Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
Shu-Dong Zhang,Jian-Jun Jin,Si Yun Chen,Mark W. Chase,Mark W. Chase,Douglas E. Soltis,Douglas E. Soltis,Hong Tao Li,Jun-Bo Yang,De-Zhu Li,Ting-Shuang Yi +10 more
TLDR
The robust phylogenetic backbone and time estimates the authors provide establish a framework for future comparative studies on rosaceous evolution and highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics.Abstract:
Summary
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified.
With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family.
Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments.
Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.read more
Citations
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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian-Jun Jin,Wen-Bin Yu,Wen-Bin Yu,Jun-Bo Yang,Yu Song,Yu Song,Claude W. dePamphilis,Ting-Shuang Yi,De-Zhu Li +8 more
TL;DR: GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping and are able to reassemble the circular Plastomes from 47 datasets using GetOrganelle.
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Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.
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TL;DR: The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification, although conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone.
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Plastid phylogenomic insights into the evolution of Caryophyllales.
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TL;DR: A well-resolved and well-supported phylogeny of the Caryophyllales is recovered that was largely congruent with previous estimates of this order and provides improved support for the phylogenetic position of several key families within this clade.
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An updated tribal classification of Lamiaceae based on plastome phylogenomics
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TL;DR: This article performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies.
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