terrestris the bufftailed bumble bee Native to Europe A managed pollinator Commercially available Reared in greenhouses Important pollinator in greenhouses and in agricultural fields Adorable ID: 589757
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Bombus terrestris, the buff-tailed bumble bee
Native to EuropeA managed pollinatorCommercially availableReared in greenhousesImportant pollinator in greenhouses and in agricultural fieldsAdorableSlide2
B. terrestris Transcriptome Project: Part of the “B12”
Derived from brains and abdomens of over 50 bees454 reads (76,405,196), 240 bp ave lengthUsed Roche GS Assembler
Assembly result: 42,816 unique sequences, 19,485
contigs
N50 contig length = ?
http://insectsociogenomics.illinois.edu/
Woodard et al. 2011
PNASSlide3
Details of Transcriptome Assembly
The ESTs from each species were masked to remove over-represented oligos, as identified by Roche’s gsAssembler softwareassembled, using Phrap
to generate a
nonredundant
set of sequences. Phrap (version 1.080721) was used with the following parameters: -ace, -max_group_size
0 and -vector_bound 0. Removal of clonal reads reduced the time required to assemble by one to few orders of magnitude. The assemblies reduced the number of unique sequences to about 50,000 across the species. Slide4
Read mapping not conductedSomething we can try!Pooled sample so nothing to compare…Slide5
B. Terrestris Genome Project
RAW dataFrom NCBISRA
274 Mb genome sizeSlide6
B. Terrestris Genome so far…
Assembly Bter_v1.1 publicly available at HymenopteraBaseBased on 454 WGS reads using Newbler assembler Reads from each Newbler scaffold were grouped, along with any missing mate-pairs, and reassembled using
Phrap
in an attempt to close the gaps within
Newbler scaffold. Finally,
Illumina reads were mapped to the assembly to identify and correct any errors associated with homopolymer sequences in the 454 data.236Mb of sequence and about 21.4x coverage Contigs
N50 76.0 kb, Scaffolds N50 of the scaffolds is 3.4 Mb.
The total length of all
contigs
is 236 Mb. When the gaps between
contigs
in scaffolds are included, the total span of the assembly is 245 Mb. Slide7
B. Terrestris Genome so far…
Gene predictions in progressAUGUSTUS (Katharina Hoff)FgenesH (Anna Bennett)NCBI genome viewer availableNot yet published