Figure 1.
Flow chart illustrating HTS-PEG.
The plasmids of the genomic library were sheared to yield fragments of 100–1500 bp larger than the vector (Blue). Then, the EcoR I sites were methylated and hairpin adaptors (Red) which contain non-methylated EcoR I sites were ligated to the fragment ends. After EcoR I digestion and circularization, the paired ends can be amplified by primers that are complementary to the ends of the vector. The PCR products with the desired size can be sequenced using the high-throughput sequencing method.
Figure 2.
The workflow of data processing.
The raw data were first filtered with the hairpin adaptor; reads without hairpin adaptor sequences were discarded. Then the vector sequences of the remaining reads were trimmed. The reads were then divided into left and right ends, and those reads with either end length less than 40 nt were discarded. The filtered paired-end reads were clustered and mapped to the genome.
Table 1.
Summary of the HTS-PEG data.
Figure 3.
Span distribution of the non-redundant read pairs mapped to the Chinese amphioxus genome.
Figure 4.
Increasing tendency of non-redundant read pairs.
50,000, 100,000, 150,000, 200,000, 250,000, 300,000 and 350,000 read pairs were randomly selected and clustered, and three replicates were made at each sampling size. Blue line represents the observed number of cluster, while red line represents its trend. And green line represents the number of increased cluster.
Table 2.
Improved scaffold length of the Chinese amphioxus genome using the paired BAC ends.