Draft assembly of the Acacia mearnsii genome

Abstract

A. mearnsii is an important forestry crop in South Africa occupying 7% of South Africa’s forestry estate. Despite its importance in the wood fibre and tannin industries and the rich history of wattle breeding in the country, there are still limited genomic resources for black wattle. Using high-molecular-weight DNA extraction methodology and data produced on a state-of-the-art long-read sequencing platform (Oxford Nanopore Technologies PromethION), we assessed the performance of three long-read genome assemblers for high-quality draft genome assembly of black wattle. We obtained 160 Gbp of sequencing data on a single PromethION flow cell, which amounts to 230X coverage of the black wattle genome (assuming a genome size of 686 Mbp). We produced a draft genome assembly comprising 430 contigs, with a contig N50 value of 2.3 Mbp, a total assembly size of 686 Mbp and a BUSCO (plant conserved single copy orthologs) completion score of 96.9%. De novo gene annotation identified 51,190 genes in the genome, with 62% of the genome marked as repeat content. We used single copy orthologs and a complete chloroplast genome assembly to assess the phylogenetic history of black wattle in relation to other plant taxa. Using in silico approaches, we have also identified microsatellite DNA loci and used these for the development of oligonucleotide primers for DNA fingerprinting and parentage analyses in wattle breeding. This study demonstrated the efficiency of long-read DNA sequencing technology and current genome assemblers in producing a high-quality de novo draft genome assembly for A. mearnsii, which will serve as a reference for future studies of genome biology and genetic dissection of agronomic traits in black wattle.