Nextera mp sample prep kit

The Illumina TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA) was used to construct the 400bp and 800-bp paired-end sequencing libraries. Long mate-pair libraries featuring 3-kb inserts were prepared using a CHGC kit (CHGC, China). The Nextera MP Sample Prep Kit (Illumina, San Diego, CA) was used to build long mate-pair libraries with 8-and 12-kb insert sizes. Whole-genome sequencing was performed on the Illumina HiSeq 2500 and HiSeq X Ten platforms generating 250-bp and 150-bp pairedend reads, respectively. Five libraries of nominal insert sizes, including 400 bp, 800 bp, 3-kb, 8-kb and 12kb, were sequenced at expected genome coverages of 60×, 30×, 7×, 7× and 20×, respectively. The generated clean reads from the 400 bp, 800 bp and 3-kb insert size libraries were used for the estimation of the genome size via JELLYFISH v1.116 (83) with a k-mer length of 17. The genome size of T. tridentatus was estimated using online scripts (https://github.com/josephryan/estimate_genome_size.pl) from a k-mer distribution generated by jelly sh. Contigs were assembled using Velvet (84) by cutting the short reads into k-mers and establishing the de Bruijn table to correct and complete the contigs, which were further scaffolded and gap-lled using SSPACE-STANDARD (85) with long mate-pair reads (8-and 12-kb).