Phylotranscriptomics and the radiation of pleurocarpous mosses

Synopsis: In plants, it is common to observe “rapid radiation” events associated with changes in the genomes of the plants. For example, the grasses (Poaceae, 12,000 species) share evidence of an ancient whole genome duplication (WGD), a doubling of chromosomes sometime in the past. Having multiple copies of each gene can increase the chances for new gene functions to evolve, and many have theorized that WGD events may have opened the door to the evolution of complex structures such as flowers. Mosses also have experienced a “rapid radiation” coincident with the evolution of the “pleurocarpous” (prostrate, highly branching, sporophytes attached on short lateral branches) growth form from the ancestral “acrocarpous” (erect, not branched, sporophytes attached terminally) form. Of the 12,000 species of moss (Bryophyta), about 45% are pleurocarpous, and many families of pleurocarps have diversified relatively recently (within the past 65 million years).

Hypnum, a pleurocarpous moss. Photo by M. Johnson

Hypnum, a pleurocarpous moss. Photo by M. Johnson

Our main goal with this study was to demonstrate whether signatures of rapid radiation in plants (whole genome duplication, gene family expansion, relaxed selection) are found in the radiation of pleurocarps. We used transcriptome sequencing as a “reduced complexity” representation of the genome, primarily to reduce costs compared to sequencing the whole genome from many species. When we sorted the genes in our transcriptomes into gene families (using a phylotranscriptomic approach), a clear pattern emerged– roughly one out of every twelve gene families have expanded within the pleurocarpous mosses. Specifically, many gene families have increased occupancy in pleurocarps and their closest relatives, the “proto-pleurocarpous” genus Aulacomnium. Despite the large number of gene family expansions, we did not observe evidence of a WGD event using a common method, and hypothesize that instead the genes families more gradually. We also tested for signatures of selection, and found over 500 gene families for which selection is increased in pleurocarps. We hypothesize that these genes, many of which function in reproductive development, nucleic acid synthesis, or in interactions with other organisms, may have played a role in the origin and diversification of pleurocarpy.

Phylogenetic clustering of transcriptome sequences indicates a heavy bias towards gene family expansions in pleurocarpous mosses. From: Johnson et al. 2016 MPE 98:29-40

Phylogenetic clustering of transcriptome sequences indicates a heavy bias towards gene family expansions in pleurocarpous mosses. From: Johnson et al. 2016 MPE 98:29-40

My role: This is the first paper to come out of my Post-Doc at the Chicago Botanic Garden, and my first real experience with “genome-scale” data, in the form of transcriptome assembly. I designed a workflow to process the transcriptomes from de novo assembly using Trinity to a set of filtered peptide sequences that could be used in multiple types of analysis, including the orthogroup clustering. (I came up with a name for the phylotransciptomics workflow before I even started my post-doc: Moss Transcriptome Analysis Pipeline, or MossTRAP). One of the most exciting aspects about being involved with this project is seeing first-hand how methodologies and technologies previously reserved for model organisms are now being applied to non-model systems like mosses. In 2012 when the Pleurocarpous Moss Tree of Life project was approved by NSF, the budget proposed sequencing twelve species to study gene family evolution. This paper alone included twice that amount, and we have more moss transcriptomes on the way! Our next goal is to test whether or not the gene family expansions are the result of whole genome or small scale duplication events using efficient orthogroup filtering to assign genes to gene families and broader taxon sampling to nail down the relative ages of duplication events.

The manuscript is now published in Molecular Phylogenetics and Evolution and you can download a copy here.

Citation:

Johnson, M. G., C. Malley, B. Goffinet, A. J. Shaw, and N. J. Wickett. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Mol Phylogenet Evol 98:29–40.

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