Correction to: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta.

Following the publication of this article [1], the authors reported that the link to Additional file 11 linked to the wrong set of data. The correct supplementary data is provided in this Correction article (Additional file 11).

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.

Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed; however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Here, we describe the extent of this problem using popular RNA-seq mapping tools and present a new method, called Portcullis, to rapidly filter false SJs derived from spliced alignments. We show that Portcullis distinguishes between genuine and false-positive junctions to a high degree of accuracy across different species, samples, expression levels, error profiles, and read lengths. Portcullis is portable, efficient, and, to our knowledge, currently the only SJ prediction tool that reliably scales for use with large RNA-seq datasets and large, highly fragmented genomes, while delivering accurate SJs.

Leveraging multiple transcriptome assembly methods for improved gene structure annotation.

Background: The performance of RNA sequencing (RNA-seq) aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Results: Here, we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artifacts such as erroneous transcript chimerisms. Conclusions: We have implemented this method in an open-source Python3 and Cython program, Mikado, available on GitHub.

SPECTRE: a suite of phylogenetic tools for reticulate evolution.

Summary: Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here, we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing environments. Availability and implementation: Full source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE. SPECTRE's core library is available from Maven Central at: https://mvnrepository.com/artifact/uk.ac.uea.cmp.spectre/core. Documentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/. Contact: sarah.bastkowski@earlham.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom.

Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

BACKGROUND: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. RESULTS: To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. CONCLUSIONS: Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

Motivation: De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. Results: We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. Availability and Implementation: KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . Contact: bernardo.clavijo@earlham.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta.

BACKGROUND: Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. RESULTS: The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. CONCLUSIONS: Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.

RAMPART: a workflow management system for de novo genome assembly.

MOTIVATION: The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication. RESULTS: Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available. AVAILABILITY AND IMPLEMENTATION: RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART.

MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome.

MicroRNAs (miRNAs) are a class of small non-coding RNA (sRNA) involved in gene regulation through mRNA decay and translational repression. In animals, miRNAs have crucial regulatory functions during embryonic development and they have also been implicated in several diseases such as cancer, cardiovascular and neurodegenerative disorders. As such, it is of importance to successfully characterize new miRNAs in order to further study their function. Recent advances in sequencing technologies have made it possible to capture a high-resolution snapshot of the complete sRNA content of an organism or tissue. A common approach to miRNA detection involves searching such data for telltale miRNA signatures. However, current miRNA prediction tools usually require a sequenced genome to analyse regions flanking aligned sRNA reads in order to identify characteristic miRNA hairpin secondary structures. Since only a handful of published genomes are available, there is a need for novel methods to identify miRNAs in sRNA datasets from high-throughput sequencing devices without requiring a reference genome. This paper presents miRPlex, a tool for miRNA prediction that requires only sRNA datasets as input. Mature miRNAs are predicted from such datasets through a multi-stage process, involving filtering, miRNA:miRNA* duplex generation and duplex classification using a support vector machine. Tests on sRNA datasets from model animals demonstrate that the tool is effective at predicting genuine miRNA duplexes, and, for some sets, achieves a high degree of precision when considering only the mature sequence.

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets.

SUMMARY: RNA silencing is a complex, highly conserved mechanism mediated by small RNAs (sRNAs), such as microRNAs (miRNAs), that is known to be involved in a diverse set of biological functions including development, pathogen control, genome maintenance and response to environmental change. Advances in next generation sequencing technologies are producing increasingly large numbers of sRNA reads per sample at a fraction of the cost of previous methods. However, many bioinformatics tools do not scale accordingly, are cumbersome, or require extensive support from bioinformatics experts. Therefore, researchers need user-friendly, robust tools, capable of not only processing large sRNA datasets in a reasonable time frame but also presenting the results in an intuitive fashion and visualizing sRNA genomic features. Herein, we present the UEA sRNA workbench, a suite of tools that is a successor to the web-based UEA sRNA Toolkit, but in downloadable format and with several enhanced and additional features. AVAILABILITY: The program and help pages are available at http://srna-workbench.cmp.uea.ac.uk. CONTACT: vincent.moulton@cmp.uea.ac.uk.