Organellar genomes of the four-toothed moss, Tetraphis pellucida.

Neil E Bell,Jeffrey L Boore,Jaakko Hyvönen,Brent D Mishler

doi:10.1186/1471-2164-15-383

Abstract

BackgroundMosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.ResultsAssembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).ConclusionsStructural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.

Highlights

Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods
Chloroplast genome The chloroplast genome of Tetraphis pellucida has a length of 127,489 bp and retains the general structure common to most land plants, with two inverted repeat (IR) regions of 9,564 bp separated by a small single copy region (SSC) of 18,927 bp and a large single copy region (LSC) of 89,434 bp
In common with Tortula ruralis, Tetraphis pellucida lacks the sizeable inversion of around 71 kb in the LSC that characterizes P. patens and other Funariales [30]. It shares with Tortula ruralis the absence of petN, these two species being the only land plants currently known to lack this gene in the chloroplast

Summary

Introduction

Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Land plants (embryophytes) comprise three extant gametophyte-dominant clades (mosses, liverworts and hornworts) and one extant sporophyte-dominant clade (tracheophytes). The former comprise a paraphyletic grade known as the “bryophytes”, a morphological grouping of convenience that includes all lineages in which the diploid generation (the sporophyte) is unbranched, has only a single sporangium, and remains attached to a generally. More genomic data are needed from representatives of each major clade, to solidify phylogenetic understanding as well as to investigate organellar evolution within the group. Sampling from the more isolated and morphologically distinct lineages surviving from this relatively early diversification event may be an efficient strategy for uncovering genomic diversity of relevance to organellar evolution in land plants. Results from molecular systematic studies have corroborated the conclusion of early investigations (e.g., [2,3]) that distinct peristome types define the primary phylogenetic divisions among peristomate mosses (e.g.; [4,5,6,7,8])

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