Organellar genomes of the four-toothed moss, Tetraphis pellucida

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.

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…However, this small size does not interfere with the G + C content, which is high. The plastid genomes of the closest Polytrichum species have a GC percentage of 28% to 33% [21,22] and those of seed plants range between 34% and 40% [50]. Cai et al, observed high G + C contents in the chloroplast coding regions, and certain regions had higher percentages than others, such as the IR region with its four genes with high levels of G and C [51].…”

“…The genome contains a total of 62 genes, including 2 rRNA genes as in P. juniperinum (1 rnl and 1 rns), 19 tRNAs, 3 rRNAs, 3 ORFs (ORF533, ORF622, and ORF187), 13 protein-coding genes related to mitochondrial oxidative metabolism, and 13 ribosomal proteins (4 rpl and 9 rps). The rps10 gene that encoded a protein from the 40S subunit of the ribosome was not found in Antarctic Polytrichaceae, apparently that region was lost before the split of mosses lineage since this absence is also evident in Tetraphidaceae [21] and Funariaceae [24]. The nad7 pseudogene in Marchantia polymorpha and ORF187 is frequently observed in the mtDNA of M. polymorpha [25] and contradictorily does not occur in Tetraphis pellucida but seems to be present in the Polytrichum species studied ( Table 2).…”

“…F. Weber & D. Mohr [20] and Tetraphis pellucida Hedw. [21] and was probably translocated to the nucleus in P. juniperinum and P. strictum. The BLAST analyses showed that ycf66 had 90% identity among the Antarctic Polytrichaceae species.…”

An update on sequenced chloroplast genomes of Bryophytes

“…Moreover, the gene content in the inverted repeats of both these species were found identical. Due to an increased total length of intragenic spacer regions in the large single copy region of the Tetraphis pellucida chloroplast genome, it is ~5 kb longer than those of Syntrichia ruralis and Physcomitrella patens (Bell et al, 2014).…”

Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw.

“…Recently, Bell et al (2014) published the chloroplast genome sequence of Tetraphis pellucida. It was downloaded from NCBI in FASTA and GenBank format (NC_024291, 127489bp).…”