Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C

• DOI: 10.1111/1755-0998.13574
• Publication Date: 2022-01-12T00:00:36Z
• Authors: Stephanie H. Chen; Maurizio Rossetto; Marlien van der M...; Patricia Lu‐Irving; Jia‐Yee S. Yap; Hervé Sauquet; Greg Bourke; Timothy G. Amos; Jason G. Bragg; Richard J. Edwards
• Keywords: Sequence assembly; Gene Annotation; Genome size

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, are significant from horticultural perspective. Here, we report first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads Hi-C data, assembly spans 823 Mb (scaffold N50 69.0 Mb) with 97.8% Embryophyta BUSCOs "Complete". We present new method Diploidocus (https://github.com/slimsuite/diploidocus) classifying, curating QC-filtering scaffolds, which combines read depths, k-mer frequencies BUSCO predictions. also tool, DepthSizer (https://github.com/slimsuite/depthsizer), size estimation depth single-copy orthologues estimate be approximately 900 Mb. The largest 11 scaffolds contained 94.1% assembly, conforming expected number chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs 728 tRNAs. investigated CYCLOIDEA (CYC) role determination floral symmetry, confirm presence two copies genome. Read analysis 180 "Duplicated" genes using DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all real duplications, increasing confidence highlighting possible need revise set this lineage. speciosissima reference (Tspe_v1) provides important genomic resource Proteaceae support conservation flora Australia further afield.