Figure 1.
Flow chart illustrating the physical map contig-specific fragment preparation.
The minimal tilling path BAC clones from each physical contig were selected (highlighted). The pooled BAC DNA from each physical map contig was digested with two 4-bp restriction enzymes, Mse I and Bfa I, respectively. The digestion product was then ligated with in-house designed adaptors, followed by PCR using in-house designed primers. The combination of adaptor and primer formed a specific tag representing each physical contig ID. All PCR products with a physical map contig-specific tag then were pooled together, and sequenced using Illumina HiSeq 2000 platform.
Figure 2.
The workflow of data processing.
The raw reads were first trimmed off the low quality reads (Q20) and BAC vectors. De novo assembly was then conducted with the filtered high quality reads. The assembled contigs with tag on it, plus singletons which have tag on it were then assigned to each physical contig, based on the specific tag. The tags were removed. The clean sequences were then used as queries to BLAST search against the draft catfish whole genome contigs. The targeted genome contigs were then retrieved and annotated.
Figure 3.
The distribution of contig sizes.
The X axis represents the length of sequence contigs, starting with 200-300 bp, since the minimum length of the contig is 200 bp, followed by 301-400 bp, 401-500 bp, 501-600 bp, 601-700 bp, 701-800 bp, 801-900 bp, 901-1000 bp, 1001-2000 bp and > 2000 bp. The Y axis represents the number of sequence contigs.
Figure 4.
The distribution of number of contigs per physical map contig.
The X axis represents the number of sequence contigs contained in each physical map contig, starting with 0-100, followed by 101-200, 201-300, 301-400 and > 400. The Y axis represents the number of physical map contigs.