tRNA Derived smallRNAs : smallRNAs Repertoire Has Yet to Be Decoded in Plants

Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses.Peer reviewe

Plant IsomiR Atlas : Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants

microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs: target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. ONE SENTENCE SUMMARY Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.Peer reviewe

Emerging Roles and Landscape of Translating mRNAs in Plants

Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations. More recently, ribosome-associated mRNA profiling has emerged as an alternative and a robust way of identifying translating mRNAs, which are a set of mRNAs associated with ribosomes and more likely to contribute to proteome abundance. In this article, we briefly review recent studies that examined the processes affecting the abundance of translating mRNAs, their regulation during plant development and tolerance to stress conditions and plant factors affecting the selection of translating mRNA pools. This review also highlights recent findings revealing differential roles of alternatively spliced mRNAs and their translational control during stress adaptation. Overall, better understanding of processes involved in the regulation of translating mRNAs has obvious implications for improvement of stress tolerance in plants.Peer reviewe

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C-3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5'-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.Peer reviewe

Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen

We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.Peer reviewe

Complete plastid genome sequence of African nightshade (Solanum scabrum) and comparative plastomics across Solanales

Solanaceae are a particularly interesting angiosperm family, not only because they include many major crop species such as potato, tomato, eggplant, pepper, tobacco and ornamentals like petunias, but also because numerous species are used as biological models. They have been widely used for understanding crop genetics and plant genome evolution in general. Sequencing efforts have been concentrated mostly to sequence genomes of important crop species of Solanaceae to understand the links between wild and cultivated members of the family. We present the complete plastome of African nightshade (Solanum scabrum Mill.) a hexaploid (2n = 6x = 72) species of the S. nigrum L. complex or Solanum sect. Solanum, a widely cultivated species across Africa. Recent studies highlight S. scabrum as a “super-vegetable” for its nutritional and environmental benefits with potential of global importance. The leaves and berries are the source of coloring plant extracts, inks and dyes, and they are rich in proteins, fibres, iron, vitamins and amino acids. Using 12,413,264 paired end reads deposited in the sequence read archive (SRA) we have assembled the plastid genome sequence of African nightshade with an estimated coverage of 123×. The plastid genome sequence had a total size of 155,522 bp, typical of Solanaceae with a large single copy (LSC) region of 85,896 bp and small single copy (SSC) region of 18,406 bp while the IRs comprised of 25,610 bp. We illustrate the role of Solanum scabrum and its comparative plastomics across Solanaceae and Convolvulaceae to understand the plastomics of Solanales.Peer reviewe

Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen

We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment

Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina

[EN] Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed. Duplicates with higher expression levels exhibit greater divergence between their gene copies. Duplicates that exhibit higher expression divergence are those enriched for TATA-containing promoters. These duplicates also show transcriptional plasticity, which seems to be involved in the origin of adaptations to environmental stresses in yeast. While the expression properties of genes strongly affect their duplicability, divergence and transcriptional plasticity are enhanced after gene duplication. We conclude that highly expressed genes are more likely to be preserved as duplicates due to their promoter architectures, their greater tolerance to expression noise, and their ability to reduce the noise-plasticity conflict.We would like to thank members of Fares' Lab for a careful reading and discussion of the results in the manuscript. We are also grateful to colleagues at Trinity College for helpful discussions. This work was supported by a grant from the Spanish Ministerio de Economia y Competitividad (MINECO-FEDER; BFU2015-66073-P) to M.A.F. F.M. is supported by a PhD grant from the Spanish Ministerio de Economia y Competitividad (reference: BES-2016-076677). C.T. was supported by a grant Juan de la Cierva from the Spanish Ministerio de Economia y Competitividad (reference: JCA-2012-14056).Mattenberger, F.; Sabater-Muñoz, B.; Toft, C.; Sablok, G.; Fares Riaño, MA. (2017). Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Research. 24(6):559-570. https://doi.org/10.1093/dnares/dsx025S559570246Ohno, S. (1999). Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Seminars in Cell & Developmental Biology, 10(5), 517-522. doi:10.1006/scdb.1999.0332Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151Otto, S. P., & Whitton, J. (2000). Polyploid Incidence and Evolution. Annual Review of Genetics, 34(1), 401-437. doi:10.1146/annurev.genet.34.1.401Carretero-Paulet, L., & Fares, M. A. (2012). Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications. Molecular Biology and Evolution, 29(11), 3541-3551. doi:10.1093/molbev/mss162Cui, L. (2006). Widespread genome duplications throughout the history of flowering plants. Genome Research, 16(6), 738-749. doi:10.1101/gr.4825606Holub, E. B. (2001). The arms race is ancient history in Arabidopsis, the wildflower. Nature Reviews Genetics, 2(7), 516-527. doi:10.1038/35080508Lespinet, O. (2002). The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes. Genome Research, 12(7), 1048-1059. doi:10.1101/gr.174302Wendel, J. F. (2000). Plant Molecular Biology, 42(1), 225-249. doi:10.1023/a:1006392424384Soltis, D. E., Albert, V. A., Leebens-Mack, J., Bell, C. D., Paterson, A. H., Zheng, C., … Soltis, P. S. (2009). Polyploidy and angiosperm diversification. American Journal of Botany, 96(1), 336-348. doi:10.3732/ajb.0800079De Peer, Y. V. (2004). Computational approaches to unveiling ancient genome duplications. Nature Reviews Genetics, 5(10), 752-763. doi:10.1038/nrg1449Hoegg, S., Brinkmann, H., Taylor, J. S., & Meyer, A. (2004). Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish. Journal of Molecular Evolution, 59(2), 190-203. doi:10.1007/s00239-004-2613-zGrant, S. G. N. (2016). The molecular evolution of the vertebrate behavioural repertoire. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1685), 20150051. doi:10.1098/rstb.2015.0051Green, S. A., & Bronner, M. E. (2013). Gene duplications and the early evolution of neural crest development. Seminars in Cell & Developmental Biology, 24(2), 95-100. doi:10.1016/j.semcdb.2012.12.006Conant, G. C., & Wolfe, K. H. (2007). Increased glycolytic flux as an outcome of whole‐genome duplication in yeast. Molecular Systems Biology, 3(1), 129. doi:10.1038/msb4100170Wolfe, K. H., & Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387(6634), 708-713. doi:10.1038/42711Fares, M. A., Keane, O. M., Toft, C., Carretero-Paulet, L., & Jones, G. W. (2013). The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes. PLoS Genetics, 9(1), e1003176. doi:10.1371/journal.pgen.1003176Blanc, G., & Wolfe, K. H. (2004). Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes. The Plant Cell, 16(7), 1667-1678. doi:10.1105/tpc.021345Blanc, G., & Wolfe, K. H. (2004). Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution. The Plant Cell, 16(7), 1679-1691. doi:10.1105/tpc.021410Conant, G. C., & Wolfe, K. H. (2008). Turning a hobby into a job: How duplicated genes find new functions. Nature Reviews Genetics, 9(12), 938-950. doi:10.1038/nrg2482Fares, M. A., Byrne, K. P., & Wolfe, K. H. (2005). Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species. Molecular Biology and Evolution, 23(2), 245-253. doi:10.1093/molbev/msj027Freeling, M. (2009). Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition. Annual Review of Plant Biology, 60(1), 433-453. doi:10.1146/annurev.arplant.043008.092122Conant, G. C., Birchler, J. A., & Pires, J. C. (2014). Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology, 19, 91-98. doi:10.1016/j.pbi.2014.05.008Keane, O. M., Toft, C., Carretero-Paulet, L., Jones, G. W., & Fares, M. A. (2014). Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae. Genome Research, 24(11), 1830-1841. doi:10.1101/gr.176792.114Fares, M. A. (2015). The origins of mutational robustness. Trends in Genetics, 31(7), 373-381. doi:10.1016/j.tig.2015.04.008Gout, J.-F., & Lynch, M. (2015). Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. Molecular Biology and Evolution, 32(8), 2141-2148. doi:10.1093/molbev/msv095Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389Byrne, K. P. (2005). The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research, 15(10), 1456-1461. doi:10.1101/gr.3672305Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., & Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/nar/gks540Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi:10.1186/gb-2010-11-10-r106Brion, C., Pflieger, D., Souali-Crespo, S., Friedrich, A., & Schacherer, J. (2016). Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Molecular Biology of the Cell, 27(10), 1694-1705. doi:10.1091/mbc.e15-12-0816Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P., Hellwig, D., … Kurzai, O. (2015). Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Research, 43(3), 1392-1406. doi:10.1093/nar/gku1357Seoighe, C., & Wolfe, K. H. (1999). Yeast genome evolution in the post-genome era. Current Opinion in Microbiology, 2(5), 548-554. doi:10.1016/s1369-5274(99)00015-6Aury, J.-M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B. M., … Wincker, P. (2006). Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444(7116), 171-178. doi:10.1038/nature05230Gout, J.-F., Kahn, D., & Duret, L. (2010). The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution. PLoS Genetics, 6(5), e1000944. doi:10.1371/journal.pgen.1000944McGrath, C. L., Gout, J.-F., Doak, T. G., Yanagi, A., & Lynch, M. (2014). Insights into Three Whole-Genome Duplications Gleaned from theParamecium caudatumGenome Sequence. Genetics, 197(4), 1417-1428. doi:10.1534/genetics.114.163287McGrath, C. L., Gout, J.-F., Johri, P., Doak, T. G., & Lynch, M. (2014). Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research, 24(10), 1665-1675. doi:10.1101/gr.173740.114Albert, F. W., Muzzey, D., Weissman, J. S., & Kruglyak, L. (2014). Genetic Influences on Translation in Yeast. PLoS Genetics, 10(10), e1004692. doi:10.1371/journal.pgen.1004692Gout, J.-F., Duret, L., & Kahn, D. (2009). Differential Retention of Metabolic Genes Following Whole-Genome Duplication. Molecular Biology and Evolution, 26(5), 1067-1072. doi:10.1093/molbev/msp026Papp, B., Pál, C., & Hurst, L. D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature, 424(6945), 194-197. doi:10.1038/nature01771Qian, W., Liao, B.-Y., Chang, A. Y.-F., & Zhang, J. (2010). Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends in Genetics, 26(10), 425-430. doi:10.1016/j.tig.2010.07.002Birchler, J. A., & Veitia, R. A. (2012). Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proceedings of the National Academy of Sciences, 109(37), 14746-14753. doi:10.1073/pnas.1207726109Pu, S., Wong, J., Turner, B., Cho, E., & Wodak, S. J. (2008). Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research, 37(3), 825-831. doi:10.1093/nar/gkn1005Scannell, D. R., Byrne, K. P., Gordon, J. L., Wong, S., & Wolfe, K. H. (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature, 440(7082), 341-345. doi:10.1038/nature04562Landry, C. R., Lemos, B., Rifkin, S. A., Dickinson, W. J., & Hartl, D. L. (2007). Genetic Properties Influencing the Evolvability of Gene Expression. Science, 317(5834), 118-121. doi:10.1126/science.1140247Lehner, B. (2010). Conflict between Noise and Plasticity in Yeast. PLoS Genetics, 6(11), e1001185. doi:10.1371/journal.pgen.1001185Mattenberger, F., Sabater-Muñoz, B., Hallsworth, J. E., & Fares, M. A. (2017). Glycerol stress inSaccharomyces cerevisiae: Cellular responses and evolved adaptations. Environmental Microbiology, 19(3), 990-1007. doi:10.1111/1462-2920.13603Mattenberger, F., Sabater-Muñoz, B., Toft, C., & Fares, M. A. (2016). The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3: Genes|Genomes|Genetics, 7(1), 63-75. doi:10.1534/g3.116.035329Blake, W. J., Balázsi, G., Kohanski, M. A., Isaacs, F. J., Murphy, K. F., Kuang, Y., … Collins, J. J. (2006). Phenotypic Consequences of Promoter-Mediated Transcriptional Noise. Molecular Cell, 24(6), 853-865. doi:10.1016/j.molcel.2006.11.003Raser, J. M. (2005). Noise in Gene Expression: Origins, Consequences, and Control. Science, 309(5743), 2010-2013. doi:10.1126/science.1105891Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441(7095), 840-846. doi:10.1038/nature04785Tirosh, I., Weinberger, A., Carmi, M., & Barkai, N. (2006). A genetic signature of interspecies variations in gene expression. Nature Genetics, 38(7), 830-834. doi:10.1038/ng181

Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom

AbstractWe conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis presented in our study suggests a correlation, which is negative but highly correlated between Axis 1 and GC3s (r=−0.827, P<0.01), indicating that mutational bias has a significant and dominant repressive role to the choices of GC3. We also observed a strong positive correlation between codon adaptation index (CAI) and translational adaptation index (tAIg) (0.407, P<0.01), which demonstrates the facilitation of efficient translation by the optimal codon usage patterns of the highly expressed genes. We believe that the complete set of optimal codon usage patterns detected in this study will serve as a model to enhance the transgenesis in the studied cultivar of Solanum lycopersicum

Transcriptome analysis reveals the role of the root hairs as environmental sensors to maintain plant functions under water-deficiency conditions

An important part of the root system is the root hairs, which play a role in mineral and water uptake. Here, we present an analysis of the transcriptomic response to water deficiency of the wild-Type (WT) barley cultivar 'Karat' and its root-hairless mutant rhl1.a. A comparison of the transcriptional changes induced by water stress resulted in the identification of genes whose expression was specifically affected in each genotype. At the onset of water stress, more genes were modulated by water shortage in the roots of the WT plants than in the roots of rhl1.a. The roots of the WT plants, but not of rhl1.a, specifically responded with the induction of genes that are related to the abscisic acid biosynthesis, stomatal closure, and cell wall biogenesis, thus indicating the specific activation of processes that are related to water-stress signalling and protection. On the other hand, the processes involved in the further response to abiotic stimuli, including hydrogen peroxide, heat, and high light intensity, were specifically up-regulated in the leaves of rhl1.a. An extended period of severe stress caused more drastic transcriptome changes in the roots and leaves of the rhl1.a mutant than in those of the WT. These results are in agreement with the much stronger damage to photosystem II in the rhl1.a mutant than in its parent cultivar after 10 d of water stress. Taking into account the putative stress sensing and signalling features of the root hair transcriptome, we discuss the role of root hairs as sensors of environmental conditions