King Protea Genome Published
A high-quality chromosome-scale assembly of the P. cynaroides genome has been published.
Chang, J., Duong, T.A., Schoeman, C., Ma, X., Roodt, D., Barker, N., Li, Z., Van de Peer, Y. and Mizrachi, E. (2022), The genome of the King Protea, Protea cynaroides. Plant J. https://doi.org/10.1111/tpj.16044
The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability.
Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroidesis invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order.
The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient-poor soils.
Comments
Our first complete genome of a Cape Plant. Using the variety 'Little Prince’ (why on earth not the type on Table Mountain?), the first genome for any Sugarbush species. (Macadamia integrifolia and Telopea speciosissima have been done in Australia).
Here is the stats:
N50 contig length (bp) 1 068 931
Total size of contigs (bp) 1 223 600 671
Number of pseudo-chromosomes 12
Total size of pseudo-chromosomes (bp) 1 181 608 347
N50 scaffold length (bp) 100 581 735
GC content 39.59%
BUSCO (complete) 95.0%
LTR Assembly Index (LAI) 14.92
Gene models
Number of gene models 33 320
Mean gene length (bp) 8133
Mean coding sequence length (bp) 1176
Mean number of exons per gene 5.14
Mean exon length (bp) 229
Mean intron length (bp) 1683
BUSCO (complete) 98.0%
Non-coding RNA
Number of miRNA 165
Number of tRNA 1403
Number of rRNA 245
Number of snoRNA 773
Now try smoking that!
(the table legend states: "Statistics of genome assembly and annotation" - presumably this makes sense to someone ...)
Now bend your mind around this:
"Repetitive elements account for 72.15% (884 Mb) of the P. cynaroides genome. LTR-retrotransposons (LTR-RT) are the major class of transposable elements (TEs) and account for 53.11% of the assembly, while DNA TEs comprise 10.91% of the genome. Gypsy elements are the most abundant, comprising 44.88% of the assembly among the LTRs, followed by Copia elements, which occupy 7.88% of the assembly."
Proteaceae appear to have had a whole-genome duplication (WGD) likely coinciding with the K-Pg mass extinction (57–76 MYA), prior to the second major diversification of the Proteaceae. Although unusual, several unrelated plants did the same at the same time ....
Chose the variety because it is for horticulture in future.
But it is the smallest (Garden Route) form. There are 25 cultivars of the KIng Protea, some spectacular, and they choose a dwarf form?
‘Little Prince’
P. cynaroides O: ARC. S: 2000. N: G. Littlejohn-Venecourt. REG: 2007. PBR granted in ZA 2008, expires 2033. Flower head: diameter ± 14 cm, red (RHS 46A), floret mass pointed, white. August.
Who paid for the research?
who paid?
European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (No. 833522),
Ghent University (Methusalem funding, BOF.MET.2021.0005.01),
Genomics Research Institute, University of Pretoria,
South Africa's National Research Foundation (Grant UID 116239 & Grant UID 113296),
Prof. Brenda D. Wingfield, made possible by the DSI-NRF SARChI Chair in Fungal Genomics (Grant UID 98353), &
Technology Innovation Agency of South Africa,
The authors acknowledge that the King Protea is a cultural icon of South Africa, and that it is “an emblem of the beauty of our land and the flowering of our potential as a nation in pursuit of the African Renaissance. It also symbolizes the holistic integration of forces that grow from the earth, nurtured from above” (Government Communication and Information System, n.d.).
They dedicate the completion of this genome to all past, present and future researchers working on – as well as peoples benefiting from – South African Biodiversity.
then did they say, why they chose your Little Prince instead of the species?
Not that I interpreted.
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