Identification of PawS1 and PawS-Like (PawL) genes in Heliopsis helia... - SRA

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SRX659707: Identification of PawS1 and PawS-Like (PawL) genes in Heliopsis helianthoides seeds by high-throughput sequencing
1 ILLUMINA (Illumina HiSeq 1500) run: 105.3M spots, 19.8G bases, 12Gb downloads

Design: RNA extraction: Mature dry H. helianthoides seeds were purchased from the Jelitto seed company, Germany. RNA was extracted from whole seeds using the hot phenol method as described in Mylne et al., 2012, Plant Cell 24: 2765-2778. The total RNA solution was DNase treated followed by further purification using the NucleoSpin RNA Clean-up kit (Machery-Nagel). The quality of the RNA was tested by measuring the A260/280 and A260/230 ratios using a NanoDrop Spectrophotometer (ND-1000 Spectrophotometer, ThermoFisher Scientific) and visualizing on a 1% agarose gel stained with ethidium bromide. Library construction: Sequencing libraries were generated using the TruSeq RNA sample prep kit (Illumina). To do so, 300-1000 ng of total mRNA was used according to the manufacturer’s instructions. Sequencing was then performed on an Illumina HiSeq 1500, as a 2 X 101 paired-end run. Data processing: FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used for quality trimming and filtering. Raw reads were trimmed using the FASTQ quality trimmer tool to obtain a quality threshold of the read ends of 30 by maintaining the minimum length after trimming at 50. FASTQ quality filter tool was used to remove poor quality reads to maintain a quality threshold at 22 and minimum percentage of bases that match the quality threshold 22 as 90.

Submitted by: The University of Western Australia

Study: Heliopsis helianthoides seed de novo transcriptome

PRJNA255932 • SRP044725 • All experiments • All runs

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PawS1 (Preproalbumin with SFTI-1) is subjected to an unusual biosynthesis whereby a small trypsin-inhibitory cyclide peptide, SFTI-1 (Sunflower Trypsin Inhibitor-1) is processed from it in addition to a napin-type 2S albumin protein in sunflower seeds. Two PawS genes, PawS1 and PawS2 were identified in sunflower. De novo transcriptomics of seed RNA identified a PawS-Like gene (PawL1) in sunflower and Arnica montana (Elliott et al., 2014, Plant Cell 26: 981-995). The proteins encoded by PawS-Like genes share many features of PawS1, but PawL1 is matured only into a napin and no stable peptide is formed. By using a de novo transcriptomics approach we identified the three PawS1 genes in Heliopsis helianthoides seeds which were previously described by Elliott et al., 2014, Plant Cell 26: 981-995 and a novel PawL1 transcript.

Sample: Heliopsis helianthoides seed sample

SAMN02933923 • SRS664725 • All experiments • All runs

Organism: Heliopsis helianthoides

Library:

Instrument: Illumina HiSeq 1500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: unspecified

Layout: PAIRED

Spot descriptor:

1 forward102 reverse

Runs: 1 run, 105.3M spots, 19.8G bases, 12Gb

Run	# of Spots	# of Bases	Size	Published
SRR1531164	105,274,469	19.8G	12Gb	2014-11-10

ID:: 924147

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