De novo transcriptome assembly of two different Prunus salicina cultivars

Abstract

Plum is a globally grown stone fruit and can be divided into several species. In particular, the Prunus salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. The transcriptome data for Prunus salicina has not been reported to our knowledge. In this study, we performed de novo transcriptome assembly for two selected P. salicina cultivars referred to as Akihime and Formosa (commercially important plum cultivars in Korea) using next generation sequencing. We obtained a total of 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly using Trinity revealed 155,169 and 160,186 transcripts for Akihime and Formosa. Next, we identified 121,278 and 116,544 proteins from Akihime and Formosa using TransDecoder. We performed BLASTP against the NCBI non-redundant (nr) dataset to annotate proteins. Taken together, this is the first transcriptome data for P. salicina to our knowledge.

Specifications
Organism/cell line/tissue	Plum (Prunus salicina)/leaves
Sex	N.A.
Sequencer or array type	HiSeq2000
Data format	Raw and processed
Experimental factors	Transcriptome profiling of two different Japanese plum cultivars
Experimental features	Leaves of two different Chinese cultivars referred to as Formosa and Akihime were harvested for total RNA extraction. Prepared libraries were paired-end sequenced by the HiSeq 2000 system. The obtained data was subjected to 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/SRX1187015 for Prunus salicina cultivar Akihime.

http://www.ncbi.nlm.nih.gov/sra/SRX1186990 for Prunus salicina cultivar Formosa.

2. Introduction

Plum is a globally grown stone fruit and can be divided into several species. Of known cultivated plum species, the Prunus salicina species, known as Japanese plum or Chinese plum, and Prunus domestica species, known as European plum, are commercially grown. In particular, the P. salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. Transcriptome data for the P. domestica species has been recently released [1]; however, the genome and transcriptome data for P. salicina have not been reported to our knowledge. In addition, available genetic markers for P. salicina are limited [2]. In this study, we performed de novo transcriptome analyses for two selected P. salicina cultivars referred to as Akihime and Formosa, which are commercially important plum cultivars in Korea, using next generation sequencing.

3. Experimental design, materials, and methods

3.1. Plant materials

Two plum cultivars were grown in an orchard located in Kadam-ri, Hoengseong-up, South Korea (Hoengseong, 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 a single tree 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 a second strand cDNA was 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 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly was performed using Trinity, which uses the de Bruijn graphs algorithm [3]. Detailed information of assembled transcriptome was summarized in Table 1. The numbers of total transcripts for Akihime and Formosa were 155,169 and 160,186, respectively, and N50 values for Akihime and Formosa were 2051 and 1957, respectively. Next, we identified candidate coding regions within the assembled transcripts using the TransDecoder program implemented in the Trinity software distribution. We identified 121,278 and 116,544 proteins from Akihime and Formosa, respectively. To annotate proteins, we performed BLASTP against the NCBI non-redundant (nr) dataset. Taken together, this is the first transcriptome data for P. salicina to our knowledge.

Table 1.

Summary of de novo assembled two Prunus salicina transcriptomes.

Index	Akihime	Formosa
Total trinity transcripts	155,169	160,186
Total trinity components	71,901	74,663
Percent GC	41.75	41.80
Contig N50	2,080	1973
Median contig length	995	906
Average contig	1,334.67	1,256.18
Total assembled bases	207,099,385	201,221,789

Conflict of interest

The authors declare that they have no competing interests.