De novo transcriptome assembly of two different apricot cultivars

Abstract

Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.

Specifications
Organism/cell line/tissue	Apricot (Prunus armeniaca)/leaves
Sex	N.A.
Sequencer or array type	HiSeq2000
Data format	Raw and processed
Experimental factors	Transcriptome profiling of two different apricot cultivars
Experimental features	Leaves of two different apricot cultivars, referred to as Harcot and Ungarische Beste, were harvested for total RNA extraction. Prepared libraries were paired-end sequenced by HiSeq 2000 system. The obtained data was subjected for de novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. We performed BLASTP against the NCBI non-redundant (nr) dataset to annotate identified proteins.
Consent	N/A
Sample source location	Hoengseong, South Korea (37°28′49.6″N 127°58′34.3″E)

1. Direct link to deposited data

http://www.ncbi.nlm.nih.gov/sra/SRX1186946 for Apricot cultivar Harcot http://www.ncbi.nlm.nih.gov/sra/SRX1186893 for Apricot cultivar Ungarische Beste.

2. Introduction

Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree [1]. The origin of apricot is known to be Armenia, as reflected in its scientific name. Today, apricot is being cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. Turkey is the largest producer of fresh and dried apricot in the world, followed by Iran and Uzbekistan [2]. As compared to other Prunus species including peach, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars, Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing.

3. Experimental design, materials, and methods

3.1. Plant materials

Two apricot cultivars were grown in an orchard located in Kadam-ri, Hoengseong-up, South Korea (37°28′49.6″N 127°58′34.3″E). Five leaves from a single tree were harvested and immediately frozen in liquid nitrogen for further experiments.

3.2. RNA isolation, library preparation, and sequencing

Five leaves from one tree of each species were pooled and used for total RNAs extraction using Fruit-mate for RNA Purification (Takara, Shiga, Japan) and the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). For mRNA library preparation, we used a TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions (Illumina, San Diego, U.S.A.). In brief, the poly-A containing mRNAs were isolated using poly-T oligo-attached magnetic beads. The first strand cDNA followed by second strand cDNA were synthesized from purified mRNAs. End repair was performed followed by adenylation of 3′ ends. Adapters were ligated and PCR was conducted to selectively enrich DNA fragments with adapters and to amplify the amount of DNA in the library, respectively. The quality control of generated libraries was conducted using the 2100 Bioanalyzer (Agilent, Santa Clara, U.S.A.). The libraries were paired-end sequenced by Macrogen Co. (Seoul, South Korea) using the HiSeq 2000 platform.

3.3. De novo transcriptome assembly, identification protein coding regions, and annotation

We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste, respectively. De novo transcriptome assembly was performed using Trinity, which uses the de Bruijn graphs algorithm [3]. Detailed information of assembled transcriptome is summarized in Table 1. The numbers of total transcripts for Harcot and Ungarische Beste were 147,501 and 152,235, respectively. N50 values for Harcot and Ungarische Beste were 2027 and 2155, respectively. Next, we identified candidate coding regions within the assembled transcripts using the TransDecoder program implemented in the Trinity software distribution. We identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste, respectively. To annotate proteins, we performed BLASTP against the NCBI non-redundant (nr) dataset. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.

Table 1.

Summary of de novo assembled two apricot transcriptomes.

Index	Harcot	Ungarische Beste
Total trinity transcripts	147,501	152,235
Total trinity components	71,386	69,387
Percent GC	41.64	41.79
Contig N50	2027	2155
Median contig length	1024	1107
Average contig	13,14.31	1409.00
Total assembled bases	193,861,738	214,498,725

Conflict of interest

The authors declare that they have no competing interests.