The 182 Mb assembly reported here, which is a subset of the Boothby et al assembly, should not have been submitted to the NCBI as a WGS submission.
The NCBI Whole Genome Shotgun Submissions page explicitly states:
Nucleotide sequences must conform to the following standards:
Submitted sequences must be assembled from data experimentally determined by the submitter.
Please request NCBI to suppress/deprecate this WGS submission and resubmit it as a Third Party Annotation (TPA). The NCBI Third Party Annotation page clearly states that it is:
A database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data.
The assembly submission reported in this paper has additional problems:
1. Sex: pooled male and female: Boothby et al sequenced a parthenogenic animal;
2. Coverage: 1000.0x: This is a subset of the Boothby et al assembly which they report as 126.0x);
3. Genome representation: full, RefSeq category: representative genome, Expected final version: Yes: The Boothby et al assembly was markedly inferior to the Koutsovoulos et al assembly in terms of CEGMA completeness, percentage of RNAseq reads mapped, and several other metrics. Therefore the subset reported in this paper is less complete than the Koutsovoulos et al assembly.