## Haruna Nijo transcripts were retrieved from http://barleyflc.dna.affrc.go.jp/bexdb/pages/harunanijo_index.jsp

## Morex cDNA sequences were obtained from ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/

## De novo assembled transcriptomes were produced from reads first published in http://www.pnas.org/content/111/37/13403.full.pdf

#Hordeum spontaneum
XZ2	Hs	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087927	Spring Tibet, China SAMN02483491
ECI-2-0	Hs	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087933	Spring, very later Lower Nahal Oren, Israel SAMN02483497
Turkey-19-24	Hs	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087936	Unknown Bitlis, Turkey SAMN02483500

#Hordeum vulgare
Padanggamu	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087917	hulless 6 Spring Landrace Xinjiang, China SAMN02483503
Beiqing5	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087920	hulles 6 Spring Beiqing 2/11-57 Qinghai, China SAMN02483504
Himala2	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087921	hulles 6 Spring Selection from Landrace Tibet, China SAMN02483505
Yiwuerleng	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1084227	2 Spring Landrace Zhejiang, China SAMN02483506
TX9425	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087922	2 Spring Selection from Landrace Jiangsu, China SAMN02483507
Amagi Nijo	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087926	2 Spring Fuji Nijo/Seijo 17 Japan SAMN02483508
Alexis	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087925	2 Spring Br.1622/Trumof Denmark SAMN02483509
Esterel	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087924	6 Winter 7761/Plaisant France SAMN02483510
Franka	Hv	ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087923	6 Winter Vogelsanger-Gold/Senta//Dura/Dea/3/Vogelsanger-Gold Germany SAMN02483511

They were assembled as shown below for Alexis:

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR108/SRR1087925

/home/contrera/soft/sratoolkit.2.4.2-ubuntu64/bin/fastq-dump --gzip --split-files SRR1087925.sra

zcat SRR1087925_1.fastq.gz | perl -lne 's/^(\S)SRR\S+ /$1/; s/ length=\d+/\/1/; print' | gzip > 1.fq.gz
zcat SRR1087925_2.fastq.gz | perl -lne 's/^(\S)SRR\S+ /$1/; s/ length=\d+/\/2/; print' | gzip > 2.fq.gz

#nohup ~/soft/trinityrnaseq-2.0.2/util/insilico_read_normalization.pl --seqType fq --JM 56G --CPU 8 \
#	--max_cov 30 --pairs_together --PARALLEL_STATS --output norm_reads --right 1.fq.gz --left 2.fq.gz &

nohup ~/soft/trinityrnaseq-2.0.2/Trinity --seqType fq --max_memory 56G --right 1.fq.gz --left 2.fq.gz \
	--CPU 8 --trimmomatic --normalize_reads --full_cleanup --output trinity &

## De novo assembled transcriptomes were produced from reads first published in this work:

SBCC073_fLF
Scarlett_fLF