Whole genome sequencing (WGS) and RNA-sequencing analyses
The genomic DNA was isolated from leaf samples of each plant using the
CTAB method (Saghai-Maroof et al., 1984). The Illumina TruSeq® Nano DNA
Library Kit (Illumina, USA) was used to construct the DNA libraries. WGS
was performed using the Illumina HiSeq4000 platform (Macrogen Inc.,
Korea) with a paired-end sequencing method. The sequencing depth of WGS
was 137× coverage for WT and 24× coverage for the sitl1 . The
short reads were filtered by NGS QC Toolkit (Lim, Kim, Gilroy, Cushman,
& Choi, 2019). The high-quality reads were 85.45% for WT and 84.03%
for sitl1 after filtering (Figure S1a). The PCR duplicates were
removed via Samtools (http://www.htslib.org/). A total number of
298,835,366 reads for WT and 55,182,756 reads for the sitl1 were
obtained (Figure S1b). Approximately 96% of obtained reads were mapped
on the Nipponbare reference genome (Os-Nipponbare-Reference-IRGSP-1.0)
from the RAP-DB database (https://rapdb.dna.affrc.go.jp/) by
Burrows-Wheeler aligner (Patel & Jain, 2012). The properly paired reads
were 95.78% for WT and 95.92% for the sitl1 . The variant
calling was performed in the GATK program with HaplotypeCaller
(https://gatk.broadinstitute.org/hc/en-us). We removed the lower quality
variants (missing variants, GQ value < 21, Phred Quality score
< 21, missing rate > 0.4, and non-pass variants
detected by VQSR).
The RNA-seq was performed using Illumina HiSeq4000 platform with 3
independent biological replicates. The high-quality reads were obtained
from the raw data of RNA-seq as described above. Approximately 99% of
high-quality short reads were obtained (Figure S1c) and the reads were
assembled by using Cufflinks
(http://cole-trapnell-lab.github.io/cufflinks/). The Cuffdiff was used
to determine DEGs, which had the statistical significance with q value
less than 0.05. To survey the overrepresented metabolism and gene
expression patterns, we used the MapMan program
(https://mapman.gabipd.org/).