Abstract
The plants in the Papaver genus are widely known as Poppies, which is used for ornamental and medicinal purposes, to utilize its plants derived alkaloids and attractive flowers. From this genus, we have sequenced the transcriptomes of four species's (Papaver rhoeas (two cultivar), Papaver nudicaule (five cultivar), Papaver fauriei, and Papaver somniferum) leaves at three developmental stages (i.e., leaf rosette (30 days), elongation and branching (60 days), and blossom and seed formations (90 days)), to elucidate the secondary metabolite biosynthesis gene expression profiles at respective plant stages.
Keywords: Papaver, Transcriptome, Developmental stages, Alkaloids, Poppies
Specifications Table
| Subject | Biology |
| Specific subject area | Transcriptomics |
| Type of data | Table, Figure |
| How data were acquired | Illumina Hiseq™ 4000 |
| Data format | Raw sequences (FASTQ) |
| Parameters for data collection | Three developmental stages, i.e., leaf rosette (30 days), elongation and branching (60 days), and blossom and seed formations (90 days) |
| Description of data collection | Papaver plants were grown individually in multiple pots and maintained at 30 °C for 3 months. At three time points (30, 60, and 90 days (and 120 days for P. fauriei only)), individuals were selected for leaf samplings. The leaves collected for the transcriptome analysis have been frozen immediately in liquid nitrogen and stored in a deep freezer at −70 °C. For each species, the experiments were repeated in triplicates (under the same conditions). |
| Data source location | National Institute of Agricultural Science, Republic of Korea |
| Data accessibility | Raw data of the RNA-Seq are available on Sequence Read Archive (SRA) and it has been deposited at NCBI under the bioproject accession PRJNA476004 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA476004). |
Value of the Data
|
1. Data
The dataset present in this article is a transcriptome from the leaves of four Papaver species and its subspecies classified upon their flower colour, as shown in Fig. 1. The tables in this article are as follows: Table 1 explains the sampling time points of Papaver plant from its three different growth stages, and Table 2 explains the quality of the transcriptome data and the sequences mapped to the draft genome and the reference transcriptome. Totally, 590 Gb of transcriptome sequences are generated from 84 sequence libraries (i.e., 28 sampling points with three biological replicates) using Illumina Hi-Seq 4000 equipment and 481 Mb of long reads from 2 libraries using PacBio, iso-seq method. Among those, the short reads, 568.4 GB (96.2%) of bases remained after the pre-processing, as explained in the previous articles [1,2]. Complete reference transcriptome has been employed for the de-novo transcriptome assemblies, as explained in the previous articles [1,2]. Further, the pre-processed reads are mapped to the transcript references, which were obtained from the de-novo assemblies [1,2] and Papaver somniferum draft genome [3]. The coverage of sequence transcriptome is 77X per sample, which was calculated with the reference of transcripts obtained from the draft genome of Papaver somniferum. Part of this transcriptomic data was assessed to catalogue the available secondary metabolite biosynthesis transcripts and the cytochrome multi-family transcripts to the KEGG and cytochrome P450 engineering database (CYPED) [1,2]. Moreover, the differential expression profiles of those transcripts were assessed into two data models, i.e., between the stages of the developmental life cycle and between the Papaver species systematically [1,2]. Moreover, as the genome sequence has been utilized to explain the evolutionary history of morphine pathway [4], and to elucidate their core functions that exist in Papaver plant which can adapt to the whole plant community, as it is self-incompatibility to various environments [5]; hence, this data set could be valuable to assess the genetics behind the Papaver plant functions.
Fig. 1.
The morphological illustrations of Papaver species. The species from the right is Papavar somniferum, P. rhoeas (Asia red A and B), P. fauriei and P. nudicaule. Papaver nudicaule cultivars (yellow dotted lines) and different Papaver species (Red dotted lines).
Table 1.
Summary of the Papaver leaves sampled for the transcriptome sequencing.
| Plant (ID) | Flower Color | Methods | Plant age in Days |
|||
|---|---|---|---|---|---|---|
| 30 | 60 | 90 | 120 | |||
| Papaver rhoeas (RA) | Asia Red A | Illumina | ✓ | ✓ | ✓ | ° |
| Papaver rhoeas (RS) | Asia Red B | Illumina/PacBio | ✓ | ✓ | ✓ | ° |
| Papaver nudicaule (NW) | White | Illumina/PacBio | ✓ | ✓ | ✓ | ° |
| Papaver nudicaule (NO) | Orange | Illumina | ✓ | ✓ | ✓ | ° |
| Papaver nudicaule (NY) | Yellow | Illumina | ✓ | ✓ | ✓ | ° |
| Papaver nudicaule (NS) | Scarlet | Illumina/PacBio | ✓ | ✓ | ✓ | ° |
| Papaver nudicaule (NP) | Pink | Illumina | ✓ | ✓ | ✓ | ° |
| Papaver fauriei (FW) | Yellow | Illumina | ✓ | ✓ | ✓ | ✓ |
| Papaver somniferum (PS) | Scarlet | Illumina | ✓ | ✓ | ✓ | ° |
Table 2.
The sequence summary of individual samples. The reference are 1: Oh, J. et al., 2: Kim, D. et al., and 3: this article.
Pacbio transcriptome sequence libraries.
2. Experimental design, materials, and methods
2.1. Plant samples
Five Papaver nudicaule varieties with different colours of flowers, i.e., white, yellow, pink, orange, and scarlet have grown individually in multiple pots and maintained at 30 °C for 3 months. For the mRNA sequencing, leaf samples were obtained from three developmental stages (i.e., 30, 60, and 90 days). Another four Papaver species (i.e., P. rhoeas, P. nudicaule, P. somniferum, and P. fauriei) have been sampled with a similar procedure that belongs to this project [1,2]. The samples collected for transcriptomic analysis was immediately frozen in the liquid nitrogen and stored in a deep freezer at −70 °C. For each species, the experiments were repeated in triplicates (under the same conditions). Phenotypic differences among these plants, i.e., flower colour, leaves, and the visual appearance of the plant with flowers, are shown in Fig. 1.
2.2. Transcriptome sequencing
The complete sequence library preparation and sequencing experiments for the Illumina protocols were conducted by Macrogen Inc. (Seoul, Korea) (http://www.macrogen.com), the authorized sequence service providers for every individual sample. Illumina Hi-Seq 4000 system has been used to sequence all the individual samples. The details on the RNA library construction was given in the published articles [1,2]. Total raw Illumina short reads from each sample underwent the pre-processing steps, in order to remove the adapter, and low-quality reads using Trimmomatic v0.36 [6]. The processed short reads were then mapped to the assembled transcriptome using Salmon v0.9.1 [7].
2.3. Dataset
The complete sequences generated in this article have been submitted to the GenBank sequence read archive (SRA) under the bio-project ID PRJNA476004, as given in Table 2.
Acknowledgments
The data is produced with the support of the National Institute of Agricultural Science (grant no. PJ01184701), Rural Development Administration, Republic of Korea.
Contributor Information
Sathiyamoorthy Subramaniyam, Email: moorthy@insilicogen.com.
Jae-Hyeon Oh, Email: jhoh8288@korea.kr.
Conflict of Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
References
- 1.Kim D., Jung M., Ha J.I., Lee Y.M., Lee S.-G., Shin Y., Subramaniyam S., Oh J. Transcriptional profiles of secondary metabolite biosynthesis genes and cytochromes in the leaves of four papaver species. Data. 2018;3 [Google Scholar]
- 2.Oh J., Shin Y., Ha J.I., Lee Y.M., Lee S.-G., Kang B.-C., Kyeong D., Kim D. Transcriptome profiling of two ornamental and medicinal papaver herbs. Int. J. Mol. Sci. 2018;19 doi: 10.3390/ijms19103192. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Guo L., Winzer T., Yang X., Li Y., Ning Z., He Z., Teodor R., Lu Y., Bowser T.A., Graham I.A., Ye K. The opium poppy genome and morphinan production. Science. 2018;362:343–347. doi: 10.1126/science.aat4096. [DOI] [PubMed] [Google Scholar]
- 4.Hu Y., Zhao R., Xu P., Jiao Y. The genome of opium poppy reveals evolutionary history of morphinan pathway. Genom. Proteom. Bioinform. 2018;16(6):460–462. doi: 10.1016/j.gpb.2018.09.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Wang L., Lin Z., Triviño M., Nowack M.K., Franklin-Tong V.E., Bosch M. Self-incompatibility in Papaver pollen: programmed cell death in an acidic environment. J. Exp. Bot. 2019;70(7):2113–2123. doi: 10.1093/jxb/ery406. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Patro R., Duggal G., Love M.I., Irizarry R.A., Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 2017;14:417. doi: 10.1038/nmeth.4197. [DOI] [PMC free article] [PubMed] [Google Scholar]