geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum


, : De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. Bmc Genomics 12(): 99-99

Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies. 681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements. This study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant.

US$19.90

PMID: 21303537

DOI: 10.1186/1471-2164-12-99


Other references

Bongiorni, L.; Jain, R.; Raghukumar, S.; Aggarwal, R.Kumar., 2005: Thraustochytrium gaertnerium sp. nov.: a new thraustochytrid stramenopilan protist from mangroves of Goa, India. Thraustochytrids are ubiquitous, chemo-organotrophic, marine stramenipilan protists belonging to the class Labyrinthulomycetes. Their taxonomy is largely based on life cycle development stages. We describe here a new species of thraustochytrid iso...

Dolgov, VA., 1974: Diagnosis of Crocidura suavolens and C. leucodon (Insectivora, Soricidae). Zoologicheskii Zh, 536: 912-918

Ibrahim, A.S.; Bowman, J.C.; Avanessian, V.; Brown, K.; Spellberg, B.; Edwards, J.E.; Douglas, C.M., 2005: Caspofungin inhibits Rhizopus oryzae 1,3-beta-D-glucan synthase, lowers burden in brain measured by quantitative PCR, and improves survival at a low but not a high dose during murine disseminated zygomycosis. Rhizopus oryzae is the most common cause of zygomycosis, a life-threatening infection that usually occurs in patients with diabetic ketoacidosis. Despite standard therapy, the overall rate of mortality from zygomycosis remains >50%, and new str...

Ohno, Y.; Maehashi, K.; Yamashiro, Y.; Matsumoto, K., 2009: Electrolyte-gated graphene field-effect transistors for detecting pH and protein adsorption. We investigated electrolyte-gated graphene field-effect transistors (GFETs) for electrical detecting pH and protein adsorptions. Nonfunctionalized single-layer graphene was used as a channel. GFETs immersed in an electrolyte showed transconductanc...

Nagel, C.W.; Spayd, S.E., 1990: Yield and enological characteristics of grape cultivars in central Washington 1974-1987. This publication updates the previous one published in 1976 which summarized cultivar tests during the period 1963-73. The present report gives tabulated data on harvest dates, yields and must and wine analyses for 37 white and 18 red cultivars. T...

Bohac, J., 1978: Research into the relationships between biomass and dry matter in wheat. In plants of 5 cv. and 15 lines of winter wheat grown in perlite in a glasshouse and sown on 23 Sept., samples taken at 4 dates from the beginning of shooting (4 Jan.) to heading (4 Feb.) showed that total plant fresh wt. was positively correlated...

Binns, M., 1993: DNA fingerprinting as an epidemiological tool. 1. In order to elucidate the mechanism underlying the positive inotropic effect (PIE) of angiotensin II (AII), we measured changes in phosphoinositide hydrolysis and contractile force induced by AII in the rabbit ventricular myocardium. 2. AII (1....

Zielinska, W., 1964: 1st Degree Auriculoventricular Block In Typhoid Fever. Kardiologia Polska 13: 57-61

Schwartz, A.G.; Pashko, L.; Whitcomb, J.M., 1986: Inhibition of tumor development by dehydroepiandrosterone and related steroids. The naturally occurring adrenal steroid, dehydroepiandrosterone (DHEA), is a potent non-competitive inhibitor of mammalian glucose-6-phosphate dehydrogenase (G6PDH). Oral administration of DHEA to mice inhibits spontaneous breast cancer and chemic...

Beliaeva, Z.V., 1979: Autonomic-somatic components of motor responses to direct and verbal stimuli in children. Negative induction influences of one (prevailing) signal system on another (functionally weaker) were studied on the model of effector vegetative-somatic components of motor conditioned reflexes to direct (sound) and verbal ("a whistle is blo...