Table 1. Results of next-generation sequencing for oak reference assembly and polymorphism screening.
Indexed individuals of oaks were sequenced using 150 bp paired-end reads and evaluated using de novo assembly (reference assembly). Pooled individuals were sequenced using 300 bp paired-end reads and evaluated using reference-guided assembly (polymorphism screen).
| Reference Assembly | Polymorphism Screen | |||||
|---|---|---|---|---|---|---|
| QUMO5 | QUPE2 | QURO21 | QUAL | QUMON Pool | QUROB Pool | |
| Sequences | 6,183,339 | 5,281,517 | 6,676,925 | 4,280,049 | 17,370,324 | 28,438,226 |
| Bases sequenced (Gbp) | 1.747 | 1.502 | 0.977 | 1.207 | 10.42 | 17.06 |
| Proportion of reads mapping to cp genome | 3.3 | 1.9 | 7.6 | 0.4 | 0.95 | 2.25 |
| De novo contigs (length sum, Mbp) | 2,085 | 872 | 80 | 7,085 | -- | -- |
| Longest de novo contig (bp) | 135,603 | 60,701 | 27,043 | 57,523 | -- | -- |
| Chloroplast contigs | 4 | 12 | 19 | 20 | -- | -- |
| Variants relative to QUMO5 | 0 | 126 | 124 | 572 | 789 | 346 |
1 Q. robur was sequenced using 100 bp single-end reads.