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/).