Transcriptome Analysis of Sarracenia, an Insectivorous Plant

Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. To investigate these plants, we sequenced the transcriptome of two species, Sarracenia psittacina and Sarracenia purpurea, using Roche 454 pyrosequencing technology. We obtained 46 275 and 36 681 contigs by de novo assembly methods for S. psittacina and S. purpurea, respectively, and further identified 16 163 orthologous contigs between them. Estimation of synonymous substitution rates between orthologous and paralogous contigs indicates the events of genome duplication and speciation within the Sarracenia genus both occurred ∼2 million years ago. The ratios of synonymous and non-synonymous substitution rates indicated that 491 contigs have been under positive selection (Ka/Ks > 1). Significant proportions of these contigs were involved in functions related to binding activity. We also found that the greatest sequence similarity for both of these species was to Vitis vinifera, which is most consistent with a non-current classification of the order Ericales as an asterid. This study has provided new insights into pitcher plants and will contribute greatly to future research on this genus and its distinctive ecological adaptations.

[1]  T. Vision,et al.  The molecular ecologist's guide to expressed sequence tags , 2006, Molecular ecology.

[2]  D. Schnell.  NOTES ON THE POLLINATION OF SARRACENIA-FLAVA L (SARRACENIACEAE) IN THE PIEDMONT PROVINCE OF NORTH-CAROLINA , 1983 .

[3]  Ryan D. Hernandez,et al.  Natural selection on protein-coding genes in the human genome , 2005, Nature.

[4]  Antonis Rokas,et al.  Harnessing genomics for evolutionary insights. , 2009, Trends in ecology & evolution.

[5]  W. Qin,et al.  The development of the pitcher plant Sarracenia purpurea into a potentially valuable recombinant protein production system. , 2009 .

[6]  T. Miller,et al.  The evolutionary ecology of carnivorous plants , 2003 .

[7]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[8]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[9]  Itay Mayrose,et al.  The frequency of polyploid speciation in vascular plants , 2009, Proceedings of the National Academy of Sciences.

[10]  L. Hurst.  Evolutionary genomics and the reach of selection , 2009, Journal of biology.

[11]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[12]  Matthew E Hudson,et al.  Sequencing breakthroughs for genomic ecology and evolutionary biology , 2008, Molecular ecology resources.

[13]  Nicholas J Gotelli,et al.  Food-Web Models Predict Species Abundances in Response to Habitat Change , 2006, PLoS biology.

[14]  Kiyoshi Asai,et al.  The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs , 2008, Nucleic Acids Res..

[15]  D. Gallie,et al.  Signal Transduction in the Carnivorous Plant Sarracenia purpurea (Regulation of Secretory Hydrolase Expression during Development and in Response to Resources) , 1997, Plant Physiology.

[16]  R. Olmstead,et al.  A survey of tricolpate (eudicot) phylogenetic relationships. , 2004, American journal of botany.

[17]  M. A. Koch,et al.  Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). , 2000, Molecular biology and evolution.

[18]  Gabor T. Marth,et al.  Pyrobayes: an improved base caller for SNP discovery in pyrosequences , 2008, Nature Methods.

[19]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[20]  Christophe Dessimoz,et al.  Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..

[21]  R. Malmberg,et al.  Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species , 2010, Conservation Genetics Resources.

[22]  J. Hepburn,et al.  The absorption of nutrients and allied phenomena in the pitchers of the Sarraceniaceæ , 1920 .

[23]  Guillaume Blanc,et al.  Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes , 2004, The Plant Cell Online.

[24]  D. Soltis,et al.  The origin and diversification of angiosperms. , 2004, American journal of botany.

[25]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[26]  L. Tait.  Insectivorous Plants , 1875, Nature.

[27]  A. Ellison,et al.  Limits to reproductive success of Sarracenia purpurea (Sarraceniaceae). , 2006, American journal of botany.

[28]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[29]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[30]  T. Wetter,et al.  Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. , 2004, Genome research.

[31]  H. Ellegren,et al.  Genetic basis of fitness differences in natural populations , 2008, Nature.