Additional file 3: of Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress

Validation of SNPs in nine sorghum lines to determine the haplotypes for cold tolerance. (XLSX 10 kb

Peanut_denovo_transcriptome_assembly_methods_comparison_PLosOne

<p>Supporting data for article Chopra, R, G. Burow, A. Farmer, J. Mudge, C. E. Simpson, and M. D. Burow. (in press). Comparisons of De Novo Transcriptome Assemblers in Diploid and Polyploid Species Using Peanut (Arachis spp.) RNA-Seq Data. PLosOne Contains denovo assemblies from A. duranensis KSSc38901, A. ipaensis GKPSSc30076 and A. hypogaea cv OLin CV-75, PI631176. Assemblies were created with AByss, SOAP, and Trinity. The list of files follows. Files are in fasta format, gzipped using the Linux gzip command. They may be unzipped using the gunzip command. There are two files for OLin_AByss_Mmer - one (OLin_AByss_Mmer.fasta.gz) containing the kmer number and other AByss header data, and the other (OLin_AByss_Mmer_ncbi.fasta.gz) file uploaded to NCBI that was modified to omit these data, as was necessary for the NCBI software to accept the file. 30076_AByss_Mmer.fasta.gz 30076_AByss_Mmer_dedup.fasta.gz 30076_AByss_25mer.fasta.gz 30076_SOAP_25mer.fasta.gz 30076_Trinity_25mer.fasta.gz 30076_Trinity_dedup.fasta.gz 38901_AByss_Mmer.fasta.gz 38901_AByss_Mmer_dedup.fasta.gz 38901_Trinity_25mer.fasta.gz 38901_Trinity_dedup.fasta.gz 38901_AByss_25mer.fasta.gz 38901_SOAP_25mer.fasta.gz OLin_AByss_Mmer.fasta.gz OLin_AByss_Mmer_ncbi.fasta.gz OLin_AByss_Mmer_dedup.fasta.gz OLin_Trinity_25mer.fasta.gz OLin_Trinity_dedup.fasta.gz OLin_AByss_25mer.fasta.gz OLin_SOAP_25mer.fasta.gz</p

Statistics on assemblies generated after merging multiple <i>kmer</i> assemblies using Trans-<i>AByss</i> and the non-redundant assemblies from Trinity and <i>AByss</i> [dedup – no redundant sequences, Mmer – multiple merged <i>kmer</i> assemblies].

<p>Statistics on assemblies generated after merging multiple <i>kmer</i> assemblies using Trans-<i>AByss</i> and the non-redundant assemblies from Trinity and <i>AByss</i> [dedup – no redundant sequences, Mmer – multiple merged <i>kmer</i> assemblies].</p

Distribution of contigs with varying percent identity against the legume EST database.

<p>BLASTN searches were performed with the threshold value of 1×10⁻¹⁰. A) 38901, B) 30076, C) Olin.</p

Statistics on <i>de novo</i> assemblies generated at kmer = 25 using Trinity, AByss and SOAPdenovo-Trans.

<p>Statistics on <i>de novo</i> assemblies generated at kmer = 25 using Trinity, AByss and SOAPdenovo-Trans.</p

N50 and total length of the assemblies produced by AByss with different kmers.

<p>A) N50, B) contig length.</p

Statistics on the BLASTX, BLASTN and re-mapping of the raw reads to assemblies respectively.

<p>Statistics on the BLASTX, BLASTN and re-mapping of the raw reads to assemblies respectively.</p

Statistics on filtered FASTQ files using Fastx toolkit.

<p>Statistics on filtered FASTQ files using Fastx toolkit.</p

Assemblies compared in a pair-wise fashion using Mummer, and the proportions covered from each of the assemblies are shown below.

<p>The upper triangular values for each accession represent the proportion of sequences at the left that were present in the sequences at the top of the triangle. The lower triangular values represent the proportion of sequences in the accession at the top that were present in the accession at the left.</p><p>Assemblies compared in a pair-wise fashion using Mummer, and the proportions covered from each of the assemblies are shown below.</p

Distribution of contigs with varying percent identity against the legume protein database.

<p>BLASTX searches were performed with the threshold value of 1×10⁻⁶. A) 38901, B) 30076, C) Olin.</p