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

<p>Abstract</p> <p>Background</p> <p>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 (<it>Pteridium aquilinum</it>) to develop genomic resources for evolutionary studies.</p> <p>Results</p> <p>681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled <it>de novo </it>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 <it>Arabidopsis</it>, <it>Selaginella </it>and <it>Physcomitrella</it>, and identified a substantial number of potentially novel fern genes. By comparing the list of <it>Arabidopsis </it>genes identified by blast with a list of gametophyte-specific <it>Arabidopsis </it>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.</p> <p>Conclusions</p> <p>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 <it>de novo </it>transcriptome characterization and gene discovery in a non-model plant.</p

Not so different? Comparison of risk profile of gay men who acquired HIV while travelling with those who acquired HIV in Australia

© 2017 Australian Health Promotion Association Issue addressed: Many countries now identify HIV and international mobility as a priority issue within a global and shared epidemic, including Australia. To support health promotion in this complex area, we investigated recent HIV infections that occurred among Australian gay men while travelling and compared to HIV infections that occurred in Australia. Methods: 446 gay men recently diagnosed with HIV completed an on-line survey regarding the high risk event (HRE) where they believed that they acquired HIV. Those who acquired HIV while in their usual place of residence (308 men), those who were travelling within Australia (59 men), and those who were travelling overseas (79 men) were compared. Results: Those who acquired HIV while overseas had very similar risk profiles, sexual behaviour, and made similar assumptions about their partners and their own HIV status, as those who acquired HIV in Australia. Only HIV status disclosure at the HRE differed across locations (P =.030). Three quarters (74.7%) of the men who acquired HIV while overseas were not diagnosed until they returned to Australia. Conclusions: Our findings challenge the idea that there are necessarily differences in behaviour and assumptions for HIV transmission in Australia and overseas. However, the men travelling may be in communities where HIV status is less commonly disclosed, and where HIV prevalence is higher. So what?: A deeper understanding of contextual factors may be required for HIV prevention and health promotion strategies targeting gay men travelling to locations with different cultural, HIV prevalence, and HIV testing considerations. This would also identify opportunities for new tools such as Pre-Exposure Prophylaxis and self-testing