[Show abstract][Hide abstract] ABSTRACT: Reconstructing the origin and evolution of land plants and their
algal relatives is a fundamental problem in plant phylogenetics, and
is essential for understanding how critical adaptations arose, including
the embryo, vascular tissue, seeds, and flowers. Despite
advances inmolecular systematics, some hypotheses of relationships
remain weakly resolved. Inferring deep phylogenies with bouts of
rapid diversification can be problematic; however, genome-scale
data should significantly increase the number of informative characters
for analyses. Recent phylogenomic reconstructions focused on
the major divergences of plants have resulted in promising but inconsistent
results. One limitation is sparse taxon sampling, likely
resulting from the difficulty and cost of data generation. To address
this limitation, transcriptome data for 92 streptophyte taxa were
generated and analyzed along with 11 published plant genome
sequences. Phylogenetic reconstructions were conducted using up
to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses
were performed to test the robustness of phylogenetic inferences to
permutations of the datamatrix or to phylogeneticmethod, including
supermatrix, supertree, and coalescent-based approaches, maximumlikelihood
and Bayesian methods, partitioned and unpartitioned analyses,
and amino acid versus DNA alignments. Among other
results, we find robust support for a sister-group relationship
between land plants and one group of streptophyte green algae,
the Zygnematophyceae. Strong and robust support for a
clade comprising liverworts and mosses is inconsistent with a
widely accepted view of early land plant evolution, and suggests
that phylogenetic hypotheses used to understand the evolution of
fundamental plant traits should be reevaluated.
Full-text · Article · Oct 2014 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
[Show abstract][Hide abstract] ABSTRACT: Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
[Show abstract][Hide abstract] ABSTRACT: New hybrid species might be expected to show patterns of gene expression intermediate to those shown by parental species. "Transcriptomic shock" may also occur, in which gene expression is disrupted; this may be further modified by whole genome duplication (causing allopolyploidy). "Shock" can include instantaneous partitioning of gene expression between parental copies of genes among tissues. These effects have not previously been studied at a population level in a natural allopolyploid plant species. Here, we survey tissue-specific expression of 144 duplicated gene pairs derived from different parental species (homeologs) in two natural populations of 40-generation-old allotetraploid Tragopogon miscellus (Asteraceae) plants. We compare these results with patterns of allelic expression in both in vitro "hybrids" and hand-crossed F(1) hybrids between the parental diploids T. dubius and T. pratensis, and with patterns of homeolog expression in synthetic (S(1)) allotetraploids. Partitioning of expression was frequent in natural allopolyploids, but F(1) hybrids and S(1) allopolyploids showed less partitioning of expression than the natural allopolyploids and the in vitro "hybrids" of diploid parents. Our results suggest that regulation of gene expression is relaxed in a concerted manner upon hybridization, and new patterns of partitioned expression subsequently emerge over the generations following allopolyploidization.
Full-text · Article · Mar 2011 · Current biology: CB