The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

Ma, Junsheng; Sun, Pengchuan; Wang, Dandan; Wang, Zhenyue; Jiao, Yang; Liu, Ying; Mu, Wenjie; Xu, Renping; Wu, Ying; Dong, Congcong; Shrestha, Nawal; Liu, Jianquan; Yang, Yongzhi

doi:10.1038/s41467-021-26931-3

Cited by 39 publications

(56 citation statements)

References 118 publications

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“…However, the rapid rise and early diversi cation of angiosperms has remained "an abominable mystery" since the time of Darwin 21 and estimates of the ancestral chromosome base number for angiosperms vary from x=5 to x=9, although x=7 is mostly likely 22 . Increasing molecular phylogenetic analyses of extant angiosperms have identi ed four major lineages: Amborellales, Nymphaeales and Austrobaileyales as the ANA grade and a core angiosperm lineage (Mesangiospermae) that includes the vast majority of the remaining owering plant diversity [9][10][11][12][13][14][15][16][17][18][19] . Mesangiospermae is further comprised of ve well-circumscribed clades: monocots, eudicots, magnoliids, Chloranthales, and Ceratophyllales 2 .…”

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confidence: 99%

“…Mesangiospermae is further comprised of ve well-circumscribed clades: monocots, eudicots, magnoliids, Chloranthales, and Ceratophyllales 2 . However, evolutionary relationships between these lineages and Mesangiospermae clades remain highly debated or inconsistent based on different lines of evidence [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] . For example, Amborellales alone 9 or Amborellales and Nymphaeales together 10 have been identi ed as a sister to other angiosperms.…”

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confidence: 99%

“…For example, Amborellales alone 9 or Amborellales and Nymphaeales together 10 have been identi ed as a sister to other angiosperms. In addition, within Mesangiospermae, monocots have been identi ed to be sister to eudicots, magnoliids or the remaining four clades [12][13][14][15][16][17][18][19] . These con icting results may have been the result of the rapid diversi cation of early angiosperms promoted by one ancestral whole-genome duplication (WGD) (tetraploidization) 20 .…”

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confidence: 99%

“…First, the highly collinear and orthologous genes with all copies retained after WGD or WGT can be extracted across representative genomes for phylogenetic analyses. These genes may be superior to other homologs for phylogenetic constructions, for example, the single-copy or clustering-identi ed homologous genes [14][15][16][17]19 , for which paralogs with heterogeneous evolution after polyploidization may be randomly retained and ILS was modeled to occur more frequently during such phylogenetic analyses 23 .…”

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confidence: 99%

“…Second, the key and large genomic variations 24 , which rarely occur but may be evolutionarily conserved, for example, chromosomal fusions following the ancestral polyploidization, may be retained in the extant genomes and can be used to re ect phylogenetic relationships. In the past decade, chromosome-level genomes have been published for most early-diverged angiosperm lineages and clades 9,[14][15][16]19 . To date, however, no high-quality genome is available for Austrobaileyales in which most extant species have especially large genomes.…”

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confidence: 99%

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Early diversification and karyotype evolution of flowering plants

Sun

Yang

Liu³

et al. 2022

Preprint

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Flowering plants (angiosperms) dominate our planet and sustain all life on Earth. However, evolutionary relationships among the angiosperm lineages that diverged early – Amborellales, Nymphaeales, Austrobaileyales and Mesangiospermae, which further comprises monocots and other four clades – have remained highly disputed likely because of their rapid diversification promoted by an ancestral polyploidization event. Here, we present high-quality chromosomal-level genome assemblies of two species – star anise (Illicium verum: 12.5 Gb with a large size) in the Austrobaileyales and calamus (Acorus gramineus) representing the sister lineage to all other extant monocots. These two genomes filled the final gaps of all genomic representatives for major angiosperm lineages. Our phylogenetic analyses of collinear genes support Amborellales and Nymphaeales as sister lineages and they, together with Austrobaileyales and monocots are successively sister to other Mesangiospermae clades. Based on chromosome-like synteny blocks shared between extant genomes, we constructed the ancestral angiosperm karyotype to be x=16. We independently established evolutionary relationships for all sampled species based on shared polyploidizations and chromosomal fusions from the common ancestral karyotype. This phylogenetic relationship is congruent with that from collinear genes, especially the finding that Amborellales and Nymphaeales shared a rare chromosomal fusion not seen in other angiosperms. These results advance our understanding and shed new lights on early diversification and karyotype evolution of flowering plants.

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confidence: 99%

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confidence: 99%

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confidence: 99%

Section: Full Textmentioning

confidence: 99%

Section: Full Textmentioning

confidence: 99%

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Early diversification and karyotype evolution of flowering plants

Sun

Yang

Liu³

et al. 2022

Preprint

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Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

Liu

Zhang

Tumi

et al. 2022

Ecology and Evolution

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The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya . The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.

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Phylogeny and biogeography of the Cryptocaryeae (Lauraceae)

Song,

Xia,

Tan

et al. 2023

TAXON

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The biogeographical history of many lineages within the Lauraceae remains poorly known because of the difficulty of assigning macrofossils to living genera, poor pollen preservation, and the absence of sufficiently resolved or well‐supported phylogenies. Here, we utilize plastid genome sequencing to reinvestigate the phylogenetic and biogeographic history of trees in the tribe Cryptocaryeae, an important component of broad‐leaved forests worldwide, with around 800 species that rely on vertebrate frugivores to disperse their seeds. A new time‐calibrated phylogeny with high support for 176 species was used to infer the biogeographic history and speciation rates based on inferences of BAMM analyses. A monophyletic Cryptocaryeae with Aspidostemon, Beilschmiedia, Cryptocarya, Dahlgrenodendron, and Eusideroxylon clades was confirmed. The five clades of Cryptocaryeae were estimated to share a common ancestor in tropical Africa or Asia in the Early Cretaceous around 123 Ma. The Beilschmiedia and Cryptocarya clades were estimated to have originated in South America around 66 Ma. Extant subclades of the Beilschmiedia clade could colonize Australia by 35 Ma and extant subclades of the Cryptocarya clade could colonize Australia by 42 Ma. Diversification rates of the Beilschmiedia clade accelerated 14 and 12 Ma after its origin and diversification rates of the Cryptocarya clade accelerated 18 Ma after its origin. Over 45% extant Cryptocaryeae species originated in the three periods of accelerated differentiation in the Miocene of Asia and Australia. Long‐distance dispersal has had a major influence on biogeography, with dispersal to Asia likely occurring seven times, Zealandia six times, America three times, Australia three times, Africa twice, and Oceania at least once. Over 70% extant Cryptocaryeae species which diverged before the Quaternary grow in the Southern Hemisphere, while 90% extant Cryptocaryeae species which diverged in the Quaternary grow in the Northern Hemisphere. The Cryptocaryeae originated in and diversified with the first angiosperm‐dominated broad‐leaved evergreen forests, from the Cretaceous to the Paleogene. Long‐distance seed dispersal, probably by birds, although possibly also by flotation, has allowed the tribe to track these forests in space and time, despite a failure to adapt to cold, dry, or highly seasonal environments.

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The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

Cited by 39 publications

References 118 publications

Early diversification and karyotype evolution of flowering plants

Early diversification and karyotype evolution of flowering plants

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

Phylogeny and biogeography of the Cryptocaryeae (Lauraceae)

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