ABA	Abscisic acid
AtDAP	Arabidopsis DAP-seq-based TF binding occupancy
BLAST	Basic Local Alignment Search Tool
BLASTP	Protein–protein BLAST
BP	Biological process
CC	Cellular component
cCOE	Evolutionarily conserved co-expression
CMC-EnSpm	CACTA-like transposon superfamily
CNV	Copy number variation
DAP-seq	DNA affinity purification sequencing
DEG	Differentially expressed gene
DNA	Deoxyribonucleic acid
ER	Endoplasmic reticulum
ERAD	Endoplasmic-reticulum-associated degradation
FASTQ	Text-based format for sequencing reads and quality scores
FDR	False discovery rate
GENIE3	Gene network inference with ensemble of trees
GFF3	General Feature Format version 3
GO	Gene Ontology
JA	Jasmonic acid
Ka	Nonsynonymous substitution rate
Ka/Ks	Ratio of nonsynonymous to synonymous substitution rates
Ks	Synonymous substitution rate
LTR	Long terminal repeat
MAFFT	Multiple Alignment using Fast Fourier Transform
MCL	Markov Cluster Algorithm
MCScanX	Multiple Collinearity Scan toolkit X
MEME	Multiple EM for Motif Elicitation
MF	Molecular function
MS	Mild stress
MSA	Multiple sequence alignment
NAC	NAM, ATAF1/2, and CUC2
NLS	Nuclear localization signal
OCR	Open chromatin region
OGG	Orthologous gene group
PAV	Presence/absence variation
PCC	Pearson correlation coefficient
PCR	Polymerase chain reaction
PIF–Harbinger	PIF/Harbinger DNA transposon superfamily
PR	Pathogenesis-related
PWM	Position weight matrix
qRT-PCR	Quantitative reverse-transcription PCR
RNA	Ribonucleic acid
RNA-seq	RNA sequencing
SA	Salicylic acid
SD	Standard deviation
SH-aLRT	Shimodaira–Hasegawa approximate likelihood ratio test
SoyDAP	Soybean DAP-seq-based TF binding occupancy
SoyGBN	Soybean gene regulatory network database
SoyMD	Soybean multi-omics database
SoyTFBase	Soybean transcription factor database
SR	Stress recovery
SS	Severe stress
TAIR	The Arabidopsis Information Resource
TAR	Transcriptional activation or repression region
TE	Transposable element
TF	Transcription factor
TPM	Transcripts per million
UPR	Unfolded protein response
VMS	Very mild stress
WGD	Whole-genome duplication
Wm82	Williams 82
WW	Well-watered
YN	Yang–Nielsen method