Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

@article{Sun2013CompletePG,
  title={Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species},
  author={Yan-xia Sun and M. Moore and Ai-ping Meng and P. Soltis and D. Soltis and Jian-qiang Li and Heng-chang Wang},
  journal={PLoS ONE},
  year={2013},
  volume={8}
}
The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete… Expand
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References

SHOWING 1-10 OF 111 REFERENCES
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
TLDR
Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Expand
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
TLDR
A phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae. Expand
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
TLDR
Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable, and ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. Expand
Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes
TLDR
The results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes, and the non‐coding proportion of the plastid genome can be considered an important information source for plastsid phylogenomics. Expand
Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region
TLDR
Important new evidence is provided for a stable, well-supported phylogenetic framework for angiosperms and the utility of IR data for resolving the deeper levels of angiosperm phylogeny is demonstrated, reiterating the importance of carefully considering taxon sampling in phylogenomic studies. Expand
Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes
TLDR
This study indicates caution in total evidence approaches in that some of the genes employed added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree. Expand
Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA
TLDR
It appears that the combined analysis of sequence data from rapidly evolving and non-coding genomic regions leads to significantly improved statistical support values in comparison to earlier studies of basal eudicots using multiple conserved genes. Expand
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
TLDR
Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships. Expand
Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences
TLDR
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA, rbcL, and atpB representing a total of 4733 bp is presented, resulting in the most highly resolved and strongly supported topology yet obtained for angiosPerms. Expand
Expansion and Contraction of the Chloroplast Inverted Repeat in Apiaceae Subfamily Apioideae
TLDR
The frequency and large size of JLB shifts in Apioideae cpDNAs are unprecedented among angiosperms, indicating that the subfamily represents a model system to study the mechanisms leading to large-scale expansions and contractions of the IR. Expand
...
1
2
3
4
5
...