Table 1. Genome data for Populus nigra subsp. betulifolia, ddPopNigr1.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | ddPopNigr1.1 | |
| Species | Populus nigra | |
| Specimen | ddPopNigr1 | |
| NCBI taxonomy ID | 3691 | |
| BioProject | PRJEB62046 | |
| BioSample ID | SAMEA110450206 | |
| Isolate information | ddPopNigr1: leaf (DNA, Hi-C and RNA sequencing) | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 64.7 | ≥ 50 |
| k-mer completeness | 100.0% | ≥ 95% |
| BUSCO ** | C:97.8%[S:78.5%,D:19.3%],F:0.8%,M:1.4%,n:2,326 | C ≥ 95% |
| Percentage of assembly mapped to chromosomes | 99.73% | ≥ 95% |
| Sex chromosomes | None | localised homologous pairs |
| Organelles | Mitochondrial assemblies: 281.85, 335.57 and 186.15 kb
Plastid genome: 156.37 kb |
complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR11458794 | |
| Hi-C Illumina | ERR11439609 | |
| PolyA RNA-Seq Illumina | ERR12245572 | |
| Genome assembly | ||
| Assembly accession | GCA_951802175.1 | |
| Accession of alternate haplotype | GCA_951802205.1 | |
| Span (Mb) | 413.2 | |
| Number of contigs | 302 | |
| Contig N50 length (Mb) | 3.5 | |
| Number of scaffolds | 21 | |
| Scaffold N50 length (Mb) | 22.5 | |
| Longest scaffold (Mb) | 50.57 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).
** BUSCO scores based on the eudicots_odb10 BUSCO set using version 5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/ddPopNigr1_1/dataset/ddPopNigr1_1/busco.