Table 3.
A comparison of public pan-genome research in Asian rice
| Pan-genome studies | #genomes | Species | Contig N50s | Assembly | Subpopulations (K) | Sequencing Technology | Sequence validation | Inversion callers | Validated | # INVs | Data access |
|---|---|---|---|---|---|---|---|---|---|---|---|
|
Wang et al.28 Fuentes et al.11 |
3K | O. sativa | 5.44 ± 2.87 Kb | Contigs/scaffolds | 9 | Illumina | NA | DELLY & LUMPY | NO | 210,301 (raw) | |
| Zhao et al.92 | 66 |
O. sativa, O. rufipogon |
40.5 ± 13 Kb | Contigs | 4 | Illumina | NA | NA | NA | NA | http://www.ncgr.ac.cn/RicePanGenome |
| Qin et al.12 | 33 |
O. sativa, O. glaberrima |
12.6 ± 4.8 Mb | Chromosome | 9 | PacBio |
BioNanao HiC |
Nucmer & SyRI | NO | 954 | http://www.ricerc.com/ |
| Zhang et al.93 | 111 |
O. sativa, O. rufipogon |
7.4 ± 2.1 Mb | Chromosome/scaffolds | 5 & 9 | PacBio & ONT | NA | NA | NA | NA | https://cgm.sjtu.edu.cn/TGSrice/index.html |
| Shang et al.94 | 251 |
O. sativa, O. rufipogon, O. glaberrima, O. barthii |
10.9 ± 3.7 Mb | Contigs | 2/15(174 accessions from 15 subpopulations of 3K-RGP, GJ-trop2 is missing) | ONT | HiC | Minimap2, NGMLR, and Sniffles | NO | 2784 (raw) | http://www.ricesuperpir.com/ |
| Our study | 75 |
O. sativa, O. rufipogon, O. punctata |
22.7 ± 8.2 Mb | Chromosome | 15 | PacBio & ONT | BioNanao | Nucmer & SyRI | YES | 1769 (validated) | https://yongzhou2019.github.io/Rice-Population-Reference-Panel/ |