PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
- Xiao-Jian Qu, M. Moore, De‐Zhu Li, T. Yi
- BiologyPlant Methods
- 21 May 2019
Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plasts, is introduced.
Contemporaneous and recent radiations of the world's major succulent plant lineages
- Mónica Arakaki, P. Christin, E. Edwards
- Environmental ScienceProceedings of the National Academy of Sciences
- 2 May 2011
Using a hybrid phylogenomic approach, it is estimated that the cactus lineage diverged from its closest relatives ≈35 million years ago (Ma), however, major diversification events in cacti were more recent, with most species-rich clades originating in the late Miocene.
Rosid radiation and the rapid rise of angiosperm-dominated forests
- Hengchang Wang, M. Moore, D. Soltis
- BiologyProceedings of the National Academy of Sciences
- 10 March 2009
The timing of the inferred rapid radiation of rosids corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
- M. Moore, C. Bell, P. Soltis, D. Soltis
- Biology, Environmental ScienceProceedings of the National Academy of Sciences
- 4 December 2007
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.
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
- Stephen A. Smith, M. Moore, Joseph W. Brown, Ya Yang
- BiologyBMC Evolutionary Biology
- 5 August 2015
This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets.
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1
- T. Givnish, M. Ames, J. Leebens-Mack
- Environmental Science, Biology
- 17 December 2010
The results of an initial project by the Monocot AToL (Angiosperm Tree of Life) team on phylogeny and evolution in Poales are presented, using sequence data for 81 plastid genes from 83 species of angiosperms and recovered highly concordant relationships using maximum likelihood (ML) and maximum parsimony (MP).
Rapid and accurate pyrosequencing of angiosperm plastid genomes
- M. Moore, A. Dhingra, D. Soltis
- BiologyBMC Plant Biology
- 25 August 2006
The high accuracy observed in the GS 20 plastid genome sequence was generated for a significant reduction in time and cost over traditional shotgun-based genome sequencing techniques, although with approximately half the coverage of previously reported GS 20 de novo genome sequence.
Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales
- Samuel F. Brockington, R. Alexandre, P. Soltis
- BiologyINTERNATIONAL JOURNAL PLANT SCIENCES
- 1 June 2009
Parsimony and maximum likelihood analyses on separate and combined data sets find little support for anemophily as the ancestral condition of the Caryophyllales, but the early caryophyllid flower is suggested to have possessed an undifferentiated perianth.
Resolving an ancient, rapid radiation in Saxifragales.
Age estimates indicate that the early diversification of Saxifragales occurred rapidly, over a time span as short as 6 million years, and the plastid IR region may be an ideal source of slowly evolving genes for resolution of deep-level angiosperm divergences that date to 90 My or more.
Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae).