National Bioresource Project (NBRP) "Silkworm" - Genomic Resources

ナショナルバイオリソースプロジェクト「カイコ」- 分担課題：ゲノム資源の収集・保存・提供

Genomic and Transcriptomic Information of Bombycoid Silkmoths

• Analysis of NBRP Genomic Resource-related Information
  
  
  • Silkmoth BLAST Server (implemented by SequenceServer 1.0.14 (Priyam et al. (2019) Mol. Biol. Evol. 36: 2922–2924))
    
    

    Database name (Specify one of them for BLAST)	Species	Library	Clone availability
    Bm_CDS.fa	Bombyx mori (strain p50T)	Predicted protein-coding genes (CDS)	-
    Bmori Fosmid end	Bombyx mori (strain p50T)	End sequences of Fosmid clones	YES
    Bmori_EST_sequence_v2.fasta	Bombyx mori (strain p50T)	End sequences of cDNA clones (EST)	YES
    Bomo_genome_assembly.e.fa	Bombyx mori (strain p50T)	Whole genome assembly (Bmori_2016v1.0; Kawamoto et al. (2019) IBMB)	-
    S.ricini_190725_EVM.all.CDS.fasta	Samia ricini (strain UT)	Predicted protein-coding genes (CDS)	-
    Samia_ricini_EST_sequence.fasta	Samia ricini (strain UT)	End sequences of cDNA clones (EST)	YES
    Sr_genome.fa	Samia ricini (strain UT)	Whole genome assembly (Sr_UT_JL_v1.0; Lee et al. (2021) Mol. Ecol. Resour.)	-
    mandarina-fosmid	Bombyx mandarina (strain Sakado)	End sequences of Fosmid clones	YES
    sequence-Bmori_BAC_end.fasta	Bombyx mori (strain p50T)	End sequences of BAC clones	YES
    Bm_protein.fa	Bombyx mori (strain p50T)	Amino acid sequences translated from the predicted genes	-
    Sr_gene_prot_with_AnnotInf.fasta	Samia ricini (strain UT)	Amino acid sequences (with annotation) translated from the predicted genes	-

    
    
  • Silkmoth Genome Browser (implemented by JBrowse2)
    
    
  
  
• Information at NCBI and SilkwormBase (NBRP)
  
  
  
  • Bombyx mori Genome Assembly (Bmori_2016v1.0) | Strain p50T | NBRP p50
  • Bombyx mori Whole Genome Shotgun Sequences (illumina)
    • Strain c10 illumina | NBRP c10 (Origin: Kojiki)
    • Strain p21 illumina | NBRP p21 (Origin: Chiyotsuru)
    • Strain p22 illumina | NBRP p22 (Origin: Yamato-Nishiki)
    • Strain p20 illumina | NBRP p20 (Origin: Akajuku)
    • Strain k25 illumina | NBRP k25 (Origin: Shokei)
    • Strain f35 illumina | NBRP f35 (Origin: Shoko)
    • Strain b20 illumina | NBRP b20 (Origin: Watako)
    • Strain d18 illumina | NBRP d18 (Origin: Chosenshu-Tanryokken)
    • Strain n16 illumina | NBRP n16 (Origin: Ishiko)
    • Strain o55 illumina | NBRP o55 (Origin: Aojuku-Abura)
    • Strain o56 illumina | NBRP o56 (Origin: Shozan)
    • Strain e10 illumina | NBRP e10 (Origin: Gifu-Gensan-Ohara-Hakuran)
    • Strain p44 illumina | NBRP p44 (Origin: Kyusan-C101)
    • Strain c51 illumina | NBRP c51 (Origin: Kanton-Kinken)
    • Strain g53 illumina | NBRP g53 (Origin: Okyaku-Hakken-Katako)
    • Strain S30 | NBRP S30 (Origin: Fu-yo x Tsukuba-ne)
      • S30-1 illumina
      • S30-2 illumina
    • Strain p42 | NBRP p42 (Origin: Sho-on)
      • p42-1 illumina
      • p42-2 illumina
    • Strain xe28 illumina | NBRP xe28 (Origin: Tamazawa-Cre)
    • Strain xe51 | NBRP xe51 (Origin: Shuko x Ryuhaku)
      • xe51-1 illumina
      • xe51-2 illumina
  • Bombyx mandarina Whole Genome Shotgun Sequences
    • Sakado strain (illumina +PacBio)
    • Oki strain (illumina)
  • Samia ricini Genome Assembly (Sr_UT_JL_v1.0)
  • Samia cynthia pryeri Whole Genome Shotgun Sequences (illumina +PacBio)
    
    

Collection and Distribution of DNA Resources

• How to request the DNA clones
  
  
  • Please identify the DNA clone names (clone IDs) by using the Silkmoth BLAST Server described above. Send an E-mail to nbrp@bombycoid.jp to request the DNA clones. After receiving the E-mail, Gakushuin University will request you to submit an MTA (Material Transfer Agreement). According to the MTA, please complete the payment of the shipping cost (written in Japanese Yen).
  
  
• List of the Distributable DNA Resources
  
  
  
  
• Bulk Dataset of the End Sequences of Distributable DNA Resources

  Species	Data set	Sequence number	Format	Data size	Reference
  Bombyx mori (strain p50T)	End sequences of BAC clones	126,500	FASTA	88.6MB	Koike et al. (2003) Mol. Genet. Genomics
  Bombyx mori (various strains)	End sequences of cDNA clones (EST)	307,766	FASTA	268.4MB	Mita et al. (2003) PNAS ; Suetsugu et al. (2013) G3
  Bombyx mori (strain p50T)	End sequences of Fosmid clones	226,893	FASTA	102.5MB	International Silkworm Genome Consortium (2008) Insect Biochem. Mol. Biol.
  Bombyx mandarina (strain Sakado)	End sequences of Fosmid clones	153,216	FASTA	184.5MB	Sakudoh et al. (2011) Genetics
  Samia ricini (strain UT)	End sequences of cDNA clones (EST)	20,271	FASTA	12.3MB	Meng et al. (2008) Arch. Insect Biochem. Physiol.

  
  
• Charge (Shipping cost)
  
  
  • Shipping cost of the DNA clones (in Japanese Yen)
    
    
  
  
• MTA (Material Transfer Agreement)
  
  
  • MTA Form (Request to nbrp@bombycoid.jp)

• Toru Shimada (Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan)