Table 1.
O. pumila reference genome assembly statistics at different stages and combinations of scaffolding.
| Assembly | Number of contigs | Number of scaffolds | Number of contigs assigned to scaffolds | Contig N50 (Mb) | Scaffold N50 (Mb) | Number of gaps | Assembly size (Mb) |
|---|---|---|---|---|---|---|---|
| PacBioa only (Canu assembly) | 243 | — | — | 9.38 | — | — | 449.00 |
| Bionano de novo Optical Map | — | 458 | — | — | 1.68 | — | 442.00 |
| PacBio + Opticalb Map | 108 | 45 | 83 | 8.21 | 21.05 | 117 | 442.00 |
| PacBio + Hi-Cc | 213 | 34 | 198 | 9.39 | 40.80 | 96 | 441.00 |
| PacBio + Hi-C + Optical Mapd | 239 | 26 | 208 | 8.21 | 24.17 | 91 | 441.90 |
| PacBio + Optical Map + Hi-Ce | 108 | 13 | 108 | 8.21 | 37.11 | 85 | 439.00 |
| PacBio + Optical Map + Hi-C + PbJelly (PacBio) + genome polishing (final O. pumila reference genome) | 31 | 13 (11 Chromosomes + 1 MT + 1 CP) | 31 | 18.49 | 40.06 | 21 | 439.90 |
O. pumila is a medicinal plant that can produce the anticancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly, and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.
aPacBio refers to contig assembly derived using Pacbio reads only and Canu22 assembler.
bPacbio + Optical Map refers to Pacbio contig-level assembly scaffolded by Bionano de novo assembly.
cPacBio + Hi-C refers to Pacbio contig-level assembly scaffolded by Hi-C library sequencing datasets.
dPacBio + Hi-C + Optical Map refers to Pacbio + Hi-C assembly scaffolded by Bionano de novo assembly.
ePacBio + Optical Map + Hi-C refers to Pacbio + Optical Map assembly scaffolded by Hi-C library sequencing datasets.