Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species
Poppies are well-known plants in the family <i>Papaveraceae</i> that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (<i>Papaver rhoeas</i>, <i>Papaver nudicaule</i>, <i>Pap...
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MDPI AG
2018-11-01
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| author | Dowan Kim Myunghee Jung In Jin Ha Min Young Lee Seok-Geun Lee Younhee Shin Sathiyamoorthy Subramaniyam Jaehyeon Oh |
| author_facet | Dowan Kim Myunghee Jung In Jin Ha Min Young Lee Seok-Geun Lee Younhee Shin Sathiyamoorthy Subramaniyam Jaehyeon Oh |
| author_sort | Dowan Kim |
| collection | DOAJ |
| description | Poppies are well-known plants in the family <i>Papaveraceae</i> that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (<i>Papaver rhoeas</i>, <i>Papaver nudicaule</i>, <i>Papaver fauriei</i>, and <i>Papaver somniferum</i>) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three <i>Papaver</i> plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of <i>Papaver</i> species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the <i>Papaver</i> development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of <i>Papaver</i> developmental and secondary metabolite biosynthesis issues in the future. |
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| spelling | doaj.art-05d979f3a4234222a95857ce4999f2942022-12-22T04:23:42ZengMDPI AGData2306-57292018-11-01345510.3390/data3040055data3040055Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> SpeciesDowan Kim0Myunghee Jung1In Jin Ha2Min Young Lee3Seok-Geun Lee4Younhee Shin5Sathiyamoorthy Subramaniyam6Jaehyeon Oh7Genomics Division, National Institute of Agricultural Science, RDA, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 54874, KoreaResearch and Development Center, Insilicogen Inc., Yongin-si, Gyeonggi-do 16954, KoreaKorean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, KoreaKorean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, KoreaKorean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, KoreaResearch and Development Center, Insilicogen Inc., Yongin-si, Gyeonggi-do 16954, KoreaResearch and Development Center, Insilicogen Inc., Yongin-si, Gyeonggi-do 16954, KoreaGenomics Division, National Institute of Agricultural Science, RDA, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 54874, KoreaPoppies are well-known plants in the family <i>Papaveraceae</i> that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (<i>Papaver rhoeas</i>, <i>Papaver nudicaule</i>, <i>Papaver fauriei</i>, and <i>Papaver somniferum</i>) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three <i>Papaver</i> plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of <i>Papaver</i> species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the <i>Papaver</i> development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of <i>Papaver</i> developmental and secondary metabolite biosynthesis issues in the future.https://www.mdpi.com/2306-5729/3/4/55<i>Papaver</i>transcriptomecytochromesalkaloidssequencing |
| spellingShingle | Dowan Kim Myunghee Jung In Jin Ha Min Young Lee Seok-Geun Lee Younhee Shin Sathiyamoorthy Subramaniyam Jaehyeon Oh Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species Data <i>Papaver</i> transcriptome cytochromes alkaloids sequencing |
| title | Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species |
| title_full | Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species |
| title_fullStr | Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species |
| title_full_unstemmed | Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species |
| title_short | Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four <i>Papaver</i> Species |
| title_sort | transcriptional profiles of secondary metabolite biosynthesis genes and cytochromes in the leaves of four i papaver i species |
| topic | <i>Papaver</i> transcriptome cytochromes alkaloids sequencing |
| url | https://www.mdpi.com/2306-5729/3/4/55 |
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