Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation

Abstract

The genus Liriodendron belongs to the family Magnoliaceae, which resides within the magnoliids, an early diverging lineage of the Mesangiospermae. However, the phylogenetic relationship of magnoliids with eudicots and monocots has not been conclusively resolved and thus remains to be determined1–6. Liriodendron is a relict lineage from the Tertiary with two distinct species—one East Asian (L. chinense (Hemsley) Sargent) and one eastern North American (L. tulipifera Linn)—identified as a vicariad species pair. However, the genetic divergence and evolutionary trajectories of these species remain to be elucidated at the whole-genome level7. Here, we report the first de novo genome assembly of a plant in the Magnoliaceae, L. chinense. Phylogenetic analyses suggest that magnoliids are sister to the clade consisting of eudicots and monocots, with rapid diversification occurring in the common ancestor of these three lineages. Analyses of population genetic structure indicate that L. chinense has diverged into two lineages—the eastern and western groups—in China. While L. tulipifera in North America is genetically positioned between the two L. chinense groups, it is closer to the eastern group. This result is consistent with phenotypic observations that suggest that the eastern and western groups of China may have diverged long ago, possibly before the intercontinental differentiation between L. chinense and L. tulipifera. Genetic diversity analyses show that L. chinense has tenfold higher genetic diversity than L. tulipifera, suggesting that the complicated regions comprising east–west-orientated mountains and the Yangtze river basin (especially near 30° N latitude) in East Asia offered more successful refugia than the south–north-orientated mountain valleys in eastern North America during the Quaternary glacial period.

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.…”

“…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).…”

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

“…Continuity and completeness are important indicators of genome assembly. PacBio-based genome assembly plus error corrections based on Illumina data could greatly improve continuity and completeness [56][57][58][59] . Our genome assembly of I. indigotica by this strategy showed a highly resolved result with an N50 = 1.22 Mb and longest contig length = 8.99 Mb.…”