The genome assembly and the protein-coding genes annotation is submitted at the National Center for Biotechnology Information (NCBI) database under SAMN44350262 in the Bioproject PRJNA831351.
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Ranunculus_cassubicifolius.EDTA.TEanno.gff3.tar.gz: the Ranunculus cassubicifolius transposable elements (TE) annotation in gff3 format -
Ranunculus_cassubicifolius.tRNA.gff3.tar.gz: the Ranunculus cassubicifolius tRNA annotation in gff3 format -
Ranunculus_cassubicifolius.rRNA.gff.tar.gz: the Ranunculus cassubicifolius other short non-coding RNA in gff3 format -
Summary of repeat content identified in the Ranunculus genome using EDTA
| Total sequences | Total length | ||
|---|---|---|---|
| 320 | 2,690,854,146bp | ||
| ---------------------- | ---------- | -------------- | ----------- |
| Class | Count | bpMasked | %masked |
| ---------------------- | ---------- | -------------- | ----------- |
| LINE | |||
| L1 | 31842 | 21,678,526 | 0.81% |
| LTR | |||
| Copia | 147394 | 80,810,425 | 3.00% |
| Gypsy | 1105626 | 654,391,560 | 24.32% |
| unknown | 2075881 | 1,353,935,235 | 50.32% |
| SINE | |||
| tRNA | 309 | 114,573 | 0.00% |
| unknown | 347 | 444,295 | 0.02% |
| TIR | |||
| CACTA | 85851 | 32,242,719 | 1.20% |
| Mutator | 134007 | 38,209,632 | 1.42% |
| PIF_Harbinger | 86910 | 30,275,684 | 1.13% |
| Tc1_Mariner | 32184 | 12,038,336 | 0.45% |
| hAT | 133119 | 40,436,252 | 1.50% |
| nonTIR | |||
| helitron | 123174 | 38,735,549 | 1.44% |
| rDNA | -- | -- | -- |
| 45S | 191 | 42,204 | 0.00% |
| repeat_fragment | 44541 | 11822,897 | 0.44% |
| satellite_DNA | 186 | 83887 | 0.00% |
| ---------------------- | ---------- | -------------- | ----------- |
| total interspersed | 4001562 | 2,315,261,774 | 86.04% |
| ---------------------- | ---------- | -------------- | ----------- |
| Total | 4001562 | 2,315,261,774 | 86.04% |
- Summary of tRNAs identified in the Ranunculus genome using tRNA-Scan-SE
| Isotype | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ala: | 32 | AGC: | 11.0 | GCG: | CGC: | 3.0 | TGC: | 18.0 | |||||
| Gly: | 49 | ACC: | 2.0 | GCC: | 28.0 | CCC: | 10.0 | TCC: | 9.0 | ||||
| Pro: | 41 | AGG: | 15.0 | GGG: | 2.0 | CGG: | TGG: | 24.0 | |||||
| Thr: | 45 | AGT: | 16.0 | GGT: | 6.0 | CGT: | 3.0 | TGT: | 20.0 | ||||
| Val: | 55 | AAC: | 5.0 | GAC: | 26.0 | CAC: | 7.0 | TAC: | 17.0 | ||||
| Ser: | 82 | AGA: | 17.0 | GGA: | 26.0 | CGA: | 6.0 | TGA: | 15.0 | ACT: | 1.0 | GCT: | 17.0 |
| Arg: | 68 | ACG: | 35.0 | GCG: | CCG: | 3.0 | TCG: | 3.0 | CCT: | 5.0 | TCT: | 22.0 | |
| Leu: | 61 | AAG: | 5.0 | GAG: | CAG: | 4.0 | TAG: | 17.0 | CAA: | 27.0 | TAA: | 8.0 | |
| Phe: | 21 | AAA: | GAA: | 21.0 | |||||||||
| Asn: | 78 | ATT: | 29.0 | GTT: | 49.0 | ||||||||
| Lys: | 41 | CTT: | 10.0 | TTT: | 31.0 | ||||||||
| Asp: | 69 | ATC: | 4.0 | GTC: | 65.0 | ||||||||
| Glu: | 39 | CTC: | 9.0 | TTC: | 30.0 | ||||||||
| His: | 29 | ATG: | 6.0 | GTG: | 23.0 | ||||||||
| Gln: | 35 | CTG: | 8.0 | TTG: | 27.0 | ||||||||
| Ile: | 22 | AAT: | 14.0 | GAT: | CAT: | TAT: | 8.0 | ||||||
| Met/iMet: | 103 | CAT: | 103.0 | ||||||||||
| Tyr: | 56 | ATA: | 19.0 | GTA: | 37.0 | ||||||||
| Supres: | 5 | CTA: | TTA: | 4.0 | TCA: | 1.0 | |||||||
| Cys: | 32 | ACA: | 3.0 | GCA: | 29.0 | ||||||||
| Trp: | 21 | CCA: | 21.0 | ||||||||||
| TOTAL | 984 |
| ncRNA type | Number |
|---|---|
| Housekeeping ncRNAs | |
| tRNA | 984 |
| SSU rRNA | 1154 |
| LSU rRNA | 1204 |
| 5s rRNA | 3013 |
| 5.8s rRNA | 1077 |
| Spliceosomal RNA (snRNA) | 99 |
| Short regulatory RNAs | |
| Plant signal recognition particle RNA | 6 |
If you want to use the data in your research, then please cite:
Efficient assembly of plant genomes: A case study with evolutionary implications in Ranunculus (Ranunculaceae) Kevin Karbstein, Nancy Choudhary, Ting Xie, Salvatore Tomasello, Natascha D. Wagner, Birthe Hilkka Barke, Claudia Paetzold, John Paul Bradican, Michaela Preick, Axel Himmelbach, Nils Stein, Argyris Papantonis, Iker Irisarri, Jan de Vries, Boas Pucker, Elvira Hoerandl. bioRxiv 2023.08.08.552429; doi: https://doi.org/10.1101/2023.08.08.552429