Short-read library preparations and sequencing

High-molecular-weight genomic DNA of E. crypticus was quantified by using picogreen (Invitrogen), and its integrity was checked on a 1% (w/v) E-gel (Invitrogen). For the construction of a paired-end library, 2.5 µg of genomic DNA was sheared by using a Covaris S2 sonicator (Covaris), aiming for 500-bp fragments. The fragmented DNA was used to build a PCR-free sequencing library with the NEBNext Ultra II DNA library prep kit for Illumina (New England BioLabs) by using TruSeq adapters. For the construction of a mate-pair library, 1 µg of intact genomic DNA was used with the Nextera mate pair library prep kit (Illumina). Both sequencing libraries were size-selected on a 2% (w/v) agarose E-gel. Fragments ranging from 700 to 800 bp were cut out of the gel and purified with the Zymoclean gel recovery kit (Zymo Research). Library quality was checked on an Agilent Bioanalyzer by using a high-sensitivity chip (Agilent Technologies), and concentration was measured via qPCR according to the qPCR Quantification Protocol (Illumina). Paired-end and mate-pair libraries were pooled with a 75:25 percent ratio and sequenced for 2 × 150 cycles in two lanes on a HiSeq3000 (Illumina).