Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Endemic species flocks inhabiting ancient lakes, oceanic islands and other long‐lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate‐level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca‐binding muscle‐related proteins, possibly indicating adaptation to Ca‐deficient low mineralization Baikal waters.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/136009/1/mec13927.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136009/2/mec13927_am.pd

Gene Expression Maps in Plants: Current State and Prospects

For many years, progress in the identification of gene functions has been based on classical genetic approaches. However, considerable recent omics developments have brought to the fore indirect but high-resolution methods of gene function identification such as transcriptomics, proteomics, and metabolomics. A transcriptome map is a powerful source of functional information and the result of the genome-wide expression analysis of a broad sampling of tissues and/or organs from different developmental stages and/or environmental conditions. In plant science, the application of transcriptome maps extends from the inference of gene regulatory networks to evolutionary studies. However, only some of these data have been integrated into databases, thus enabling analyses to be conducted without raw data; without this integration, extensive data preprocessing is required, which limits data usability. In this review, we summarize the state of plant transcriptome maps, analyze the problems associated with the combined analysis of large-scale data from various studies, and outline possible solutions to these problems

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana

Abstract Background Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. Results The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. Conclusions Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress

Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum

The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes

The Microwave Absorption in Composites with Finemet Alloy Particles and Carbon Nanotubes

The absorption of waves of the centimeter and millimeter wavebands in composites with Finemet alloy particles and carbon nanotubes has been studied. It has been established that ferromagnetic resonance and antiresonance are observed in such composites. A method is proposed for calculating the effective dynamic magnetic permeability of a composite containing both a random distribution of ferromagnetic particles and a part of the particles oriented in the same way. In the approximation of effective parameters, the dependences of the transmission and reflection coefficients of microwaves are calculated. It is shown that the theoretical calculation confirms the existence of resonant features of these dependences caused by ferromagnetic resonance and antiresonance. The theory based on the introduction of effective parameters satisfactorily describes the course of the field dependence of the coefficients and the presence of resonance features in these dependences. The frequency dependence of the complex permittivity of the composite is determined. The dependence of the complex magnetic permeability on the magnetic field for millimeter-wave frequencies is calculated

Effect of method of deduplication on estimation of differential gene expression using RNA-seq

Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout

Origin and diversity of Capsella bursa-pastoris from the genomic point of view

Abstract Background Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. Results We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance—both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. Conclusions C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella

Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armor and reduction of appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters

Additional file 1 of Origin and diversity of Capsella bursa-pastoris from the genomic point of view

Additional file 1: Fig. S1. Scheme for data acquisition for the genetic map. Fig. S2. An example of a contig fragment with a colored state of the markers. Due to the low coverage some of the markers are "noisy". Fig. S3. An example of chimeric assembly. Two adjacent markers located at a distance of ~90 kbp have 33 "recombinations" per 100 chromosomes, which is impossible and indicates independent inheritance of markers.Fig. S4. An example of correction of a local chimeric assembly. a Insertion of a foreign fragment(s) and b view of the site after correction. The green dashed lines show the signals indicating the proximity of the sites. Fig. S5. Simulation of the subgenome separation procedure. Example of the coverage by reads of the parental species of some reference contigs created from the genomes of C. orientalis and C. rubella for subgenome separation. Fig. S6. Analysis of introgression by admixture analysis in C. bursa-pastoris, for K=6. The colors of the line names correspond to the populations in Fig. 4b.Fig. S7. Fbranch matrix plotted using Dsuite f4-statistics results for different tree topologies of parental species and lineages of C. bursa-pastoris for subgenome O. a for ((((ME,EU),ASI),Co),Cgr-Outgroup) tree; b for ((((ASI,EU),ME),Co),Cgr-Outgroup) tree; c for ((((ASI,ME),EU),Co),Cgr-Outgroup) tree; d for (((ME,EU),ASI),Co-Outgroup) tree; e for (((ASI,EU),ME),Co-Outgroup) tree; f for (((ASI,ME),EU),Co-Outgroup) tree. Co – C. orientalis, Cgr – C. rubella/C. grandiflora, and ASI, ME, EU – lineages of C. bursa-pastoris. Fig. S8. Fbranch matrix plotted using Dsuite f4-stastics results for different tree topologies of parental species and lineages of C. bursa-pastoris for subgenome R. a for ((((ME,EU),ASI),Cgr),Co-Outgroup) tree; b for ((((ASI,EU),ME),Cgr),Co-Outgroup) tree; c for ((((ASI,ME),EU),Cgr),Co-Outgroup) tree; d for (((ME,EU),ASI),Cgr-Outgroup) tree; e for (((ASI,EU),ME),Cgr-Outgroup) tree; f for (((ASI,ME),EU),Cgr-Outgroup) tree. Co – C. orientalis, Cgr – C. rubella/C. grandiflora, and ASI, ME, EU – lineages of C. bursa-pastoris. Fig. S9. F2 data processing. Fig. S10. Building the SNP Database