Improving Scaffold Contiguity of the Common House Spider, Parasteatoda tepidariorum, Genome Using Physical Mapping Techniques

The first available de novo genome of the common house spider, Parasteatoda tepidariorum, was assembled (as part of the i5K initiative at Baylor College of Medicine) using standard deep coverage sequencing methods (100x Illumina [2x100bp] and Mate Pair libraries [5kb, 8kb]). With the intention of improving overall assembly metrics, the common house spider was re-sequenced using the “chicago” library method and assembled using HiRise assembly software, available through Dovetail genomics.  Dovetail Genomics uses the proprietary methods for “chicago “ library preparation, a method that obtains physical mapping data and involves in vitro chromatin assembly to condense DNA. This method allows for the construction of long-range sequencing libraries whose inserts span all distances up to the size of the input DNA. The resulting library had maximal fragment sizes (library inserts) between 100 -150 KB. Additionally, the resulting assembly improved scaffold N50/N90 coverage by ten fold (starting assembly - N50 816 scaffolds, min length 0.466 Mb; N90: 4824 scaffolds, min length 0.025 Mb/final assembly – N50: 94 scaffolds, min length 4.05 Mb; N90: 448 scaffolds, min length 0.487 Mb). For the physical mapping data, the signal density was lower in smaller scaffolds and as such, larger improvements were concentrated in longer starting scaffolds. Increased scaffold continuity for the common house spider genome will allow for greater insights on genome evolution, including investigating evidence of whole genome duplications and of gene cluster duplications.