We conducted whole-genome sequencing for males of C. uenoi (table S2). Total DNA was extracted from the testes of three males using Genomic Tip (Qiagen, Hilden, Germany) and used for Illumina paired-end and mate-pair sequencing with insert lengths of 170 bp, 2 kbp, and 5 kbp on a HiSeq 2000 sequencer (Illumina, San Diego, CA, USA). One lane of a HiSeq 2000 run each was used for the 170-bp paired-end library and the combined 2- and 5-kbp mate-pair libraries. In addition, we sequenced 170-bp paired-end libraries of an additional four C. uenoi, five C. iwawakianus, and six C. maiyasanus males (for details of libraries, see table S2). Library construction and sequencing were performed at Beijing Genomics Institute (Shenzhen, China).

We also obtained transcriptome sequence data for two third-instar larvae of C. uenoi 10 to 11 days after molting. The tissues were fixed in RNAlater and stored in a freezer until RNA extraction. Total RNA was extracted from the abdominal part containing genital part (primordial) and the head to mid-body using a Qiagen RNeasy kit. For each larva, two paired-end libraries with 170-bp insertions were constructed (one each for abdominal and head-mid body) and sequenced using an Illumina HiSeq 2000 at Beijing Genomics Institute, Shenzhen, China (for details of the libraries, see table S2).

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