Transcriptome Dataset of Halophyte Beach Morning Glory, a Close Wild Relative of Sweet Potato

摘要

Introduction Soil salinity is one of the major environmental factors causing crop loss worldwide. Currently, 33% of the global arable land is affected by salinity, hampering crop production in these fields (Flowers and Colmer, 2008 ). As the global population continues to rise, crop production is facing increasing demands (Flowers and Muscolo, 2015 ). With the combined pressures to sustain or even increase the world's food supply, salt tolerance is becoming an important agronomic trait to support crop plant growth and production in marginal and high saline soils.Salt tolerance is a genetically complex trait that has evolved independently by different mechanisms in numerous lineages (Bromham, 2015 ). Efforts to improve salt tolerance in crops through selective breeding have proven difficult (Ruan et al., 2010 ) due to a lack of genetic resources and limited salt tolerance associated with known molecular markers (Deinlein et al., 2014 ).We conducted a transcriptome analysis of a wild relative of the salt-sensitive sweet potato ( Ipomoea batatas ): the beach morning glory ( Ipomoea imperati ). Beach morning glory is a halophyte that thrives in beach ecosystems of high salt content. Our objective was to better understand the genetic basis for salt tolerance in I. imperati , so that future studies might transfer the salt tolerance genes into sweet potatoes. Value of the data Beach Morning is closely related to sweet potatoes, but commonly grows in high salt conditions. This creates a potential genetic source for adding much-needed salt tolerance into future sweet potato breeding strategies. To date, there is no well-characterized transcriptome for either sweet potato or morning glory and no source for gene annotation when exposed to high levels of salt. This dataset of biological triplicates can help in the further understanding of the plant pathways involved under varying salt levels. These data will help identify relevant genes that are significant differentially expressed under salt stress as well as identify genes that are detectable under normal growing conditions in both root and leaf tissue. Gene expression can be compared between the 2 tissue types to identify how different tissues respond within the plant to salt exposure. Data Experimental design, materials, and methods Plant materials Total RNA extraction and quality control, library preparation, and RNA-seq Seeds from I. imperati were collected from St. George Island, Florida as seed and grown in the lab. At 2 weeks of growth 600 mM NaCl solution (treatment) or water (control) was applied to the soil, daily, for 7 days. Three biological replicates for each treatment and species were harvested at 0, 3, 24 h, and 7 days. Total RNA was extracted from the roots and leaves using the Qiagen protocol and treated with DNAse (Qiagen). Quantity and integrity of the extracted total RNA were determined using an Agilent 2100 bioanalyzer (Agilent), respectively, to be RIN >9. A total of 12 RNA-Seq libraries, including three biological replicates, were prepared using Illumina TruSeqRNA sample Preparation Kit (Illumina). Twelve normalized cDNA libraries were constructed and sequenced using the Illumina Hiseq2500 platform (North Carolina State University) to generate 100 bp paired-end raw reads.Raw reads were deposited into the Short Read Archive (SRA database, http://www.ncbi.nlm.nih.gov/sra ) with the following accession information: Bioproject ID = PRJNA322032 Biosample accession Roots = SAMN05007696, SAMN05271550, SAMN05271551 Leafs = SAMN05271552, SAMN05271553, SAMN05271554 SRA Root tissue experiment = SRX1771615, SRX1858743, SRX1858745 SRA Leaf tissue experiment = SRX1858747, SRX1858786, SRX1858810 Root and leaf tissue experiments contain sequence reads of triplicate runs for both salt treated and control. Transcriptome De novo assembly Sequence reads were filtered using the Fastx-toolkit (Gordon and Hannon, 2010 ) for quality and adapter removal using the fastq_quality_trimmer tool with the following parameters: -Q33 -v -t 20. Paired ends were corrected and repaired using Perl script, PE_FIX_POSTQC.pl (all scripts described herein are available at https://github.com/bioinformagical/SweetPotatoRNA-Seq ). Paired reads were validated using validateHiseqPairs.pl.Reads were combined across all conditions and de novo assembled via Trinity (Grabherr et al., 2011 ; version r2013-02-25) using default settings in order to build a suitable set of reference contigs (column 4 of Table 1 ). These contigs are used for the purposes of determining differential gene expression and pathway level analysis (paper in preparation). Assembly is publicly available on Figshare at: https://figshare.com/articles/Morning_Glory_Transcriptome_assembly/3498239 . Table 1 Summary of assembly, from sequencing reads produced to final unigenes assembled . Pre assembly Number of reads Post assembly Number of sequences Raw reads Leaf + Root 252,166,154 Trinity 94,728 Filtered reads Leaf + Root 201