Table 1.
T‐DNA integration sites in Laccaria genome located in ORFs and their upstream or downstream elements.
| Best blast hit | Predicted functions | Cellular functional group | |
|---|---|---|---|
| Fungal transgenic strains with ORF integrations | |||
| 2. Exon integration in Protein ID: 296957 | Hypothetical protein SNOG_16556 [Phaeosphaeria nodorum SN15]. Score (Bits): 317. E‐value: 2e‐84 | Reverse transcriptase | Transposon activity |
| 4. Exon integration in Protein ID: 318751 | Predicted protein [Coprinopsis cinerea okayama7#1]. Score (Bits): 344. E‐value: 9e‐93 | Zinc finger, MYND type | Chromatin structure and dynamics |
| 23. Exon integration in Protein ID: 316402 | Copia‐type polyprotein, putative [Arabidopsis thaliana]. Score (Bits): 556. E‐value: 6e‐156 | Zinc finger Integrase core domain. Reverse transcriptase | Transposon activity |
| 24. Exon integration in Protein ID: 379393 | Hypothetical protein CC1G_06600 [Coprinopsis cinerea okayama7#130]. Score (Bits): 791. E‐value: 0.0 | Serine/Threonine protein kinase | Signal transduction |
| 28. Exon integration in Protein ID: 318121 | Predicted protein [Coprinopsis cinerea okayama7#130]. Score (Bits): 41.6. E‐value: 0.041 | Unknown | nd |
| 33. Exon integration in Protein ID: 394044 | Hypothetical protein CC1G_09476 [Coprinopsis cinerea okayama7#130]. Score (Bits): 489. E‐value: 1e‐136 | Fungal transcriptional regulatory protein | DNA‐dependent regulation of transcription |
| 34. Exon integration in Protein ID: 316757 | Hypothetical protein CC1G_03966 [Coprinopsis cinerea okayama7#130]. Score (Bits): 174. E‐value: 3e‐41 | Reverse transcriptase | Transposon activity |
| 35. Exon integration in Protein ID: 308902 | Hypothetical protein CC1G_04991 [Coprinopsis cinerea okayama7#130]. Score (Bits): 934. E‐value: 0.0 | RPAP1‐like | Global gene expression |
| 36. Intron integration in Protein ID: 318555 | Hypothetical protein CC1G_08098 [Coprinopsis cinerea okayama7#130]. Score (Bits): 156. E‐value: 2e‐36 | Protein with similarities to di‐tricarboxylate transporter | Transporter |
| 39. Intron integration in Protein ID: 385818 | Predicted protein [Coprinopsis cinerea okayama7#130]. Score (Bits): 103. E‐value: 2e‐20 | Unknown | nd |
| 43a. Exon integration in Protein ID: 306930 or in Protein ID: 304244 | Predicted protein [Coprinopsis cinerea okayama7#130]. Score (Bits): 84.7. E‐value: 1e‐14 | Unknown | nd |
| 51. Exon integration in Protein ID: 317247 | Predicted protein [Coprinopsis cinerea okayama7#130]. Score (Bits): 634. E‐value: 1e‐179 | Unknown | nd |
| Fungal transgenic strains with upstream integrations | |||
| 11. Protein ID: 333685 | Hypothetical protein RUMOBE_00303 [Ruminococcus obeum ATCC 29174]. Score (Bits): 33.5. E‐value: 3.9 Unknown | Unknown | nd |
| 12. Protein ID: 298746 | Predicted protein [Coccidioides immitis RS]. Score (Bits): 37.4. E‐value: 0.25Unknown | Unknown | nd |
| 49. Protein ID: 315197 | Predicted protein [Coprinopsis cinerea okayama7#130]. Score (Bits): 283. E‐value: 1e‐74 | Unknown | nd |
| Fungal transgenic strains with downstream integrations | |||
| 16. Protein ID: 387352 | Ubiquitin‐conjugating enzyme E2‐16 kDa [Ustilago maydis 521]. Score (Bits): 279. E‐value: 3e‐74 | Ubiquitin protein ligase | Protein modification, ubiquitin cycle |
| 18. Protein ID: 296295 | Hypothetical protein CC1G_01879 [Coprinopsis cinerea okayama7#130]. Score (Bits): 312. E‐value: 8e‐83 | RNA binding | Control of meiosis |
a.
Transgenic strain 43 sequence was found twice in Laccaria genome in two different scaffolds.
Rescue plasmids obtained from fungal transgenic strains were subjected to sequencing with the Post‐RB primer that binds within the T‐DNA at 43–62 bases upstream from the RB nick site. A blastn search was performed with the obtained sequences on the JGI Laccaria genome portal (http://genome.jgi‐psf.org/Lacbi1/Lacbi1.home.html) and the T‐DNA–gDNA junctions identified.
nd, not determined.