Data from: A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land
plants comprising about 6,000 species that share the development of female
sex organs on short lateral branches, a derived trait within mosses. Many
of the families within Hypnales, the largest order of pleurocarpous
mosses, trace their origin to a rapid radiation less than 100 million
years ago, just after the rise of the angiosperms. As a result, the
phylogenetic resolution among families of Hypnales, necessary to test
evolutionary hypotheses, has proven difficult using one or few loci. We
present the first phylogenetic inference from high-throughput sequence
data (transcriptome sequences) for pleurocarpous mosses. To test
hypotheses of gene family evolution, we built a species tree of 21
pleurocarpous and six acrocarpous mosses using over one million sites from
659 orthologous genes. We used the species tree to investigate the genomic
consequences of the shift to pleurocarpy and to identify whether patterns
common to other plant radiations (gene family expansion, whole genome
duplication, or changes in the molecular signatures of selection) could be
observed. We found that roughly six percent of all gene families have
expanded in the pleurocarpous mosses, relative to acrocarpous mosses.
These gene families are enriched for several gene ontology (GO) terms,
including interaction with other organisms. The increase in copy number
coincident with the radiation of Hypnales suggests that a process such as
whole genome duplication or a burst of small-scale duplications occurred
during the diversification. In over 500 gene families we found evidence of
a reduction in purifying selection. These gene families are enriched for
several terms in the GO hierarchy related to “tRNA metabolic process.” Our
results reveal candidate genes and pathways that may be associated with
the transition to pleurocarpy, illustrating the utility of
phylotranscriptomics for the study of molecular evolution in non-model
species.