Gossypium turneri (D10) genome NSF_v1_a2

Material and Methods

DNA was extracted from Gossypium turneri (accession D10-3) using CTAB techniques (Kidwell and Osborn 1992). DNA concentration was measured by a Qubit Fluorometer (ThermoFisher, Inc.). The sequencing library was constructed according to PacBio recommendations at the BYU DNA Sequencing Center (DNASC). Fragments >18 kb were selected for sequencing via BluePippen (Sage Science, LLC). Prior to sequencing, the size distribution of fragments in the libraries was evaluated using a Fragment Analyzer (Advanced Analytical Technologies, Inc). Eight and eleven PacBio cells were sequenced from a single library for G. turneri, respectively, on the Pacific Biosciences Sequel system. For both genomes, the raw PacBio sequencing reads were assembled using Canu V1.6 using default parameters (Koren et al. 2017).

Leaf tissue of G. turneri was shipped to DoveTail Genomics for DNA extraction and construction of Hi-C sequencing libraries. These HiC sequencing libraries were sequenced on the Illumina HiSeq 2500 (PE125 bp) at the BYU DNASC. Reads were mapped to the G. raimondii (Paterson et al. 2012) reference genome, and a scaffolded assembly was created for G. turneri by Dovetail Genomics. Whole genome alignments identified in-silico assembly errors where a contiguous 25.7 MB of Chromosome 9 (D10_09) was initially placed on D10_12, and the remainder of that chromosome was in smaller scaffolded pieces. Similar to the process above, manual iterations of scaffolding correctly assembled D10_09 and D10_11 using Juicebox (Durand 2016). The final genome sequence of G. turneri was constructed using a custom python script developed by PhaseGenomics, LLC and consists of 13 assembled chromosomes.

About the assembly

This is the first de novo genome sequence for G. turneri. The G. turneri genome was assembled from 73.2x PacBio of raw sequence reads. The assembly consisted of 220 contigs with an N50 of 7.9MB (Table 1). Similar to the G. raimondii sequence, these contigs were scaffolded by Dovetail Genomics and the pseudomolecules were manually adjusted using JuiceBox. Bionano data was not collected for G. turneri. The G. raimondii Bionano data was uninformative when aligned to the G. turneri genome sequence (because the distances between labeled recognition sites were too different). After creation of the sequence assembly, the G. raimondii HiC sequence reads were also mapped to the G. turneri genome sequence (and vice versa). While the number of mapped reads was reduced significantly (29.90% and 12.67%, respectively), there were no association anomalies detected between genomes.

Table 1. Assembly metrics of the G. turneri genome, the G. raimondii (our current assembly, D5), and the previous G. raimondii assembly (Paterson et al. 2012).

Publication

Udall, et al., 2019. De novo genome sequence assemblies of Gossypium raimondii and G. turneri.