Transcriptome datasets in MilletRancidDB
Mining of Rancidity Associated Transcripts/Enzymes in Transcriptome Datasets
After literature review, eighty-two publically available transcriptome datasets of different cultivar of Pearl millet were considered. They belong to different tissues like root, leaf etc and also to different stress condition, e.g. heat, drought etc with control conditions. Brief details of these studies is provided in the first table while the complete detail is provided in the next table.
Raw reads were taken for each dataset from SRA database. After then they were assembled using Pearl millet genome sequence available from ICRISAT. After assembly, each transcriptome sequence was aligned against the rancidity genes/enzymes which were taken from 15 different plant species, i.e., 11 species of Pennisetum glaucum, 01 species each of Setaria italica, Eleusine coracana, Oryza sativa and Arabidopsis thaliana.
On this basis, four rancidity associated enzymes, Lipase, Lipoxygenase, Polyphenol Oxidase and Peroxidase were identified in these transcriptome datasets.
| S. No. | Bioproject | Cultivar | Plant part | Country | Reference |
|---|---|---|---|---|---|
| 1. | PRJNA574746 | PRLT2/89-33 | Leaves | Shivhare R, Asif MH, & Lata C. Comparative transcriptome analysis reveals the genes and pathways involved in terminal drought tolerance in pearl millet. Plant Mol Biol 103, 639 | India |
| 2. | PRJNA688001 | Tifleaf 3 | Root | Zhang A, Ji Y, Sun M, et al. Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage. BMC Genomics 22, 568 (2021). https://doi.org/10.1186/s12864-021-07888-5 | China |
| 3. | PRJNA689619 | Tifleaf 3 | Root | Sun M, Lin C, Zhang A, et al. Transcriptome sequencing revealed the molecular mechanism of response of pearl millet root to heat stress. J Agro Crop Sci. 2021; 207: 768 | China |
| 4. | PRJNA756390 | Tifleaf 3 | Leaves | Huang D, Sun M, Zhang A, Chen J, Zhang J, Lin C, Zhang H, Lu X, Wang X, Yan H, Tang J, Huang L. Transcriptional Changes in Pearl Millet Leaves under Heat Stress. Genes. 2021; 12(11):1716. https://doi.org/10.3390/genes12111716 | China |
| 5. | PRJNA766308 | Tifleaf 3 | Root | Ji Y, Lu X, Zhang H, Luo D, Zhang A, Sun M, Wu Q, Wang X, Huang L. Transcriptome Reveals the Dynamic Response Mechanism of Pearl Millet Roots under Drought Stress. Genes. 2021; 12(12):1988. https://doi.org/10.3390/genes12121988 | China |
Detailed information about each of these studies is provided below:
| S. No. | Bioproject | Species / Cultivar | Plant Part | Stress | Replicate(s) | SRA id |
|---|---|---|---|---|---|---|
| 1. | PRJNA574746 | PRLT2/89-33 | Leaves | water stressed (WS) | NA | SRR10198587 |
| 2. | PRJNA574746 | PRLT2/89-33 | Leaves | water stressed (WS) | NA | SRR10198585 |
| 3. | PRJNA574746 | PRLT2/89-33 | Leaves | well-watered (WW) | NA | SRR10198586 |
| 4. | PRJNA574746 | PRLT2/89-33 | Leaves | well-watered (WW) | NA | SRR10198588 |
| 5. | PRJNA688001 | Tifleaf 3 | Root | drought 1 hour | replicate 1 | SRR13355949 |
| 6. | PRJNA688001 | Tifleaf 3 | Root | drought 1 hour | replicate 2 | SRR13355948 |
| 7. | PRJNA688001 | Tifleaf 3 | Root | drought 1 hour | replicate 3 | SRR13355947 |
| 8. | PRJNA688001 | Tifleaf 3 | Root | drought 3 hour | replicate 1 | SRR13355943 |
| 9. | PRJNA688001 | Tifleaf 3 | Root | drought 3 hour | replicate 2 | SRR13355958 |
| 10. | PRJNA688001 | Tifleaf 3 | Root | drought 3 hour | replicate 3 | SRR13355957 |
| 11. | PRJNA688001 | Tifleaf 3 | Root | drought 7 hour | replicate 1 | SRR13355953 |
| 12. | PRJNA688001 | Tifleaf 3 | Root | drought 7 hour | replicate 2 | SRR13355952 |
| 13. | PRJNA688001 | Tifleaf 3 | Root | drought 7 hour | replicate 3 | SRR13355951 |
| 14. | PRJNA688001 | Tifleaf 3 | Root | without drought 1hour | replicate 1 | SRR13355960 |
| 15. | PRJNA688001 | Tifleaf 3 | Root | without drought 1hour | replicate 2 | SRR13355959 |
| 16. | PRJNA688001 | Tifleaf 3 | Root | without drought 1hour | replicate 3 | SRR13355950 |
| 17. | PRJNA688001 | Tifleaf 3 | Root | without drought 3hour | replicate 1 | SRR13355946 |
| 18. | PRJNA688001 | Tifleaf 3 | Root | without drought 3hour | replicate 2 | SRR13355945 |
| 19. | PRJNA688001 | Tifleaf 3 | Root | without drought 3hour | replicate 3 | SRR13355944 |
| 20. | PRJNA688001 | Tifleaf 3 | Root | without drought 7hour | replicate 1 | SRR13355956 |
| 21. | PRJNA688001 | Tifleaf 3 | Root | without drought 7hour | replicate 2 | SRR13355955 |
| 22. | PRJNA688001 | Tifleaf 3 | Root | without drought 7hour | replicate 3 | SRR13355954 |
| 23. | PRJNA689619 | Tifleaf 3 | Root | control_1h | replicate 1 | SRR13354584 |
| 24. | PRJNA689619 | Tifleaf 3 | Root | control_1h | replicate 2 | SRR13354583 |
| 25. | PRJNA689619 | Tifleaf 3 | Root | control_1h | replicate 3 | SRR13354592 |
| 26. | PRJNA689619 | Tifleaf 3 | Root | control_3h | replicate 1 | SRR13354591 |
| 27. | PRJNA689619 | Tifleaf 3 | Root | control_3h | replicate 2 | SRR13354590 |
| 28. | PRJNA689619 | Tifleaf 3 | Root | control_3h | replicate 3 | SRR13354589 |
| 29. | PRJNA689619 | Tifleaf 3 | Root | control_7h | replicate 1 | SRR13354588 |
| 30. | PRJNA689619 | Tifleaf 3 | Root | control_7h | replicate 2 | SRR13354587 |
| 31. | PRJNA689619 | Tifleaf 3 | Root | control_7h | replicate 3 | SRR13354586 |
| 32. | PRJNA689619 | Tifleaf 3 | Root | heat_1h | replicate 1 | SRR13354585 |
| 33. | PRJNA689619 | Tifleaf 3 | Root | heat_1h | replicate 2 | SRR13354582 |
| 34. | PRJNA689619 | Tifleaf 3 | Root | heat_1h | replicate 3 | SRR13354581 |
| 35. | PRJNA689619 | Tifleaf 3 | Root | heat_3h | replicate 1 | SRR13354598 |
| 36. | PRJNA689619 | Tifleaf 3 | Root | heat_3h | replicate 2 | SRR13354597 |
| 37. | PRJNA689619 | Tifleaf 3 | Root | heat_3h | replicate 3 | SRR13354596 |
| 38. | PRJNA689619 | Tifleaf 3 | Root | heat_7h | replicate 1 | SRR13354595 |
| 39. | PRJNA689619 | Tifleaf 3 | Root | heat_7h | replicate 2 | SRR13354594 |
| 40. | PRJNA689619 | Tifleaf 3 | Root | heat_7h | replicate 3 | SRR13354593 |
| 41. | PRJNA756390 | Tifleaf 3 | Leaves | control_1h | replicate 1 | SRR15532987 |
| 42. | PRJNA756390 | Tifleaf 3 | Leaves | control_1h | replicate 2 | SRR15532986 |
| 43. | PRJNA756390 | Tifleaf 3 | Leaves | control_1h | replicate 3 | SRR15532977 |
| 44. | PRJNA756390 | Tifleaf 3 | Leaves | control_48h | replicate 1 | SRR15532976 |
| 45. | PRJNA756390 | Tifleaf 3 | Leaves | control_48h | replicate 2 | SRR15532975 |
| 46. | PRJNA756390 | Tifleaf 3 | Leaves | control_48h | replicate 3 | SRR15532974 |
| 47. | PRJNA756390 | Tifleaf 3 | Leaves | control_96h | replicate 1 | SRR15532973 |
| 48. | PRJNA756390 | Tifleaf 3 | Leaves | control_96h | replicate 2 | SRR15532972 |
| 49. | PRJNA756390 | Tifleaf 3 | Leaves | control_96h | replicate 3 | SRR15532971 |
| 50. | PRJNA756390 | Tifleaf 3 | Leaves | heat_1h | replicate 1 | SRR15532970 |
| 51. | PRJNA756390 | Tifleaf 3 | Leaves | heat_1h | replicate 2 | SRR15532985 |
| 52. | PRJNA756390 | Tifleaf 3 | Leaves | heat_1h | replicate 3 | SRR15532984 |
| 53. | PRJNA756390 | Tifleaf 3 | Leaves | heat_48h | replicate 1 | SRR15532983 |
| 54. | PRJNA756390 | Tifleaf 3 | Leaves | heat_48h | replicate 2 | SRR15532982 |
| 55. | PRJNA756390 | Tifleaf 3 | Leaves | heat_48h | replicate 3 | SRR15532981 |
| 56. | PRJNA756390 | Tifleaf 3 | Leaves | heat_96h | replicate 1 | SRR15532980 |
| 57. | PRJNA756390 | Tifleaf 3 | Leaves | heat_96h | replicate 2 | SRR15532979 |
| 58. | PRJNA756390 | Tifleaf 3 | Leaves | heat_96h | replicate 3 | SRR15532978 |
| 59. | PRJNA766308 | Tifleaf 3 | Root | drought 144 hour | D_R144h_1 | SRR16071963 |
| 60. | PRJNA766308 | Tifleaf 3 | Root | drought 144 hour | D_R144h_2 | SRR16071962 |
| 61. | PRJNA766308 | Tifleaf 3 | Root | drought 144 hour | D_R144h_3 | SRR16071961 |
| 62. | PRJNA766308 | Tifleaf 3 | Root | drought 24 hour | D_R24h_1 | SRR16071960 |
| 63. | PRJNA766308 | Tifleaf 3 | Root | drought 24 hour | D_R24h_2 | SRR16071959 |
| 64. | PRJNA766308 | Tifleaf 3 | Root | drought 24 hour | D_R24h_3 | SRR16071958 |
| 65. | PRJNA766308 | Tifleaf 3 | Root | drought 48 hour | D_R48h_1 | SRR16071954 |
| 66. | PRJNA766308 | Tifleaf 3 | Root | drought 48 hour | D_R48h_2 | SRR16071975 |
| 67. | PRJNA766308 | Tifleaf 3 | Root | drought 48 hour | D_R48h_3 | SRR16071974 |
| 68. | PRJNA766308 | Tifleaf 3 | Root | drought 96 hour | D_R96h_1 | SRR16071970 |
| 69. | PRJNA766308 | Tifleaf 3 | Root | drought 96 hour | D_R96h_2 | SRR16071969 |
| 70. | PRJNA766308 | Tifleaf 3 | Root | drought 96 hour | D_R96h_3 | SRR16071968 |
| 71. | PRJNA766308 | Tifleaf 3 | Root | without drought 144 hour | CK_R144h_1 | SRR16071967 |
| 72. | PRJNA766308 | Tifleaf 3 | Root | without drought 144 hour | CK_R144h_2 | SRR16071966 |
| 73. | PRJNA766308 | Tifleaf 3 | Root | without drought 144 hour | CK_R144h_3 | SRR16071964 |
| 74. | PRJNA766308 | Tifleaf 3 | Root | without drought 24 hour | CK_R24h_1 | SRR16071977 |
| 75. | PRJNA766308 | Tifleaf 3 | Root | without drought 24 hour | CK_R24h_2 | SRR16071976 |
| 76. | PRJNA766308 | Tifleaf 3 | Root | without drought 24 hour | CK_R24h_3 | SRR16071965 |
| 77. | PRJNA766308 | Tifleaf 3 | Root | without drought 48 hour | CK_R48h_1 | SRR16071957 |
| 78. | PRJNA766308 | Tifleaf 3 | Root | without drought 48 hour | CK_R48h_2 | SRR16071956 |
| 79. | PRJNA766308 | Tifleaf 3 | Root | without drought 48 hour | CK_R48h_3 | SRR16071955 |
| 80. | PRJNA766308 | Tifleaf 3 | Root | without drought 96 hour | CK_R96h_1 | SRR16071973 |
| 81. | PRJNA766308 | Tifleaf 3 | Root | without drought 96 hour | CK_R96h_2 | SRR16071972 |
| 82. | PRJNA766308 | Tifleaf 3 | Root | without drought 96 hour | CK_R96h_3 | SRR16071971 |