Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

Telopea speciosissima, the New South Wales waratah, is an Australian
endemic woody shrub in the family Proteaceae. Waratahs have great
potential as a model clade to better understand processes of speciation,
introgression and adaptation, and are significant from a horticultural
perspective. Here, we report the first chromosome-level genome for T.
speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium
linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of
69.0 Mb) with 97.8 % of Embryophyta BUSCOs ‘Complete’. We present a new
method in Diploidocus (https://github.com/slimsuite/diploidocus) for
classifying, curating and QC-filtering scaffolds, which combines read
depths, k-mer frequencies and BUSCO predictions. We also present a new
tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome
size estimation from the read depth of single-copy orthologues and
estimate the genome size to be approximately 900 Mb. The largest 11
scaffolds contained 94.1 % of the assembly, conforming to the expected
number of chromosomes (2n = 22). Genome annotation predicted 40,158
protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA
(CYC) genes, which have a role in determination of floral symmetry, and
confirm the presence of two copies in the genome. Read depth analysis of
180 ‘Duplicated’ BUSCO genes using a new tool, DepthKopy
(https://github.com/slimsuite/depthkopy), suggests almost all are real
duplications, increasing confidence in the annotation and highlighting a
possible need to revise the BUSCO set for this lineage. The
chromosome-level T. speciosissima reference genome (Tspe_v1) provides an
important new genomic resource of Proteaceae to support the conservation
of flora in Australia and further afield.