Grasscutter Genome Database
Grasscutter Genome Database (GGD) is the database for grasscutter (Thryonomys swinderianus), also known as greater cane rat, providing genomic information to support the studies using this rodent.
List of members for the GGD Project
- National Institute of Genetics, Mouse Genomics Resource Laboratory (Japan)
- Tsuyoshi Koide, Ph.D.
- Kyoto University, Wildlife Research Center (Japan)
- Miho Inoue-Murayama, Ph.D.
- University of Ghana, College of Basic & Applied Sciences (Ghana)
- Boniface B. Kayang, Ph.D.
- Christopher Adenyo, Ph.D.
Contributing organizations
- University of Ghana
- National Institute of Genetics
- Kyoto University
- Grasscutter Initiative for Rural Transformation (GIfT)
The grants contributing to this database are:
Grants-in-Aid for Scientific Research KAKENHI (19KK0177): Contribution to African food security by domestication of a giant rodent and development of a new experimental animal.
Japan Science and Technology Agency, JST-aXis (JPMJAS2017): Promotion of domestication of giant rodent grasscutters for environmental protection and food safety in West Africa.
National Institute of Genetics, NIG-Joint (1B2020): Genome survey for domestication of large rodent grasscutter in Ghana
Statistics
| Build | ThrSwi_NIG_v1 |
| Assembler | Platanus v1.2.4 |
| Total length | 2,181,956,919bp |
| Number of scaffolds | 20,779 |
| Scaffold N50 | 20,890,746bp |
| Contig N50 | 26,644bp |
| GAP length | 37,159,237 |
| Library | # Reads | # Bases | Avg. Size | Read Cov. | Clone Cov. |
|---|---|---|---|---|---|
| PE600 | 1,035M | 259Gb | 638bp | 118x | 150x |
| MP3000 | 182M | 18Gb | 3,147bp | 8x | 130x |
| MP6000 | 170M | 17Gb | 6,157bp | 8x | 238x |
| MP10000 | 174M | 17Gb | 9,575bp | 8x | 379x |
| MP15000 | 191M | 19Gb | 13,457bp | 9x | 585x |
| Tissue | Index | # Reads | # Bases |
|---|---|---|---|
| testis | AR001_ATCACG | 86M | 8.6Gb |
| heart | AR002_CGATGT | 85M | 8.5Gb |
| lung | AR003_TTAGGC | 113M | 11.3Gb |
| muscle | AR004_TGACCA | 91M | 9.1Gb |
| hippocampus | AR005_ACAGTG | 108M | 10.8Gb |
| spleen | AR006_GCCAAT | 101M | 10.1Gb |
| frontal_cortex | AR007_CAGATC | 83M | 8.3Gb |
| dentate_gyrus | AR008_ACTTGA | 78M | 7.8Gb |
| pituitary | AR009_GATCAG | 101M | 10.1Gb |
| hypothalamus | AR010_TAGCTT | 79M | 7.9Gb |
| olfactory_bulb | AR011_GGCTAC | 79M | 7.9Gb |