Dating dispersal and radiation in the gymnosperm gnetum
Yet compared to angiosperms, little is known about the patterns of diversification and genome evolution in gymnosperms.
We assembled a phylogenetic supermatrix containing over 4.5 million nucleotides from 739 gymnosperm taxa.
This study first synthesizes the available phylogenetically informative sequences to build a phylogenetic hypothesis of gymnosperms that reflects the recent advances in sequencing and computational phylogenetics.
The resulting tree provides a starting point for large-scale evolutionary and ecological analyses of gymnosperms and will hopefully be a resource to promote and guide future phylogenetic and comparative studies.
Similarly, recent sequencing of 10 BAC (bacterial artificial chromosome) clones from Pinus taeda identified many conifer-specific LTR (long terminal repeat) retroelements .
These comprise the Acrogymnospermae clade described by Cantino et al. Many gymnosperms have exceptionally large genomes (e.g., [5–7]), and this has hindered whole-genome sequencing projects, especially among economically important Pinus species.For the r8s analysis, we used the same time constraints on seed plant clades used by Won and Renner .The most recent common ancestor of seed plants was constrained to a maximum age of 385 million years ago (mya).To identify sets of homologous sequences from the Gen Bank data, we clustered sequences less than 10,000 bp in length based on results from an all-by-all pairwise BLAST analysis.The all-by-all blastn search was done with blastall using the default parameters .