Highly Contiguous A4 Genome Assembly

A4 DNA was extracted from females and used in SMRTbell library
preparation following¹² . We
sequenced this library on 30 SMRTcells using P6-C4 chemistry on a Pacific
Biosciences RSII platform at the UC Irvine Genomics Facility, yielding 18.7 Gb
of sequence. We then followed¹² to assemble the A4 genome. We assembled a draft genome
using PBcR-MHAP^{41 (link)} in
wgs 8.3rc1 and PacBio reads only (NG50 = 13.9 Mb, 147 Mb
total), then generated a hybrid assembly with DBG2OLC^{42 (link)} using the longest 30×
PacBio reads and 75× paired end Illumina reads from¹² (assuming 130 Mb genome size;
NG50 = 4.23 Mb, 129 Mb total). We merged the two assemblies using
quickmerge v0.1 with default settings except hco = 5, c =
1.5, and l = 2 Mb. The merge yielded an assembly (NG50 = 21.3 Mb, 130 Mb total)
that was both smaller than expected^{43 (link)} and smaller than the PacBio-only assembly. Therefore,
we added contigs unique to the PacBio assembly to the hybrid assembly using
quickmerge as above but with I = 5 Mb. Finally, we
generated the final assembly by running finisherSC^{44 (link)} with default settings,
polishing the assembly twice with quiver (smrtanalysis v2.3),
and finally finishing with Pilon v1.3^{45 (link)} (using A4 reads from¹² ). This yielded a final assembly of 144 Mb with
N50 = 22.3 Mb (Supplementary
Table 1).