
short = AC,
long = accessory chromosome,
}

\DeclareAcronym{cc}{
short = CC,
long = core chromosome,
}

\DeclareAcronym{bp}{
short = bp,
long = base pair,
}

\DeclareAcronym{tir}{
short = TIR,
long = Terminal Invert Repeat,
}

\DeclareAcronym{prr}{
short = PRRs,
long = pattern recognition receptors,
}

\DeclareAcronym{nlr}{
short = NLR,
long = nucleotide-binding leucine-rich receptor,
}

\DeclareAcronym{pamp}{
short = PAMPs,
long = pathogen-associated molecular patterns,
}

\DeclareAcronym{pti}{
short = PTI,
long = PAMP-triggered immunity,
}


\DeclareAcronym{pcr}{
short = PCR,
long = polymerase chain reaction,
}
  
\DeclareAcronym{eti}{
short = ETI,
long = effector-triggered immunity,
}

\DeclareAcronym{ets}{
short = ETS,
long = effector-triggered susceptibility,
}

\DeclareAcronym{rprot}{
short = R proteins,
long = resistance proteins,
}

\DeclareAcronym{rgene}{
short = R gene,
long = resistance gene,
}

\DeclareAcronym{nafld}{
short = NAFLD,
long = Non-Alcoholic Fatty Liver Disease,
}

\DeclareAcronym{nafl}{
short = NAFL,
long = Non-Alcoholic Fatty Liver,
}

\DeclareAcronym{nash}{
short = NASH,
long = Non-Alcoholic Steato-Hepatitis,
}
                   
%Bioinf 
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\DeclareAcronym{blast}{
short = BLAST,
long = Basic Local Alignment Tool,
}

\DeclareAcronym{orf}{
short = ORF,
long = Open Reading Frame,
}

\DeclareAcronym{busco}{
short = BUSCO,
long = Benchmarking Universal Single-Copy Orthologs,
}

\DeclareAcronym{maei}{
short = MAEI,
long = \textit{Mimp}-Associated Effector Identification,
}

\DeclareAcronym{star}{
short = STAR,
long = Spliced Transcripts Alignment to a Reference,
}

\DeclareAcronym{ml}{
short = ML,
long = machine learning,
}

\DeclareAcronym{phibase}{
short = PHI-base,
long = Pathogen-Host Interaction Database,
}               

%Stats
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\DeclareAcronym{anova}{
short = ANOVA,
long = Analysis of Variance,
}

\DeclareAcronym{plsda}{
short = PLS-DA,
long = Partial Least Squares-Discriminant Analysis,
}

\DeclareAcronym{hmm}{
short = HMM,
long = Hidden Markov Model
}

\DeclareAcronym{fc}{
short = FC,
long = fold change
}



%Experimental Terms and Techniques
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\DeclareAcronym{hpi}{
short = hpi,
long = hours post-inoculation,
}

\DeclareAcronym{dpi}{
short = dpi,
long = days post-inoculation,
}

\DeclareAcronym{wpi}{
short = wpi,
long = weeks post-inoculation,
}

\DeclareAcronym{ont}{
short = ONT,
long = Oxford Nanopore Technologies,
}

\DeclareAcronym{hplc}{
short = HPLC,
long = high-performance liquid chromatography,
}

\DeclareAcronym{lcms}{
short = LC-MS,
long = Liquid Chromatography-Mass Spectrometry,
}

\DeclareAcronym{esi}{
short = ESI,
long = electrospray ionisation,
}

\DeclareAcronym{lamp}{
short = LAMP,
long = Loop-mediated isothermal amplification
}

\DeclareAcronym{pda}{
short = PDA,
long = potato dextrose agar,
}

\DeclareAcronym{pdb}{
short = PDB,
long = potato dextrose broth,
}

\DeclareAcronym{ypgb}{
short = YPGB,
long = {yeast, peptone, and glucose broth},
}

\DeclareAcronym{ypga}{
short = YPGA,
long = {yeast, peptone, and glucose agar},
}

\DeclareAcronym{rpm}{
short = rpm,
long = revolutions per minute
}

\DeclareAcronym{sdw}{
short = SDW,
long = sterile distilled water
}

\DeclareAcronym{um}{
short = UM,
long = untargeted metabolomics,
}

\DeclareAcronym{srm}{
short = SRM,
long = selected reaction monitoring,
}

%Organisations
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\DeclareAcronym{FAO}{
short = FAO,
long = Food and Agriculture Organisation of the United Nations}

\DeclareAcronym{wbf}{
short = WBF,
long = World Banana Forum}

\DeclareAcronym{ncbi}{
short = NCBI,
long = National Center of Biotechnology Information}

\DeclareAcronym{ngdc}{
short = NGDC,
long = National Genomics Data Centre}

\DeclareAcronym{tnau}{
short = TNAU,
long = Tamil Nadu Agricultural University }

\DeclareAcronym{niab}{
short = NIAB,
long = National Institute of Agricultural Botany}


%Misc
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\DeclareAcronym{rs}{
short = RS,
long = remote sensing }

\DeclareAcronym{uav}{
short = UAV,
long = Unmanned Aerial Vehicle}

\DeclareAcronym{vi}{
short = VI,
long = Vegetation Indices}

\DeclareAcronym{ps2}{
short = PSII,
long = Photosystem II}




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%Prelimary Sections
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\clearpage
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\addcontentsline{toc}{chapter}{Acknowledgements}
\chapter*{\huge\centering Acknowledgements}
\input{Preamble/0.1_Acknowledgments}

\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{Thesis Declaration}
\chapter*{\huge\centering Thesis Declaration}
\input{Preamble/0.2_Declarations}

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\phantomsection
\addcontentsline{toc}{chapter}{Abstract}
\chapter*{\huge\centering Abstract}
\input{Preamble/0.3_Abstract}

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\addcontentsline{toc}{chapter}{Abbreviations}
\chapter*{\huge\centering Abbreviations}  
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\chapter{General Introduction}\label{Chap1}
\chaptermark{Introduction}
\pagenumbering{arabic} %! Begins arabic numerals start from page 1.
    \input{Chapters/1_Introduction.tex}
    
\chapter{A potential Newly Described \textit{Fusarium} Pathogen of Banana Identified in India}\label{Chap2}
    \input{Chapters/2_PotentialNovelFusarium.tex}
    
\chapter{Improving Genomic Tools for Identifying Virulence Factors in  \textit{Fusarium oxysporum formae specialis}}\label{Chap3}
     \input{Chapters/3_ImprovingGenomicTools.tex}
    
\chapter{The Banana-pathogen Metabolome}\label{Chap4}
     \input{Chapters/4_Metabolomics.tex}

\chapter{The Future of Fusarium Wilt of Banana Research is Multi-omic: A General Discussion}\label{Chap5}
    \input{Chapters/5_GeneralDiscussion}

% \chapter*{Covid-19 Impact Statement}
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\addcontentsline{toc}{chapter}{Bibliography}
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\begin{appendices}

\input{Appendices/Chap2-Appendix}

\input{Appendices/Chap3-Appendix}

\input{Appendices/Chap4-Appendix}

\end{appendices}

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