1 / 7

Bombus terrestris , the buff-tailed bumble bee

Bombus terrestris , the buff-tailed bumble bee. Native to Europe A managed pollinator Commercially available Reared in greenhouses Important pollinator in greenhouses and in agricultural fields Adorable. B. t errestris Transcriptome Project: Part of the “B12”.

orsen
Télécharger la présentation

Bombus terrestris , the buff-tailed bumble bee

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Bombusterrestris, the buff-tailed bumble bee • Native to Europe • A managed pollinator • Commercially available • Reared in greenhouses • Important pollinator in greenhouses and in agricultural fields • Adorable

  2. B. terrestrisTranscriptome Project: Part of the “B12” • Derived from brains and abdomens of over 50 bees • 454 reads (76,405,196), 240 bpave length • Used Roche GS Assembler • Assembly result: 42,816 unique sequences, 19,485 contigs • N50 contig length = ? Woodard et al. 2011 PNAS http://insectsociogenomics.illinois.edu/

  3. Details of Transcriptome Assembly • The ESTs from each species were masked to remove over-represented oligos, as identified by Roche’s gsAssembler software • assembled, 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.

  4. Read mapping not conducted • Something we can try! • Pooled sample so nothing to compare…

  5. B. TerrestrisGenome Project 274 Mb genome size RAW data From NCBI SRA

  6. B. TerrestrisGenome so far… • Assembly Bter_v1.1 publicly available at HymenopteraBase • Based 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.

  7. B. TerrestrisGenome so far… • Gene predictions in progress • AUGUSTUS (Katharina Hoff) • FgenesH (Anna Bennett) • NCBI genome viewer available • Not yet published

More Related