Would you please tell me which strains are used for genome sequence analysis? For example, we have 29 strains for C. remanei. (I am sure it should be indicated in somewhere in Wormbase, but I am sorry I could not find it…)
CB5161 Caenorhabditis sp.
EM464 C. remanei ssp. vulgaris
JU724 Wild isolate.
JU727 Wild isolate.
JU800 Wild isolate.
KC322 C. remanei (wx23) A.
KC421 C. remanei (wx32) A.
KC422 C. remanei (wx36) A.
KC423 C. remanei (wx42) A.
KC427 C. remanei (wx29) A.
KC431 C. remanei (wx34) A.
KC435 C. remanei (wx30) X.
KC436 C. remanei (wx33) X.
KC440 C. remanei (wx49) A.
KC441 C. remanei (wx51) A.
KC442 C. remanei (wx41) X.
KC443 C. remanei (wx50) A.
KC467 C. remanei (wx38) A.
KC470 C. remanei (wx53) A.
PB201 Cr-ung-1(bd201).
PB206 Caenorhabditis remanei.
PB212 Caenorhabditis remanei.
PB219 Caenorhabditis remanei.
PB227 Caenorhabditis remanei.
PB228 Caenorhabditis remanei.
PB229 Caenorhabditis remanei.
PB4641 Caenorhabditis remanei.
SB146 Rhabditis (Caenorhabditis) remanei ssp. remanei.
VT733 C. remanei ssp. vulgaris
I would like to know the strain names for following species:
C. remanei
C. briggsae (AF16?)
C. brenneri
C. japonica
I also would like to know where I could obtain these species. I have checked CGC, but C. brenneri, C. japonica may not be available from CGC.
Thanking you in advance.
Hiroshi KAGOSHIMA
Kohara lab, National Institute of Genetics, Japan
LaDeana wrote in Hillier LW et al.: 2007 . Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny. PLoS Biol 5 : e167
that the AF16 strain was used for the C.briggsae sequencing.
But, according to the paper, the sequenced strain of C. briggsae may be neither of AF16 nor HK104… Does somebody know if the strain is available, which was used for the genome sequence?
I would also greatly appreciate it if somebody inform me about other sequenced strains
Hiroshi KAGOSHIMA
References:
[Hillier LW et al. 2007]
C. briggsae strains were obtained from the Caenorhabditis Genetics Center. AF16 was originally isolated in Gujarat, India. HK104 and HK105 were derived from collections in Okayama, Japan (H Kagawa). VT847 was collected in Hawaii, United States (V Ambrose), whereas PB800 was isolated in Ohio, United States. AF16 and VT847 group in the tropical clade of C. briggsae, whereas HK104, HK105, and PB800 group in the temperate clade [Baird SE et al. 2005].
C. briggsae recombinant inbred lines (RILs) were constructed from the AF16 and HK104 parental strains and AF16 and VT847 parental strains [Baird SE et al. 2005]. RILs were constructed from F2 progeny of crosses between HK104 (or VT847) males and sperm-depleted AF16 hermaphrodites. F2 larvae were picked as L4s and propagated through one hermaphrodite per generation from F2 to F11.
[Baird SE et al. 2005]
C. briggsae strains AF16, and HK104 are available from the Caenorhabditis Genetics Center. These strains were maintained on agar plates seeded with E. coli strain OP50. Recombinant inbred lines (RIL) were constructed starting with HK104 males mated to sperm-depleted AF16 hermaphrodites. Each RIL was initiated with a single F2 hermaphrodite and propagated through F11, one hermaphrodite per generation.
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, et al. PLoS Biology Vol. 1, No. 2, e45 doi:10.1371/journal.pbio.0000045
from the Material and Methods section:
… Physical mapping and sequencing was performed on C. briggsae strain AF16 (Fodor et al. 1983). We constructed a physical map for C. briggsae using a high-throughput fingerprinting scheme (Marra et al. 1997). Our substrates were two large-insert C. briggsae libraries: a 6.5-fold coverage fosmid library (M. A. Marra, unpublished data) and a 10-fold coverage bacterial artificial chromosome (BAC) library (M. A. Marra and P. deJong, unpublished data) …
Looking at the Washington University Genome Sequencing Center’s 2003 “Whitepaper”, I see the following:
C. remanei
Scott Baird has inbred the EM464-derivative PB4641 20 generations, and we will thus use this strain.
CB5161, since renamed C. brenneri
The strain CB5161 defines the new species called here Caenorhabditis n. sp. CB5161. To ensure homozygosity, we are inbreeding CB5161 20 generations, which is expected to be completed this fall. The inbred strain will be permanently archived as a frozen culture at the Caenorhabditis Genetics Center.
Note the plans appear to have changed for C. brenneri since 2003, because the CGC says:
This (PB2801) is a 20X inbred (one gravid female per generation) derivative of LKC28, which is conspecific with CB5161. This is the strain that will be used for genome sequencing by Erich Schwarz/John Spieth. sp. 4 in Kiontke and Sudhaus Wormbook Ecology chapter.
C. japonica
Karin Kiontke and D. Fitch (pers. comm.) have two healthy, 17-generation inbred strains of C. japonica that have been sent to the Caenorhabditis Genetics Center. One will be chosen for sequencing.
In brief,
the following strains were used for the genome sequencing.
C. briggsae: AF16
C. remanei: PB4641
C. brenneri: PB2801
C. japonica: DF5081
and all strains are available from CGC, except for DF5081.
I have send an inquiry mail to Genome Sequence Center about DF5081.
I will post again if I could have any information.
This is the final report about sequenced nematode strains.
I asked Prof. Sternberg and Dr. Schwarz about the C. elegans-related strains used for the genomic sequencing, and they kindly confirm the all the information by Dr. Schwartz were correct.
C. briggsae: AF16 C. remanei: PB4641 C. brenneri: PB2801 C. japonica: DF5081
AF16, PB4641, PB2801 are available from CGC, and DF5081 should be requested to Dr. Schwarz [Caltech]. (He also advised me that DF5081 i s a highly mutable strain, so it may not be genetically identical to everybody else’s copy of DF5081.)
Again, I thank all the community members for the help!