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Major difference in short RNA populations among plants - the results of interaction with pathogen?
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Department of Plant Biology and Forest Genetics, Swedish University of Agriculture Science.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Small RNA (sRNA) including miRNA and siRNA are important in the regulation of diverse biological processes. Comparative studies of sRNA from plants have mainly focused on miRNA even though this group in most cases is just a mere fraction of the total sRNA diversity. In the present study we report results from an in-depth analysis of the sRNA population from the conifer Picea abies and compared the results to those of a range of species from the plant kingdom. The vast majority of sRNA in P. abies was 21 nucleotides long siRNA, of which a large fraction originate from degradation of transcribed sequences related to TIR-NBS-LRR (Toll/Interleukin-1-Nucleotide Binding Site-Leucine Rich Repeats) type resistance genes. Over 90% of all genes predicted to contain either a TIR or an NBS domain showed evidence of siRNA degradation. Data further suggests that those phased siRNA are initiated from miRNA guided cleavage, often by an abundant 22 nt miRNA. Comparative analysis over a range of divergent plant species revealed a large variation between species in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis thaliana, Oryza sativa and non-vascular plants, while particularly high frequencies were observed in Vitis vinifera and Populus thrichocarpa. This divergent pattern between species might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding NBS-LRR gene families. Alternatively it might reflect variation in a counter-counter defence mechanism partly affected by differences in life history traits, e.g. perennial versus annual life cycles. A major difference between annuals and perennials, affecting the evolution of resistance, is that perennials will with almost certainty encounter many different pathogens before reproduction, and that the long generation times confers problems in matching the evolutionary rates of the pathogens.

National Category
Evolutionary Biology Genetics
Research subject
Biology with specialization in Evolutionary Functional Genomics
Identifiers
URN: urn:nbn:se:uu:diva-177475OAI: oai:DiVA.org:uu-177475DiVA: diva2:541009
Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2013-06-27
In thesis
1. Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus
Open this publication in new window or tab >>Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Evolutionary process can be inferred at three different levels: the species level, the population level and the molecular level. In this thesis, I applied approaches at these three levels and aimed to get a comprehensive picture of conifer evolution, from speciation and demography to geographic variation and local adaptation, and then to the molecular evolution of proteins and small regulatory RNAs.

Spruce species have been observed to possess a large number of trans-species shared polymorphisms. Using an “Isolation with migration” model, we found that the large effective population size of spruce retained these shared polymorphisms, inheriting them from the common ancestor. Post-divergence gene flow only existed between Picea abies and P. glauca, and between P. wilsonii and P. schrenkiana. The combination of Tajima’s D and Fay & Wu’s H at most of loci suggested an ancient and severe bottleneck for most species except P. breweriana.

Furthermore, I investigated the effect of local selection in two parallel clines, which is one of the major forces that can cause divergence or even speciation. The timing of bud set and growth cessation was found correlated with latitude in populations of P. abies and P. obovata. Using allele frequency spectrum analyses we identified three genes under local selection in both species including two circadian-clock genes GI and PRR7, and one photoperiodic gene FTL2. This indicated that parallel evolution could occur through groups of genes within related pathways. Clinal variation at expression level provided stronger evidence of selection in FTL2, which has previously been associated with bud set in P. abies.

Finally we focused on the molecular evolution of mRNA and small regulatory RNAs in P. abies. With the help of Next-Generation sequencing, we have achieved in spruce the first de novel assembly of the needle transcriptome and a preliminary characterization of sRNA populations. Along with features common in plants, spruce also exhibited novelties in many aspects including lower substitution rate and protein evolutionary rate, dominance of 21-nt sRNA, and a large proportion of TIR-NBS-LRR genes as sRNA sources and targets.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 52 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 947
Keyword
Speciation, Demographics, clinal variation, convergent evolution, transcriptome, small regulatory RNA
National Category
Evolutionary Biology Genetics
Research subject
Biology with specialization in Evolutionary Functional Genomics; Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-177482 (URN)978-91-554-8411-8 (ISBN)
Public defence
2012-09-14, Lindahlsalen, EBC, Norbyvägen 18A, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2012-08-24 Created: 2012-07-13 Last updated: 2013-01-22Bibliographically approved

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Lagercrantz, Ulf

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