De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome. (13th June 2014)

• Record Type: Journal Article
• Authors: Szövényi, Péter; Perroud, Pierre‐François; Symeonidi, Aikaterini; Stevenson, Sean; Quatrano, Ralph S.; Rensing, Stefan A.; Cuming, Andrew C.; McDaniel, Stuart F.
• Is Part Of: Molecular ecology resources. Volume 15:Number 1(2015:Jan.)
• Page Start: 203
• Page End: 215
• Publication Date: 2014-06-13
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12284
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12284-abs-0001"> <title>Abstract</title> <p>The bryophytes are a morphologically and ecologically diverse group of plants that have recently emerged as major model systems for a variety of biological processes. In particular, the genome sequence of the moss, <italic>Physcomitrella patens</italic>, has significantly enhanced our understanding of the evolution of developmental processes in land plants. However, to fully explore the diversity within bryophytes, we need additional genomic resources. Here, we describe analyses of the transcriptomes of a male and a female isolate of the moss, <italic>Ceratodon purpureus</italic>, generated using the 454 FLX technology. Comparative analyses between <italic>C. purpureus</italic> and <italic>P. patens</italic> indicated that this strategy generated nearly complete coverage of the protonemal transcriptome. An analysis of the overlap in gene sets between <italic>C. purpureus</italic> and <italic>P. patens</italic> provides new insights into the evolution of gene family composition across the land plants. In spite of the overall transcriptomic similarity between the two species, <italic>K</italic><sub><italic>a</italic></sub>/<italic>K</italic><sub><italic>s</italic></sub> analysis of <italic>P. patens</italic> and <italic>C. purpureus</italic> suggests considerable physiological and developmental divergence. Additionally, while the codon usage was very similar between these two mosses, <italic>C. purpureus</italic> genes showed a slightly greater codon usage bias than <italic>P. patens</italic> genes potentially because of the contrasting mating system of the two species. Finally, we found evidence of a genome doubling ~65–76 MYA that likely coincided with the contemporaneous polyploidy event inferred for <italic>P. patens</italic> but postdates the divergence of <italic>P. patens</italic> and <italic>C. purpureus</italic>. The powerful laboratory tools now available for <italic>C. purpureus</italic> will enable the research community to fully exploit these genomic resources.</p> </abstract>