Whose genome has been sequenced? Anas platyrhynchos
Starting with a great deal of attention for the bird flu in 2005, nearly every year a potential Influenza epidemic is discussed in the media. This leads to greater awareness for influenza research projects. A well suited research tool for influenza viruses are ducks. Ducks harbor nearly all hemagluttinin (HA) and neuraminidase subtypes and the harm for the ducks is often neglectable.
Huang and his research team have now sequenced the ducks genome to search for defense mechanisms in ducks against influenza viruses (Huang et. al., Nature Genetics).
What was sequenced?
A 10-week-old female Beijing duck (Anas platyrhynchos)
Sequencing strategy: Whole genome sequencing
- Libraries: 8 shotgun libraries and 5 mate-pair libraries (insert sizes: SG lib 185 – 530 bp, mate-pair lib 2 – 10 kb), (50 bp reads) using the Illumina GA Solexa technology
note: sequencing method according to the de novo Panda Genome project
- Read output: >77 Gb of paired-end reads (~ 64x coverage)
- Data output: 78.487 scaffolds with a contig N50 length of 26 kbp and a scaffold N50 length of 1.2 Mbp; total covered length of 1.1 Gb (~ 95% of the genome)
- Bioinformatics: Genome assembly using SOAPdenovo
- Additional comparative studies with the duck genetic and physical map resulted in 47 superscaffolds which contained 225 scaffolds and spanned 289 Mbp
- Libraries: Infected as well as control duck transcriptomes were sequenced using the Roche GS FLX instruments. In addition cDNA-libraries were sequenced using the Illumina GA instrument
- Data output after BI: 319,996 contigs with an average length of 307 bp
- Bioinformatics: Illumina transcriptome mapping and assembly was performed using SOAPaligner and SOAPdenovo software. Re-assembly together with 454 data was performed using Phrap software
The intensive study of the ducks genome using de novo genome and transcriptome sequencing approaches helped to identify significant changes in the genetic pattern compared to other bird species: the duck genome […] includes genes that are not present in the other three species whose genomes have been sequenced .” (Huang et. al)
I think it’s a quite interesting approach to learn more about a virus and its infectivity by studying the interaction between host – virus.
Read the complete publication here.
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