DOI: 10.5061/dryad.475g7
title: Data from: A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

description: 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.
description: mosstrap-masked-coding.tarRNA-Seq was conducted on Illumina Hi-Seq 2000 platform, and reads were quality trimmed using Trimmomatic. De novo transcriptome assemblies were generated using Trinity, which can produce many isoforms. We used a phylogenetic approach to decide whether to retain isoforms. Transcripts which contained a valid protein with a BLASTp hit to a known land plant proteome were clustered using mcl, and gene trees were built from sequences in each cluster. To generate the "masked" dataset, the gene trees were searched for monophyletic clades containing sequences from the same species. Only one transcript per clade was retained, and the others were pruned from further analysis. This archive contains a multi-FASTA file of coding (DNA) sequences for each of the transcriptomes generated for the study.masked_orthogroup_tableThis file contains a correspondence between assembled transcripts and the orthogroups generated by the Yang/Smith Pipeline (see manuscript for details). Each species is separated by a tab, and transcripts from the same species in the same orthogroup are separated by commas.singlegene.tarThis archive contains single gene sequence alignments for 657 "1-to-1 orthologs" used go generate a species phylogeny for the study. Each directory contains the single-gene sequence alignment in multi-FASTA format, and the results of a maximum likelihood search in RAXML. Nucleotide sequences were aligned with MAFFT and trimmed with trimal to remove columns represented by fewer than 5 taxa. Phylogenies were reconstructed with the GTRGAMMA substitution model and nodal support was evaluated with 200 "fast bootstrap" replicates.supermatrix_cds_bootstrap_MLPhylogeny reconstructed from concatenated nucleotide matrix of single genes in RAXML version 8. A single GTRGAMMA partition was specified for each locus. Support values are from 200 full bootstrap replicates.species_tree_astral_jackknife_cdsASTRAL species tree reconstructed from nucleotide RAXML gene trees for 657 genes. Support values generated by jack-knife (sampling (without replacement) 65 gene trees 1000 times).cluster_gocatsGene ontology (GO) annotations for each orthogroup generated from the masked dataset. The Trinotate transcriptome annotation pipeline was used go assign GO annotations to transcripts using BLASTp searches of the UniProt database and HMM searches of the pfam protein domain database. All unique GO annotations for sequences in an orthogroup are shown.sequenceID_to_speciesIDCorrespondence between sequenceIDs used in data files and the family, genus, and species names of samples used in the analysis.