Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure
Methods – A shotgun library developed from total genomic liverwort DNA was subjected to high-throughput pyrosequencing using the Roche 454 platform. Plastid reads were bioinformatically identified, assembled and annotated. To maximize usage of the vast number of reads generated using 454 sequencing technology, combined nuclear, mitochondrial and plastid contigs were also screened for microsatellite markers, and presumed nuclear contigs were scanned for protein domains.
Key Results – This is the first plastid genome to be assembled for a leafy liverwort (i.e. Ptilidium) and also the first such genome to be sequenced using next generation technology for any bryophyte. The 119,007 base long plastid genome of Ptilidium pulcherrimum contains 88 protein-coding genes, four rRNAs and thirty tRNAs. The Inverted Repeat occurs between trn V-GAC and trn N-GUU. Functional copies of the two plastid-encoded sulphate import protein-coding genes (cysA and cysT) are absent, although pseudogenes are present in the same position that the functional genes occupy in Marchantia. Microsatellites: 197 novel potential primer pairs for P. pulcherrimum were found. Presumed nuclear Ptilidium contigs gave multiple hits to Class I transposable elements.
Conclusions – The arrangement of genes is identical to the plastid of the complex thalloid liverwort Marchantia, suggesting that structural rearrangements are rare in hepatics. This dataset represents a valuable resource for novel phylogenetic and population level marker design in hepatics.
Document Type: Regular Paper
Publication date: 2011-03-01
Plant Ecology and Evolution (a continuation of Belgian Journal of Botany, incorporating Systematics and Geography of Plants) is an international journal devoted to ecology, phylogenetics and systematics of all 'plant' groups in the traditional sense (including algae, cyanobacteria, fungi, myxomycetes), also covering related fields such as comparative and developmental morphology, conservation biology, ecophysiology, evolution, phytogeography, pollen and spores, population biology, and vegetation studies. It is published by the Royal Botanical Society of Belgium and the Botanic Garden Meise and contains original research papers, review articles, checklists, short communications and book reviews.
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