maps and genomic sequencing identify candidate genes in the Usher 1C locus.
Multiple contiguous sequences were created automatically for each mega-amplicon by using a de novo assembly program in CLC, and 4-8 contigs
supported by high coverage rate of sequence reads were generated (online Technical Appendix Table 2).
PacBio's single molecule, real-time (SMRT([R])) technology offers very long reads that reduce the number of contiguous sequences, or contigs
, to simplify and improve genome assembly.
virescens sequence database, a 664 base pair contig
encoding a 199 amino acid polypeptide with 3 CS-[alpha][beta] motifs highly homologous to the X-Tox proteins isolated previously from other Lepidoptera.
Finally, the protein domain ratio in each bacterial species, of which definition was the portion of cellulase-like protein domain to the assembled and annotated contigs
, was analyzed to evaluate the richness of protein domain with cellulase activity in the dominant bacterial species (Supplementary Figure 4).
We created a more complete and accurate assembly of the draft sequences by rearranging the sequence contigs
inside each clone to conform to our maps and by comparing small overlapping portions of contigs
from different clones.
8%) and were distributed in 42-52 large (>500 bp) contigs
Comparison of representative contig
sequences for these clusters against public domain rat sequences showed no significant hits for 555 sequences (20%).
KM077139), a region of the spike only had 5x coverage and ambiguity bases in the consensus contig
whereas the coverage across the remaining PEDV genome was 50x.
The cDNA was then used as a template in PCR reactions employing Taq DNA polymerase (TaKaRA, Japan) and a pair of primers, MxF1: 5'-AAATGGCTCAAGAGGTGGA-3' and MxR1: 5'-TATCGCTGACAGTTGGGTG -3', designed based on an EST contig
in the NCBI database, and a PCR product of 420 bp was amplified.
The resulting sequences were assembled into a contig
with Sequencher[R] based on the same parameters used above.
Sequence data files were assembled into contigs
by use of Pregap4, a contig
assembly program available as part of the Staden analysis package (23).