ABA	Abscisic acid
AVR	Avirulence
BUSCO	Benchmarking Universal Single-Copy Orthologs
CDPK	Calcium-dependent protein kinase
CDS	Coding sequence
CN	Coiled-coil nucleotide-binding
CNL	Coiled-coil nucleotide-binding leucine-rich repeat
CTAB	Cetyltrimethylammonium bromide
DP	Depth of coverage
DREB	Dehydration-responsive element-binding
ETI	Effector-Triggered Immunity
GO	Gene ontology
HRM	His Royal Majesty
HSP	Heat shock protein
InDel	Insertion & Deletion
LAI	LTR Assembly Index
LD	Linkage disequilibrium
LINE	Long interspersed nuclear element
LTR	Long Terminal Repeats
MHR	Moruga Hill Rice
MITE	Miniature inverted-repeat TEs
MQ	Mapping quality
NB-ARC	Nucleotide-binding adaptor shared by APAF-1, R proteins and CED-4
NLR	Nucleotide-binding leucine-rich repeat
ONT	Oxford Nanopore Technologies
PCA	Principal component analysis
PIP	Plasma membrane intrinsic protein
PYL	Pyrabactin Resistance-like
QD	Quality by depth
QTL	Quantitative trait locus
QV	Quality value
R	Resistance gene
RBH	Reciprocal best BLAST hit
RLK	Receptor-like kinase
RLP	Receptor-like protein
sHSP	Small heat shock protein
SINE	Short interspersed nuclear element
SNP	Single Nucleotide Polymorphism
T	Tolerance gene
TE	Transposable element
TIR	Terminal inverted repeat
TNL	Toll/interleukin-1 receptor nucleotide-binding leucine-rich repeat
Ts/Tv	Transition/Transversion