%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