Supporting Information legends:
Figure S1. Numbers and computationally estimated physical sizes of ‘Kasalath’ BAC
contigs along each chromosome.
Figure S2. Length and chromosomal distribution of 938 sequences assembled from
MTP BAC clones of ‘Kasalath’ chromosome 1.
Figure S3. Numbers and distribution of SNPs and indel sites detected along rice
chromosome 1 between ‘Nipponbare’ and ‘Kasalath’.
Figure S4. Annotation of transcripts through chromosomal mapping of short-read
sequences derived individually from total RNAs of leaves and roots of ‘Nipponbare’
and ‘Kasalath’.
Table S1. Detailed information of 'Kasalath' MTP clones assigned along 'Nipponbare'
pseudomolecule sequences (IRGSP, Build5).
Table S2. Detailed results of sequencing and sequence assembly of MTP BAC clones
from 'Kasalath' chromosome 1.
Table S3. Detailed results obtained from comparison and characterization of genomic
sequences and structure of chromosome 1 between 'Nipponbare' and 'Kasalath'.
Table S4. Search for indel sites detected in genic regions on chromosome 1 within 94
accessions of O. sativa and O. rufipogon through PCR amplification and/or Sanger
sequencing.
Table S5. Sequence and structural comparison of all annotated genes on rice
chromosome 1 between 'Nipponbare' and 'Kasalath'.
Table S6. Chromosomal positions and repeat contents of large indel sites (> 1 kb).
Table S7. List of indica full-length cDNAs mapped within insertion or PS sites on
'Kasalath' chromosome 1 through a BLAST search.
Table S8. Transcripts annotated within insertion sites on 'Kasalath' chromosome 1
through piling up of mapped short reads from RNA-Seq analysis.