The Drosophila americana Sequencing Project



News (3/3/2013): Draft assembly of two strains of D. americana publicly available.


Draft assembly of D. americana

A draft assembly of two strains of D. americana (H5 and W11) is now complete. Strain H5 is from Lake Hurricane and strain W11 is from Lake Wappapelo (Reis et al. 2008). A brief historical perspective on the research on D.americana is available here.

The two genome assemblies are available for download here. They may also be searched using BLAST.

Assembly Statistics

The assembly of the strain H5 comprises 24,251 scaffolds with a total sequence length of 163 Mbp. The assembly of the strain W11 comprises 34,687 scaffolds with a total sequence length of 166 Mbp. More details are presented bellow.

Strain H5 W11
Size (Kbp) 163,287 166,080
Scaffolds 24,251 34,687
Max.(bp) 229,288 135,613
Mean (bp) 6,733 4,788
Min. (bp) 200 200
N50 Length (bp) 28,025 19,358
N50 1,328 1,939
N90 Length (bp) 11,961 8,256
N90 4,083 5,955
GC % 40.57 40.42
Ns 732,237 641,609
Ns% 0.45 0.39

We started with approximately 180 million reads produced from 3 paired-end sequencing libraries with insert sizes of about 220 base pairs (bp), 280 bp, and 480 bp, encompassing a total of approximately 18 GB of sequence with an average read length of 100 bp.

A de novo assembly of the two strains was performed using Abyss (1.2.6), SSPACE and Minimus2. Small scaffolds with less than 200bp were discarded. Finally, using the Virilis genome (release 1.2 02/2010) as reference, the scaffolds were clustered into the six Muller's elements and then ordered and oriented using Mauve.

Funding

This project is sponsored by Fundação para a Ciência e Tecnologia (National Agency for Sciences and Tecnology), through Programme COMPETE - reference PTDC/BIA-BDE/66765/2006.

Credits:


Last update:

Valid HTML 4.01 Transitional Valid CSS!