Study of terpene biosynthetic pathways in medicinal plants based on big data analysis
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23. Sept. 2025
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Online veröffentlicht: 23. Sept. 2025
Eingereicht: 12. Jan. 2025
Akzeptiert: 08. Mai 2025
DOI: https://doi.org/10.2478/amns-2025-1109
Schlüsselwörter
© 2025 Xiaoqian Zhang et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.
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Quality indicators of Unigene
| Sample | Genome | Total length | Mean length | N50 | N70 | N90 | GC(%) |
|---|---|---|---|---|---|---|---|
| R1-1 | 43889 | 24414215 | 455 | 610 | 401 | 202 | 40.23 |
| R1-2 | 31285 | 43781698 | 527 | 774 | 486 | 217 | 39.59 |
| R1-3 | 39983 | 32687437 | 494 | 696 | 448 | 210 | 40.05 |
| R2-1 | 55141 | 49431632 | 688 | 1113 | 681 | 270 | 40.1 |
| R2-2 | 56317 | 58566372 | 618 | 1041 | 589 | 225 | 40.26 |
| R2-3 | 41928 | 61193397 | 641 | 1012 | 605 | 249 | 38.89 |
| R3-1 | 38344 | 50372121 | 683 | 1122 | 669 | 262 | 40.12 |
| R3-2 | 40886 | 47304575 | 676 | 1106 | 667 | 261 | 40.16 |
| R3-3 | 43889 | 49739930 | 678 | 1070 | 663 | 274 | 39.98 |
| All-Unigene | 116731 | 118032214 | 978 | 1456 | 978 | 397 | 39.55 |
Quality indicators of transcripts
| Sample | Genome | Total length | Mean length | N50 | N70 | N90 | GC(%) |
|---|---|---|---|---|---|---|---|
| R1-1 | 46420 | 29653187 | 467 | 736 | 429 | 180 | 40.15 |
| R1-2 | 84358 | 55318339 | 500 | 844 | 460 | 181 | 39.47 |
| R1-3 | 63630 | 41105112 | 484 | 794 | 443 | 180 | 39.92 |
| R2-1 | 77553 | 61553228 | 631 | 1161 | 632 | 214 | 40.05 |
| R2-2 | 99127 | 72837938 | 580 | 1085 | 552 | 192 | 40.19 |
| R2-3 | 99391 | 75704223 | 606 | 1082 | 588 | 209 | 38.88 |
| R3-1 | 80400 | 63786716 | 632 | 1167 | 631 | 214 | 40.05 |
| R3-2 | 73577 | 58385161 | 629 | 1162 | 631 | 213 | 40.09 |
| R3-3 | 77548 | 61459178 | 630 | 1136 | 634 | 218 | 39.92 |
| Total | 702004 | - | 654 | 1053 | - | - | - |
Annotation results of gene function
| Values | Total | NR | Nt | Swissprot | KEGG | COG | Interpro | GO | Intersection | Overall |
|---|---|---|---|---|---|---|---|---|---|---|
| Quantity | 116731 | 61243 | 27632 | 41652 | 46542 | 52155 | 51432 | 34326 | 13757 | 67564 |
| Total ratio | 100% | 52.47% | 23.67% | 35.68% | 39.87% | 44.68% | 44.06% | 29.41% | 11.79% | 57.88% |
Experimental instrument
| Instrument name | Instrument Model |
|---|---|
| Agilent 1290 type super. high performance liquid chromatograph | 1290 Infinity |
| Electron fraction | Sartorius BT125D |
| Kq5200 super | KQ5200 |
| Youku. Pure water | ULUP-IV-10T |
| Liquid nitrogen research | JXFSTPRP-64 |
| Automatic pressure. Sterilized pan | SANYO MLS-3020 |
| coagulator | DYY-III 33B |
| Gels. Like systems | GELD.OCEQ |
| ptera | T100™ The.ermal cycler |
| High density centrifuge | D-37520 |
| trace | Rese.arch plus |
| Nanophotm-n60 micro. Volume spectrophotometer | N60 Touch |
Experimental reagent
| Reagent name | Reagent type |
|---|---|
| acetonitrile | chromatogram |
| Phosphoric acid | chromatogram |
| Methyl alcohol | Analytical purity |
| Tiangen polysaccharide polyphenol plant total RNA extraction kit | DP441 |
| Nebnext ltram RNA library prep kit | #E7530 |
| DNA 1000 assay kit | 5067-1504 |
| Agencourt AMPure XP | 63881 |
| Agarosey (AGAR sugar) | TSJ001 |
Quality indicators of sample sequencing
| Sample | Original reading (Mb) | Clean reading (Mb) | Clean base (Gb) | Q20 (%) | Q30 (%) | Ratio (%) |
|---|---|---|---|---|---|---|
| R1-1 | 67.92 | 64.96 | 4.59 | 95.35 | 87.47 | 90.83 |
| R1-2 | 70.46 | 63.74 | 4.47 | 95.71 | 88.72 | 86.05 |
| R1-3 | 67.97 | 64.54 | 4.55 | 95.71 | 88.68 | 90.2 |
| R2-1 | 65.48 | 64.17 | 4.51 | 95.76 | 88.95 | 92.96 |
| R2-2 | 65.42 | 63.69 | 4.46 | 95.74 | 88.78 | 92.36 |
| R2-3 | 65.48 | 63.32 | 4.42 | 95.57 | 88.35 | 91.74 |
| R3-1 | 65.48 | 63.03 | 4.4 | 95.61 | 88.44 | 91.32 |
| R3-2 | 65.42 | 63.56 | 4.45 | 95.6 | 88.31 | 92.16 |
| R3-3 | 65.48 | 63.67 | 4.46 | 95.69 | 88.71 | 92.25 |