Hippophae rhamnoides Information Archive
Hippophae rhamnoides Information Archive
- A hybrid approach that integrates Illumina paired-end and PacBio long-read sequencing data was employed to assemble the sea buckthorn plant genome. The ALLpaths-LG was first used to de novo assembly the raw illumina sequencing data, and the WTDBG and DBG2OLC were used to de novo assembly the PacBio sequencing data. Finally，Quickmerge was used to produce a more contiguous assembly, and LACHESIS was used to assemble to pseudo-chromosomes.
| Genome Characteristic | |
|---|---|
| Estimated genome size (Mb) | 978.77 |
| Number of scaffolds | 3642 |
| Total length of scaffolds (bp) | 849,035,029 |
| N50 of scaffolds (bp) | 69,524,443 |
| N90 of scaffolds (bp) | 1,800,000 |
| Longest scaffolds (bp) | 92,334,523 |
| Number of contigs | 6,357 |
| Total length of contigs (bp) | 846,833,702 |
| N50 of contigs (bp) | 2,151,660 |
| N90 of contigs (bp) | 58,930 |
| Longest contigs (bp) | 25,098,727 |
| GC content of the genome (%) | 30.09 |
References:
Kajitani, R. et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Research 24, 1384-1395 (2014).
English, A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PloS one 7, e47768 (2012).
Huang, S. et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Research 22, 1581-1588 (2012).