%0 Generic %A Huang, Zhongyun %A Kelly, Shannon %A Matsuo, Rika %A Li, Lin-Feng %A Li, Yaling %A M. Olsen, Kenneth %A Jia, Yulin %A L. Caicedo, Ana %D 2018 %T Supplemental Material for Huang et al., 2018 %U https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Huang_et_al_2018/6853244 %R 10.25387/g3.6853244.v1 %2 https://gsajournals.figshare.com/ndownloader/files/12477653 %2 https://gsajournals.figshare.com/ndownloader/files/12484709 %2 https://gsajournals.figshare.com/ndownloader/files/12996926 %2 https://gsajournals.figshare.com/ndownloader/files/12996929 %2 https://gsajournals.figshare.com/ndownloader/files/12996932 %K red rice %K weed evolution %K candidate genes %K seed shattering %K seed dormancy %K Evolutionary Biology %X
Supplementary tables contain genotype and phenotype of Oryza accessions included in the study, and genomic regions sequenced by target capture. Figure S1 contains phylogeny tree based on SNPs.

A series of in-house Perl scripts to convert the polymorphisms from variant call format (VCF) to FASTA format; estimate of nucleotide diversity including Nei’s average pairwise nucleotide diversity (π) and Watterson’s estimator of theta (θw)

Fasta format files of gene fragments (~1500 base pair) upstream and downstream of the five candidate genes. These fragments were captured following the Agilent (Agilent, Santa Clara, CA) SureSelect Target Enrichment method (Gnirke et al., 2009). A total of 123 loci close to the five candidate genes were targeted and sequenced (Table S2)
%I GSA Journals