CandiSSR: an efficient pipeline used for identifying candidate polymorphic SSRs based on multiple assembled sequences

Simple Sequence Repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing (NGS) and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs based on the multiple assembled sequences. The pipeline allows users to identify putative polymorphic SSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation (SD) and missing rate (MR) of the SSR repetitions are provided to systematically assess the feasibility of the detected polymorphic SSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified polymorphic SSR are also automatically designed and further evaluated by the global sequence similarities of the primer-binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of polymorphic SSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the polymorphic SSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html

Pyrosequencing Reveals a Core Community of Anodic Bacterial Biofilms in Bioelectrochemical Systems from China

Bioelectrochemical systems (BESs) are promising technologies for energy and product recovery coupled with wastewater treatment, and the core microbial community in electrochemically active biofilm in BESs remains controversy. In the present study, 7 anodic communities from 6 bioelectrochemical systems in 4 labs in southeast, north and south-central of China are explored by 454 pyrosequencing. A total of 251,225 effective sequences are obtained for 7 electrochemically active biofilm samples at 3% cutoff level. While Alpha-, Beta- and Gamma-proteobacteria are the most abundant classes (averaging 16.0-17.7%), Bacteroidia and Clostridia are the two sub-dominant and commonly shared classes. Six commonly shared genera i.e. Azospira, Azospirillum, Acinetobacter, Bacteroides, Geobacter, Pseudomonas and Rhodopseudomonas dominate the electrochemically active communities and are defined as core genera. A total of 25 OTUs with average relative abundance >0.5% were selected and designated as core OTUs, and some species relating to these OTUs have been reported electrochemically active. Furthermore, cyclic voltammetry and chronoamperometry tests show that two strains from Acinetobacter guillouiae and Stappia indica, bacteria relate to two core OTUs, are electrochemically active. Using randomly selected bioelectrochemical systems, the study presented extremely diverse bacterial communities in anodic biofilms, though, we still can suggest some potential microbes for investigating the electrochemical mechanisms in bioelectrochemical systems