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Cryptomeria japonica
Description about sugi genome reference sequence (SUGI ver. 1)
Cryptomeria japonica (sugi) is an endemic conifer in Japan and is widely grown due to their rapid growth and high wood quality. It belongs to Cupressaceae sensu lato (s.l.). It has 11 pairs of chromosomes, unlike most species in the Pinaceae, which have 12 pairs (or, rarely, 11 or 13) of chromosomes. The estimated C-values is ~10100 Mbp (Hizume et al. 2001); approximately half the mean genome size of Pinaceae species (22470Mbp) (Leitch et al. 2001). C. japonica is a monoecious species, and the allergic reactions caused by its pollen have become a serious public-health problem in Japan.In this version, reference genome sequences were constructed by whole genome shotgun sequencing using HiFi read (PacBio). The assembled contigs were scaffolded by Illumina short read from Hi-C library.
SUGI ver. 1 release information
| Reference/Feature | #Total | Download (file size) |
md5sum |
|---|---|---|---|
| Scaffold | 2,699 | SUGI_1.genome.fa.gz (2.6 GB) |
63aa6c0eb8e1e4d14d66d2367bf2aa3d |
| Standard gene set | 55,246 | SUGI_1.std.gene.gff3.gz (5.5 MB) |
4e7c055b90a659374fcdf2f3352081cc |
| SUGI_1.std.cds.fa.gz
(15 MB) |
778de81853db7721ae7ba243cec10367 | ||
| Permissive gene set | 152,527 | SUGI_1.pmsv.gene.gff3.gz (11 MB) |
41783713b84aa25668543022a51dfee7 |
| SUGI_1.pmsv.cds.fa.gz
(29 MB) |
34cfcb79de0b6800ccf7da82fbaf99c6 |
| Chromosome | size (bp) |
|---|---|
| chr1 | 718,876,227 |
| chr2 | 680,319,432 |
| chr3 | 1,007,622,168 |
| chr4 | 781,262,672 |
| chr5 | 933,584,362 |
| chr6 | 683,545,021 |
| chr7 | 862,687,481 |
| chr8 | 746,363,822 |
| chr9 | 754,841,075 |
| chr10 | 924,125,822 |
| chr11 | 736,731,119 |
| chrCh (chloroplast) | 131,654 |
Functional annotation
| Download (file size) | md5sum |
|---|---|
| SUGI_1.EnTAP.tsv (77 MB) | 2619deeee4ea42a34f5f492495498d0d |
| SUGI_1.EnTAP.extra.tsv (81 MB) | 0c118dc62b1e2f7fb0054ce9dfeabe6e |
| SUGI_1.EnTAP.extra.xlsx (33 MB) | fdbd6b05537364d158d0fdd244822bb7 |
| SUGI_1.EnTAP.annot (61 MB) | 605b4eec24affdead193c113bb903a47 |
Another information
- # Acknowledgement #
- This work has been supported in part by FFPRI Grant (#201406, #201421, #201906), JSPS KAKENHI Grant Number JP16H06279 (PAGS), and JP20H03239, Bio-oriented Technology Research Advancement Institution (BRAIN) Grant (JPJ007097; Project ID 28013B), and NIBB Collaborative Research Program (15-829, 16-403, 17-405, 18-408, 19-420, 20-428, 21-302, and 22NIBB402).
- # References #
-
- Fujino, T., K. Yamaguchi, T. Yokoyama, T. Hamanaka, Y. Harazono, H. Kamada, W. Kobayashi, T. Ujino-Ihara, K. Uchiyama, A. Matsumoto, A. Izuno, Y. Tsumura, A. Toyoda, S. Shigenobu, Y. Moriguchi, S. Ueno, and M. Kasahara, A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don. BioRxiv, 2023, doi: https://doi.org/10.1101/2023.02.24.529822
- Fujino, T., K. Yamaguchi, T. Yokoyama, T. Hamanaka, Y. Harazono, H. Kamada, W. Kobayashi, T. Ujino-Ihara, K. Uchiyama, A. Matsumoto, A. Izuno, Y. Tsumura, A. Toyoda, S. Shigenobu, Y. Moriguchi, S. Ueno, and M. Kasahara. Chromosome-Level Genome Assembly of Japanese Cedar (Cryptomeria japonica D. Don). in Plant and Animal Genome Conference / PAG30. 2023. San Diego, CA.
- # Links to our research groups #
- Department of Forest Molecular Genetics and
Biotechnology, Forestry and Forest Products Research Institute
- Graduate
School of Frontier Sciences, The University of Tokyo
- Trans-Scale
Biology Center, National Institute for Basic Biology
- Graduate School of Science and Technology,
Niigata University
- Faculty
of Life and Environmental Sciences, University of Tsukuba
- Comparative Genomics Laboratory, National
Institute of Genetics
- # Contact #
- If you have any tracks to be displayed in the JBrowse, feel free to send an email to cj-genome@ffpri.affrc.go.jp
