Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution

Abstract

We present reference-quality genome assembly and annotation for the stout camphor tree (Cinnamomum kanehirae (Laurales, Lauraceae)), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry than monocots. Two whole-genome duplication events were inferred within the magnoliid lineage: one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small-scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of the terpenoid synthase gene subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

“…This contrasts with recent studies in magnoliids (Chaw et al 2019;Chen et al 2019), where the authors found WGD with lower Ks values (thus potentially more recent), and hypothesized them to be shared in magnoliids and thus older than the divergence between Lauraceae and Magnoliaceae.…”

“…In addition to the standard GMM method, we also used the BGMM method and confirmed that fitting more complex Gaussian models only resulted in components of negligible weights (results not shown). Considering two components for Annona and Liriodendron, and twothree components for Cinnamomum (as indicated by the results above), the main peak in Annona was found around 1.3-1.5 Ks units, whereas it occured around 0.8 Ks units (two components) or 0.4 and 1.3-1.4 Ks units (three components) in Cinnamomum (partially comparable -for the two components -with results from previous studies (Chaw et al 2019), as we did not identify a peak at 0.76). Notably, the oldest peak in…”

“…Scaffolds longer than 100kb totaled 646.64Mb (98.45% of the total length). This level of contiguity is similar to the one obtained in Liriodendron chinensis (N50=3.5 Mb (Chen et al 2019)) but smaller than obtained in Cinnamomum kanehirae (N50=50.4Mb after Hi-C scaffolding (Chaw et al 2019), and better than other genomes assembled at scaffold-level (e.g. (Yang et al 2018;Arimoto et al 2019;Zhang et al 2019)).…”

“…However, the results strongly disagreed on the position of magnoliids, supporting either a sister relationship to eudicots and monocots (Chen et al 2019), or to eudicots alone (Chaw et al 2019). This disagreement could be an analytical artefact caused by whole genome duplication (WGD) and chromosomal rearrangements as apparent in both Liriodendron chinense (the Chinese tulip poplar) and Cinnamomum kanehirae (the stout camphor tree) after their divergence from monocots or eudicots.…”

“…Reconstruction of the ancestral angiosperm genome shows a reduction in the number of chromosomes between the divergence of the putative sister taxa of all remaining angiosperms Amborella and the most recent common ancestor (MRCA) of eudicots (Murat et al 2017). In addition to this assessment of early angiosperm genomic features, Sauquet et al (Sauquet et al 2017) suggested that the early evolution of angiosperm flowers was marked by published to date (Chaw et al 2019;Chen et al 2019). Analysis of such genomic data was expected to resolve the still unclear relationships of magnoliids with the rest of angiosperms (Soltis and Soltis 2019).…”