First, the maximum percentage of variation was calculated among the six randomly produced read packages of the North Dakota accession, as above, for each superfamily or family (supplementary material S2, Supplementary Material online); then, these values were used as threshold to compare frequencies of different superfamilies and families.
The presence of KBV reads could potentially bias SNP estimation for IAPV in this sample, but given that the two accessions listed above have a genome-average identity of only 77.6%, we believe this effect should be negligible.
A panel of 50 accessions (above) possessing a range of leaf sheath colors were used to assess genetic diversity of OsC1.
TRDJ sequences were truncated to include sequence between the RS (5' end) and splice site (3' end) and comprised those from bovine (identified here in Btau_3.1), human, mouse, ovine and swine (see accession numbers above).
TRDV sequences were truncated to include the V-REGION (IMGT amino acid positions 1 through 108) and comprised those from bovine (identified here in Btau_3.1), human, mouse and ovine (see accession numbers above).
These results suggested that the accessions of the above species were heterozygous.
For Gremlin 1 (~329 bp) Grem1F: 5'-CAAGGMTCAGCMCAATGAYTC-3', Grem1R: 5'-YTTCTTGGGCTTGCAGAAG-3'. GenBank accession numbers for the above amplified fragments are [GenBank: KR081935-KR081937].
A similar study was carried out on all 8 accessions selected above as displaying a SNP1Ws/SNP2Ws or SNP1Ws/SNP2Col haplotype (Fig. 5A).
Principal coordinate analysis was also used to reveal the relationships among the 250 accessions based on the above dissimilarity matrices, with the help of NTSYS-pc version2.1 software [43].
Since it was not possible to study expression in all accessions, we chose the above described "cold core" for detailed analysis.
