The complete plastome sequences of four orchid species: insights into the evolution of the Orchidaceae and the utility of plastomic mutational hotspots

Z Niu, Q Xue, S Zhu, J Sun, W Liu, X Ding - Frontiers in plant science, 2017 - frontiersin.org
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species
in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and …

Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and …

N Korotkova, L Nauheimer, H Ter-Voskanyan… - PLoS …, 2014 - journals.plos.org
Plastid genomes exhibit different levels of variability in their sequences, depending on the
respective kinds of genomic regions. Genes are usually more conserved while noncoding …

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

MJ Moore, CD Bell, PS Soltis… - Proceedings of the …, 2007 - National Acad Sciences
Although great progress has been made in clarifying deep-level angiosperm relationships,
several early nodes in the angiosperm branch of the Tree of Life have proved difficult to …

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone

J Leebens-Mack, LA Raubeson, L Cui… - Molecular Biology …, 2005 - academic.oup.com
While there has been strong support for Amborella and Nymphaeales (water lilies) as
branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently …

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae

RW Ness, SW Graham… - Molecular Biology and …, 2011 - academic.oup.com
Most plant phylogenetic inference has used DNA sequence data from the plastid genome.
This genome represents a single genealogical sample with no recombination among genes …

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

PF Ma, MS Vorontsova, OP Nanjarisoa, J Razanatsoa… - BMC Plant …, 2017 - Springer
Background Heterogeneous rates of molecular evolution are universal across the tree of life,
posing challenges for phylogenetic inference. The temperate woody bamboos (tribe …

[HTML][HTML] Genome size evolution of the extant lycophytes and ferns

FG Wang, AH Wang, CK Bai, DM Jin, LY Nie, AJ Harris… - Plant Diversity, 2022 - Elsevier
Ferns and lycophytes have remarkably large genomes. However, little is known about how
their genome size evolved in fern lineages. To explore the origins and evolution of …

Single-copy genes as molecular markers for phylogenomic studies in seed plants

Z Li, AR De La Torre, L Sterck… - Genome Biology and …, 2017 - academic.oup.com
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms,
remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and …

Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation

S Nie, XC Tian, L Kong, SW Zhao, ZY Chen… - Frontiers in Plant …, 2022 - frontiersin.org
Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging
diverged genomes) were previously revealed, although there is significant evidence for the …

A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

JR Mandel, RB Dikow, VA Funk… - Applications in plant …, 2014 - Wiley Online Library
• Premise of the study: The Compositae (Asteraceae) are a large and diverse family of
plants, and the most comprehensive phylogeny to date is a meta‐tree based on 10 …