high-quality genome assembly for the European barn swallow
DNA extraction was performed on blood cells portion of centrifuged whole blood containing nucleated erythrocytes and leukocytes using the Wizard genomic DNA purification kit (Promega, Cat. No. A1125). SMRTbell Express Template Prep Kit (Pacific Biosciences, Cat. No. 101357000) was used to produce the insert library. Input gDNA concentration was measured on a Qubit Fluorometer dsDNA Broad Range (Life Technologies, Cat. No. 32850). 10g of gDNA was mechanically sheared to an average size distribution of 40-50 kbp, using a Megaruptor Device (Diagenode, Cat. No. B06010001). FEMTO Pulse capillary electrophoresis was employed to assess the size of the fragments. 5 g of sheared gDNA was DNA-damage repaired and end-repaired using polishing enzymes. Blunt-end ligation was used to create the SMRTbell template. A Blue Pippin device (Sage Science, Cat. No. BLU0001) was used to size-select the SMRTbell template and enrich for fragments > 30 kbp, excluding the first two cells for which the library was enriched for fragments > 15 kbp. The size-selected library was checked using FEMTO Pulse and quantified on a Qubit Fluorometer. A ready to sequence SMRT bell-Polymerase Complex was created using the Sequel binding kit 2.0 (Pacific Biosciences, Cat. No. 100862200). The Pacific Biosciences Sequel instrument was programmed to sequence the library on 18 Sequel SMRT Cells 1M v2 (Pacific Biosciences, Cat. No. 101008000), taking one movie of 10 hours per cell, using the Sequel Sequencing Kit 2.1 (Pacific Biosciences, Cat. No. 101310400). After the run, sequencing data quality was checked via the PacBio SMRT Link v5.0.1 software using the run QC module.