AcolM1

An. coluzzii Mali-NIH, formerly Anopheles gambiae M form, was sequenced by the Washington University School of Medicine Genome Sequencing Center (Lawniczak et al. 2010, PMID: 20966253). DNA samples derived from whole mosquitoes were provided by the University of Notre Dame and MR4. BAC libraries were provided by the Clemson University Genomics Institute (CUGI), and are available through CUGI or MR4. The number of traces per genome was ~2.755 million M sequence reads deposited in the NCBI Trace Archives. For the M project, 94% of the traces were from plasmids (5-6kb inserts), 4% from fosmids (40kb inserts), and 2% from BACs. Based on the source DNA of these libraries, 94% of reads were generated from males, resulting in lower X-chromosome sequence coverage relative to autosomes.

Whole genome shotgun (WGS) sequences were assembled de novo for each genome by both sequencing centers: at WUGSC using the PCAP assembler (S3), and at JCVI using the Celera assembler (http://wgs-assembler.sf.net). WUGSC assemblies based on the original PCAP algorithm were nearly twice the expected ~260 Mb size (S4). This outcome reflected considerable numbers of high quality base discrepancies (polymorphisms), owing to relatively high allelic variation in the non-isogenic genome samples. Although a modification of PCAP (Pcap.rep.poly) resulted in smaller assembled genome sizes, the Celera assembler algorithms specifically developed to accommodate heterozygosity gave improved assemblies. By mutual agreement, the JCVI assemblies (available via GenBank accessions ABKP00000000 and ABKQ00000000) and served as the basis for the VectorBase genome browsers.