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Additional file 7. Review history.

Additional file 1: Fig. S1. Divergent transcriptomic changes of leaves and flowers in heat. Fig. S2. Comparison of m6A enrichment in two biological replications. Fig. S3. Detected sequence motifs of m6A-modified sites. Fig. S4. m6A peaks detected in different clusters. Fig. S5. Correlation between m6A and expression levels. Fig. S6. Correlation between FC m6A and FC expression. Fig. S7. Increased m6A RNA modification in Arabidopsis flowers. Fig. S8. Overlap of lowly variable genes identified from different datasets. Fig. S9. Inverse correlation of m6A levels and gene expression variability. Fig. S10. Lowly variable genes show stronger m6A RNA modification. Fig. S11. Enrichment of genes associated with low expression variability. Fig. S12. Expression profiling of genes encoding RNA demethylases. Fig. S13. An exemplary locus for increased m6A in 10b-1. Fig. S14. Density distribution of m6A enrichment in Arabidopsis leaves. Fig. S15. Exemplary loci with decreased expression variability in 10b-1. Fig. S16. Stress-granule association of lowly variable transcripts.

Additional file 2.

Sustainable goals for contemporary world seek viable solutions for interconnected challenges, particularly in the fields of food and energy security and climate change. We present bamboo, one of the versatile plant species on earth, as an ideal candidate for bioeconomy for meeting some of these challenges. With its potential realized, particularly in the industrial sector, countries such as China are going extensive with bamboo development and cultivation to support a myriad of industrial uses. These include timber, fiber, biofuel, paper, food, and medicinal industries. Bamboo is an ecologically viable choice, having better adaptation to wider environments than do other grasses, and can help to restore degraded lands and mitigate climate change. Bamboo, as a crop species, has not become amenable to genetic improvement, due to its long breeding cycle, perennial nature, and monocarpic behavior. One of the commonly used species, moso bamboo (Phyllostachys edulis) is a potential candidate that qualifies as industrial bamboo. With its whole-genome information released, genetic manipulations of moso bamboo offer tremendous potential to meet the industrial expectations either in quality or in quantity. Further, bamboo cultivation can expect several natural hindrances through biotic and abiotic stresses, which needs viable solutions such as genetic resistance. Taking a pragmatic view of these future requirements, we have compiled the present status of bamboo physiology, genetics, genomics, and biotechnology, particularly of moso bamboo, to drive various implications in meeting industrial and cultivation requirements. We also discuss challenges underway, caveats, and contextual opportunities concerning sustainable development.

Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies. We offer a glimpse into a program which detects TE insertion polymorphisms and discuss practical issues arising from the diversity of TEs and genome architectures. Detecting TE polymorphisms relies on a series of ad hoc criteria because, in contrast to single nucleotide polymorphisms, there is no general way to model TE activity. Signatures of TE polymorphisms in reference-aligned reads depend on the type of TE as well as on the complexity of the genomic background. As a consequence, a basic understanding of the limitations imposed by the data and of what the algorithm is doing is important to obtain reliable results. Here, we hope to convey such a basic understanding and help researchers to avoid some of the common pitfalls of TE polymorphism detection.

Transposable elements (TEs) are the main component of eukaryotic genomes. Besides their impact on genome size, TEs are also functionally important as they can alter gene expression and influence phenotypic variation. In plants, most top-down studies focus on extremely clear phenotypes such as the shape or the color of individuals and do not explore fully the role of TEs in evolution. Assessing the impact of TEs in a more systematic manner, however, requires identifying active TEs to further study their impact on phenotypes. In this chapter, we describe an in planta approach that consists in activating TEs by interfering with pathways involved in their silencing. It enables to directly investigate the functional impact of single TE families at low cost.

Most plants associate with beneficial arbuscular mycorrhizal (AM) fungi that facilitate soil nutrient acquisition. Prior to contact, partner recognition triggers reciprocal genetic remodelling to enable colonisation. The plant Dwarf14-Like (D14L) receptor conditions pre-symbiotic perception of AM fungi, and also detects the smoke constituent karrikin. D14L-dependent signalling mechanisms, underpinning AM symbiosis are unknown. Here, we present the identification of a negative regulator from rice, which operates downstream of the D14L receptor, corresponding to the homologue of the Arabidopsis thaliana Suppressor of MAX2-1 (AtSMAX1) that functions in karrikin signalling. We demonstrate that rice SMAX1 is a suppressor of AM symbiosis, negatively regulating fungal colonisation and transcription of crucial signalling components and conserved symbiosis genes. Similarly, rice SMAX1 negatively controls strigolactone biosynthesis, demonstrating an unexpected crosstalk between the strigolactone and karrikin signalling pathways. We conclude that removal of SMAX1, resulting from D14L signalling activation, de-represses essential symbiotic programmes and increases strigolactone hormone production.

Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.

It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species., eLife digest An organism’s genome contains all of the DNA the individual needs to survive and grow. Transposons are pieces of DNA that can move around the genome. They make up almost half of human DNA and over 85% of the DNA of major crop plants like maize, barley and wheat. When transposons move they can cause harmful changes in the regions where they insert into the DNA and so cells have mechanisms in place to tightly control the activities of the transposons. However, some transposons cause changes to DNA that are beneficial to the organism. Thus, the relationship between transposons and their host organisms is an example of a delicate but mostly peaceful coexistence. Although the cellular mechanisms controlling transposons are quite well known, the extent to which the transposons affect the ability of organisms to survive, develop and reproduce is poorly understood. A family of proteins known as the SCARECROW-like transcription factors are important for the roots of plants to develop properly. In other organs such as the leaves or flowers these proteins can cause developmental defects, so the plants carefully control where the proteins are made. Thus, plants normally produce a molecule called miR171 in leaves and flowers, but not in roots, that inhibits protein production by binding to and destabilising the RNA molecules that act as templates to make these proteins. Cho and Paszkowski have now identified a transposon that produces an RNA molecule with similarities to the RNA templates used to make the SCARECROW-like transcription factors. The experiments show that this transposon RNA is found in very high amounts in roots and mimics the transcription factor RNA so well that miR171 binds to it. This inactivates miR171 in roots to allow the SCARECROW-like transcription factors to be produced. These findings reveal a new mechanism by which transposons may regulate how plants develop and provide possible new approaches for boosting the growth of rice and other crop plants. Similar regulatory interactions between transposons and their host DNA may also be present in animals and other organisms.