Lamprotornis superbus isolate:SS15 Genome sequencing and assembly

Lamprotornis superbus whole genome sequencing, ALLPATHS-LG v49414 genome assembly and MAKER v2.31.8 annotation.DNA was extracted using a Qiagen DNeasy Blood & Tissue Kit from liver tissue obtained from one female individual (SS15) captured at the Mpala Research Centre, Kenya in April 2008. Elutions were quantified with a Nanodrop, and samples were sent to the New York Genome Center for library preparation and sequencing. Two Illumina paired end libraries, with 200 and 400 bp of average insert size, were constructed using the Illumina TruSeq kit. These two libraries were sequenced on the Illumina HiSeq 2500 sequencing platform (2 X 125 bp), generating 244 and 176 M read pairs, respectively. Extracted DNA was also used as input to create two mate pair libraries, utilizing the Illumina Nextera Mate Pair Library Prep Kit v1. Size selection of tagmented and strand displaced DNA fragments was carried out on a Blue Pippin (Sage Science, Beverly, MA, USA) to select two sets of fragments, with lengths distributed between 3 and 5 kbp and between 5 and 8kb. Size selected fragments were then circularized and processed to produce two final mate pair libraries that were sequenced on the Illumina HiSeq 2500 sequencing platform (2 X 125 bp), producing 187 and 174 M read pairs, respectively.Processed reads were de novo assembled using ALLPATHS-LG v49414 (Gnerre et al., Proc Natl Acad Sci, 2011) to produce a high-quality draft genome reference. Gene completeness was evaluated using BUSCO v3.0.2 (Simao et al., Bioinformatics, 2015) against the aves_odb9 dataset.For version 2 genome assembly, CU_Lasu_v2, Olga Dudchenko at Baylor College of Medicine and DNA Zoo Project used SRX13161229 Hi-C sequencing of SAMN23245411 to misjoin-correct, anchor, order and orient into chromosomes the original SAMN16294059 sequences. 3D Assembly was performed with 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome assembly was reviewed with Juicebox Assembly Tools (Dudchenko et al., bioRxiv, 2018). MAKER annotations were lifted over to the new assembly with Liftoff v1.6.1 (Shumate et al., 2020, Bioinformatics).