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Last updated: 2017/04/21
 
cDNA    The complete sequences of the FL-cDNA clones   piRNA    ChIP-seq   Assembled RNA-seq    ORF from Assembled RNA-seq
SAGE    MPSS   Transposon    GeneModel (2017)    Old GeneModel (2008)   Scaffold    Fosmid   BAC
Hypothetically reconstructed genomes of 18 Bombyx mori strains    18 Re-sequenced Genome DNA libraries (Partial RAW Reads)

cDNA libraries

Lib. name #clones Strain/Race Organ/Tissue Development stage Sex Vector Cloning site Sequence direction
an-- 606  Strain: Shuko x Ryuhaku  Antenna  Adult moth    pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
bmmt 21180  p50T  Malpighan tube  5th-instar larva , spinning stage: day-0 to day-6 mixed  female/male mixed  pGCAP10,V-capping method    single-pass sequencing from both ends (5' end 3') 
BmN 20736  Strain: Unknown; BmN cultured cell  cultured cell (derived from ovary)      Oligo-cap, full-length    sequenced from 5' 
bmnc 20635  BmN4  cultured cell (derived from ovary)  NPV infected; 20hr postinfection    pGCAP10,V-capping method    single-pass sequencing from both ends (5' end 3') 
bmov 21573  p50T  ovary  P4  female  pGCAP10,V-capping method    single-pass sequencing from both ends (5' end 3') 
bmte 21503  p50T  testis  P4  male  pGCAP10,V-capping method    single-pass sequencing from both ends (5' end 3') 
br-- 1017  Strain: p50  Brain  P0 (just after pupation)  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
brP- 1587  Strain: p50  Brain  P1-P7  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
brS- 798  Strain: p50  Brain  Larva of S0-S4  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
ce-- 1621  Strain: C202 x J201  Compound eyes  Mixed stages fifth-instar to pupa  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
ceN- 3812  The same as ce-- but a different preparation  Compound eyes  Mixed stages fifth-instar to pupa  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
cesb 83  The same as ce--: Subtracted library from ce-- library with the mixed probe containing 20 highly expressed housekeeping genes  Compound eyes  Mixed stages fifth-instar to pupa  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
e40h 756  Strain: p50  Diapause-destined embryo  40 hr after oviposition  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
e96h 710  Strain: p50  Diapause-destined embryo  96 hr after HCl treatment (HCl at 20 hr after oviposition)  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
epV3 1969  Strain: p50  Epidemis  5th-instar day-3 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
fbpv 698  Strain: Shuko x Ryuhaku  fat body  S2 (Spinning day 2); BmNPV infected; 2 hr postinfection  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
fbS2 281  Strain: C202 x J201  fat body  S2 (Spinning day 2)  male  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
fbVf 298  Strain: p50  fat body  5th-instar day-3 larva  female  cloned into pUC18 SmaI  SmaI-Blunt-end  primer (direction unknown) 
fbVm 708  Strain: p50  fat body  5th-instar day-3 larva  male  cloned into pUC18 SmaI  SmaI-Blunt-end  primer (direction unknown) 
fcaL 33462  Strain: p50T  corpora allata  5th instar larvae    pGCAP1,V-capping method    single-pass sequencing from both ends (5' end 3') 
fdpe 9984    diapause-destinated embryos  12-40hr after oviposition  female/male mixed  pGCAPI, G-capping, full-length    Sequenced from 5' with T8 primer 
fe100 5024  Strain: p50T  whole egg includeing embryo  100 hours after oviposition    pGCAP1,V-capping method    single-pass sequencing from both ends (5' end 3') 
fmgV 38020  Strain: p50T  midgut  5th instar larvae    pGCAP1,V-capping method    single-pass sequencing from both ends (5' end 3') 
fner 37074  Strain: p50T  ventral nerve cord including brain  5th instar larvae    pGCAP1,V-capping method    single-pass sequencing from both ends (5' end 3') 
fprw 6008  Strain: p50T  prothoracic gland  5th instar larvae    pGCAP1,V-capping method    single-pass sequencing from both ends (5' end 3') 
FWD 24960  Strain: p50T  Wing disc  5th-instar larva - spinning stage: mixed  female/male mixed  Oligo-cap, full-length    sequenced from 5' 
heS0 831  Strain: C108  Hemocyte  Spinning stage day-0  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
heS3 606  Strain: C108  Hemocyte  Spinning stage day-3  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
maV3 1697               
MFB 10368  Strain: p51T  Microbe-infected fat body  5th-instar larva  female/male mixed  pGCAPI, G-capping, full-length    Sequenced from 5' with T9 primer 
mg-- 605  Strain: p50  Midgut  5th-instar day-3 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
msgV 645  Strain: N02 x C02  Middle silkgland  5th-instar larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
N--- 757  Strain: Unknown; BmN clutured cell  cultured cell (derived from ovary)      pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
Nnor 221  BmN normalized library        pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
NRPG 1521  Strain: p50, Normalized Library  Pheromone gland  Adult  female  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
NV02 558  Strain: Unknown, BmN cultured cell  cultured cell (derived from ovary)  BmNPV infected; 2 hr postinfection    pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
NV06 684  Strain: Unknown, BmN cultured cell  cultured cell (derived from ovary)  BmNPV infected; 6 hr postinfection    pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
NV12 646  Strain: Unknown, BmN cultured cell  cultured cell (derived from ovary)  BmNPV infected; 12 hr postinfection    pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
ovS3 2709               
P5PG 811  Strain: p50  Pheromone gland  Pupation day-5 stage  female  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
pg-- 553  Strain: Shuko x Ryuhaku  Pheromone gland  Newly-eclosed adult  female  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
prgv 813  Strain: p50  Prothoracic gland  5th-instar day-4 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
ps4M 312  Strain: p50  Posterior silkgland  4th molting stage  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
psV3 740  Strain: p50  Posterior silkgland  5th-instar day-3 larva    pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
tesS 944  Strain: p50  testis  Spinning stage day-3  male  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
tesV 324  Strain: p50  testis  5th-instar day-3 larva  male  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdS0 866  Strain: C108  Wing disc  Spinning stage day-0  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdS2 760  Strain: C108  Wing disc  Spinning stage day-2  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdS3 774  Strain: C108  Wing disc  Spinning stage day-3  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdV1 327  Strain: C108  Wing disc  5th-instar day-1 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdV3 843  Strain: C108  Wing disc  5th-instar day-3 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
wdV4 749  Strain: C108  Wing disc  5th-instar day-4 larva  female/male mixed  pBluescript SK-  EcoR1 for 5', Xho1for 3'  sequenced from T3 primer (5' -> 3') 
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EST libraries (you can see it only by BLAST search)

Lib. name #clones Strain/Race Organ/Tissue Development stage Sex Vector Cloning site Sequence direction
F1mg 2128F1 (J150 x J203)midgutfourth instar larval stage D2mixedpBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')
FJsb 1030       
J150 2847J150midgutfifth instar larval stage D2mixedpBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')
JFsb 500       
caL- 10831p50corpora allatafifth instar larval stagemixedpBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')
famL 25972N137 X C146mixture of antenna and maxillary galeafifth instar larval stage (day-2 to day-3)mixedpGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
fcP8 3779p50Tfollicle cellspupal stage P8femalepBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')
fe8d 18731p50Tembryofertilized egg stage H200mixedpGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
fepM 5620p50Tepidermisfourth molting stagemixedpGCAPI, G-capping, full-lengthUnknownSequenced from 5' with T7 primer
ffbm 9843p50Tfat bodyfifth instar larval stagemalepGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
fmxg 4370p50Tmaxillary galeafifth instar larval stage D3mixedpGCAPI, G-capping, full-lengthUnknownSequenced from 5' with T7 primer
fphe 334p50Tpheromone glandadult stage D0femalepGCAPI, G-capping, full-lengthUnknownSequenced from 5' with T7 primer; Sequenced from 3' with modified pT primer
ftes 29670p50Ttestisfifth instar larval stagemalepGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
fufe 17095p50Tembryounfertilized egg stagemixedpGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
fwgP 17521p50Twingpupal stagemixedpGCAP10, V-capping, full-lengthUnknownSequenced from 5' with PGCAP-F-21 primer; Sequenced from 3' with degenerate oligo dT primer
ovS0 2600p50Tovaryspinning stage S0femalepBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')
vg4M 2481p50TVerson's glandfourth molting stage D2malepBluescript SK-EcoR1 for 5' Xho1for 3'sequenced from T3 primer (5' -> 3')

The complete sequences of the FL-cDNA clone libraries

Lib. name #clones Description
Complete_Seq11833The complete sequences of the FL-cDNA clones
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GeneModel (2017) libraries

Lib. name #clones Description
KWMTBOMO 16880GeneModel based on the new assembled genome
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Old GeneModel (2008) libraries

Lib. name #clones Description
BGIBMGA 14623GeneModel based on scaffold build2
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Assembled RNA-seq libraries

Lib. name #reads Strain Organ/Tissue Development stage
A_BomoFB35635p50TFat body5th-instar
A_BomoMG43914p50TMidgut5th-instar
A_BomoSK49310p50TSkin5th-instar
A_BomoEE221677p50TwholeEarly embryo
A_BomoN4EE144953N4wholeEarly embryo
A_BomoOtmSK47999otmSkin5th-instar
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ORF from Assembled RNA-seq libraries

i
Lib. name #reads Strain Organ/Tissue Development stage
O_BomoFB25536p50TFat body5th-instar
O_BomoMG16985p50TMidgut5th-instar
O_BomoSK33939p50TSkin5th-instar
O_BomoEE95730p50TwholeEarly embryo
O_BomoN4EE51699N4wholeEarly embryo
O_BomoOtmSK35878otmSkin5th-instar
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piRNA libraries

Lib. name #reads Strain Organ/Tissue Development stage Sex
OV687407p50TOvary-Female
TE601621p50TTestis-Male
MW7869133MW (Bombyx mori with Bombyx mandarina W chromosome)Ovary-Female
WF7766937WF (DfZ-DfW) (Fujii et al. 2006)Testis-Male
LY8485411LY (T(W:2)Y-Abe) (Abe et al. 2008)Ovary-Female
GFP #89548321----
0h Egg8987706p50TWhole0 hour post-fertilization embryo-
6h Egg9724369p50TWhole6 hours post-fertilization embryo-
12h Egg13619042p50TWhole12 hours post-fertilization embryo-
24h Egg10304686p50TWhole24 hours post-fertilization embryo-
40h Diapause Egg325606----
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ChIP-seq libraries

Lib. name #reads Strain Description
Input22560725BmN4-
pIZ33593500BmN4Control for BmHP1a and Cdp1
BmHP1a38801571BmN4Bombyx mori heterochromatin protein 1 homolog
Cdp136251377BmN4Chromodomain protein 1
IgG-R36337532BmN4Rabbit IgG (Control for H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K9me3, H3K27ac, H3K27me3, and H3K36me3)
H3K4me131735270BmN4Histone H3 monomethyl Lys4 (Euchromatic modifications)
H3K4me237613798BmN4Histone H3 dimethyl Lys4 (Euchromatic modifications)
H3K4me325595873BmN4Histone H3 trimethyl Lys4 (Euchromatic modifications)
H3K9ac35094666BmN4Histone H3 acetyl Lys9 (Euchromatic modifications)
H3K9me229450531BmN4Histone H3 dimethyl Lys9 (Heterochromatic modifications)
H3K9me334783792BmN4Histone H3 trimethyl Lys9 (Heterochromatic modifications)
H3K27ac34707965BmN4Histone H3 acetyl Lys27 (Euchromatic modifications)
H3K27me334719405BmN4Histone H3 trimethyl Lys27 (Heterochromatic modifications)
H3K36me333361047BmN4Histone H3 trimethyl Lys36 (Heterochromatic modifications)
IgG-M27303327BmN4Mouse IgG (Control for Pol2)
Pol234323768BmN4RNA polymerase II
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SAGE libraries

Lib. name #clones Strain Organ/Tissue Development stage Sex
3'SAGE57051p50TOviduct (germarium to stage3)PupaFemale
5'SAGE25176p50Twhole96 hours after oviposition-
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MPSS libraries

Lib. name #clones Strain Organ/Tissue Development stage Sex
MPSS44872p50TOviduct (germarium to stage3)PupaFemale
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Transposon libraries

Lib. name #clones Description
121TEs121121 well-annotated transposons
BmTE16901690 transposons library
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Genome library

Lib. name #clones Description
Bomo_Chr28Genome assembly (2017) sequencing was performed on the PacBio RS II. Chromosome number was determined. Scaffolds were connected with N.
Bomo_Scaf668Genome assembly (2017) sequencing was performed on the PacBio RS II. Chromosome number was not determined.
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Old scaffold library

Lib. name #clones Description
Bm_scaf43462Scaffold build2 (2008)
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Fosmid library

Lib. name #clones Description
RO, GBMFno274342Fosmid end
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BAC libraries

Lib. name #clones Description
BE137219BAC end
BAC55BAC (assembled)
W-BAC_BABU479W chromosome-derived BAC
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Hypothetically reconstructed genomes of 18 Bombyx mori strains

Lib. name #clones Strain Geographic race Sex
R_C108T43462C108T (p62)Chinese practical racesMale
R_N443462N4 (p55)Tropical polyvoltinismMale
R_b2043462b20Ryukyu localMale
R_c1043462c10Japanese bivoltineMale
R_c5143462c51South Chinese localMale
R_d1843462d18Korean univoltineMale
R_e1043462e10-Male
R_f3543462f35Chinese bivoltineMale
R_g5343462g53-Male
R_k2543462k25Chinese univoltineMale
R_n1643462n16Japanese and Europian practical racesMale
R_o5543462o55Japanese bivoltineMale
R_o5643462o56Chinese univoltineMale
R_p2043462p20Japanese univoltineMale
R_p2143462p21Japanese bivoltineMale
R_p2243462p22Japanese bivoltineMale
R_p4443462p44Chinese practical racesMale
R_u4843462u48European univoltineMale
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18 Re-sequenced Genome DNA libraries (Partial RAW Reads)

Lib. name #reads Strain Geographic race Sex
DNA_C108T10000000C108T (p62)Chinese practical racesMale
DNA_N410000000N4 (p55)Tropical polyvoltinismMale
DNA_b2010000000b20Ryukyu localMale
DNA_c1010000000c10Japanese bivoltineMale
DNA_c5110000000c51South Chinese localMale
DNA_d1810000000d18Korean univoltineMale
DNA_e1010000000e10-Male
DNA_f3510000000f35Chinese bivoltineMale
DNA_g5310000000g53-Male
DNA_k2510000000k25Chinese univoltineMale
DNA_n1610000000n16Japanese and Europian practical racesMale
DNA_o5510000000o55Japanese bivoltineMale
DNA_o5610000000o56Chinese univoltineMale
DNA_p2010000000p20Japanese univoltineMale
DNA_p2110000000p21Japanese bivoltineMale
DNA_p2210000000p22Japanese bivoltineMale
DNA_p4410000000p44Chinese practical racesMale
DNA_u4810000000u48European univoltineMale
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The construction of this database has been supported by
Grant-in-Aid for Publication of Scientific Research Results,
JSPS, Japan (1999-2003, 2005-2017).

The EST sequencing was supported by the Genome Analysis Program,National Bioresource Project (NBRP),
Grants-in-Aid for Scientific Research, MEXT,and the Agrigenome Program, NIAS/MAFF.
The maintenance and distribution of the DNA clones are supported by the National Bioresource Project (NBRP).