ForestGEN
Forest EST and Genome database

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.

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

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

# 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. BMC Genomics 25:1039, 2024, doi: https://doi.org/10.1186/s12864-024-10929-4

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