New paper published – Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Text by Lauri Laanisto /EMÜ Press

With the help of Ülo Niinemets and Leila Pazouki from our work group, researchers led by Finnish plant scientists have described the whole genome of silver birch – one of the most distinct and widespread woody species in boreal forest ecosystems of Eurasia. Here is the press release from our university:

Researchers of the Estonian University of Life Sciences involved in publishing silver birch (Betula pendula) genome


A research team led by Professors Jarkko Salojärvi and Jaakko Kangasjärvi (Dept. Biosciences, University of Helsinki, Finland), involving multiple partners from research institutions in Finland, Estonia, UK, and USA published the birch genome. Two researchers from the Estonian University of Life Sciences, Dr. Leila Pazouki and Prof. Ülo Niinemets, were involved in this pioneering research.

Silver birch is an extremely wide-spread Eurasian tree, often dominating temperate and boreal forests. Due to high growth rates and high-quality timber, it is the main tree species for commercial forestry in northern countries. Despite its high commercial value, the genome of silver birch had not been sequenced yet.

Due to its wide geographic dispersal, populations of this plant species are and have been strongly affected by environmental changes. Particularly, temperature is the main factor affecting its growth and development. At present, temperature has increased more than 1.5 °C in several birch habitats, and a warming of 4–11 °C is predicted to be reached by the end of current century. To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes.

In this study, 80 individuals of B. pendula were sequenced. Sampling was done through Finland, Germany, Norway, Ireland, and Siberia. These 80 sequenced genomes allowed the team to identify several key mutations important for understanding the environmental adaptation of birch and also serve as relevant targets for tree breeding. Such primary mutations may affect growth and development of birth trees and the way they respond to light at different latitudes and longitudes and under varies environmental conditions.

As very few tree genomes have been fully sequenced, this study provides particularly valuable information for genome structure and evolution of long-living plants such as trees. Furthermore, this research is expected to serve as a springboard for more efficient breeding of birch towards achieving higher yield and timber quality in different environments. As birch trees have local adaptations to site climates, understanding these natural adaptations will provide a major means for genetic engineering and forest biotechnology studies.

The study was published in the journal Nature Genetics.

Citation: Salojärvi, J., Smolander, O. P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., … & Rastas, P. (2017). Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics, doi:10.1038/ng.3862. (link to full text)



Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

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Public lecture by Steffen M. Noe

On Thursday, 18th of May, our senior researcher Steffen Manfred Noe will held a public lecture in our university – in Kreutzwaldi 5-1B27.

The lecture is titled: “Forest, Climate and Grand Challenges” and it will be in English


Steffen in Estonian Public Broadcasting (link from here)

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New publication – Schola Biotheoretica XLIII: BAER

Text by Lauri Laanisto

On February 17th, in 1792 – thus 225 years ago – Karl Ernst von Baer (died 1876) was born in Piibe manor, in North-East Estonia (back then, of course, it was Russian Empire). Von Baer is probably the most eminent Estonian scientist ever (though, technically he was ethnic German, but he spoke Estonian as well).


Young von Baer (pic from here)

He´s the guy who (re)discovered mammalian ovum. He is also the father of embryology and formulated the Baer’s laws of embryology:

  1. General characteristics of the group to which an embryo belongs develop before special characteristics.
  2. General structural relations are likewise formed before the most specific appear.
  3. The form of any given embryo does not converge upon other definite forms, but separates itself from them.
  4. The embryo of a higher animal form never resembles the adult of another animal form, such as one less evolved, but only its embryo.

He also studied geography, river erosion dynamics, freshwater fish populations. Baer was the first researcher to study perception of time in different organisms. A true polymath. “The great Von Baer” as Darwin mentioned him in “The Origin of Species”, even though Baer was not really proponent of evolution via natural selection.

Therefore this year´s Schola Biotheoretica – annual journal accompanying the Spring School of Theoretical Biology (edited by yours truly) is dedicated to von Baer and all the topics he studied. I´ll paste here the English version of the Table of Contents (the text themselves are in Estonian), and also add the beautiful cover by Vahram Muradyan, and then I have to start driving to the spring school. It starts in couple of hours…


Table of contents:

Kalevi Kull ja Lauri Laanisto – Introduction: Of Baer, theoretical biology and Estonian culture 7
Maie Remmel – Scientific research program „Baer and Darwin“ 13
Mati Kaal – Karl Ernst von Baer, discoverer of the mammalian ovum 87
Toomas Kukk ja Thea Kull – Baer´s herbarium 93
Raik-Hiio Mikelsaar – 225 years from the birth of Karl Ernst von Baer, appraising his scientific contribution in Estonia 107
Toivo Maimets – Randomness during the development of an organism 113
Elo Madissoon – From ovum to embryo: the role of genes 121
Kersti Tepp – Changes in the energy transfer pathways during development; systems biology approach 127
Oive Tinn – The embryos of our predecessors – who laid the first egg? 135
Tuul Sepp – Does urbanization slow down life-history continuum? 143
Sirgi Saar – Cognitive architecture and plant behaviour 149
Siim-Kaarel Sepp – Glomeromycota and human impact 157
Tanel Vahter – Chicken or crocodile – Glomeromycota inoculates in the environment 163
Mart Viikmaa – Francis Galton – XIX century polymath 173
Lauri Laanisto – Restless polymath Alexander von Humboldt 191
Margus Ott – Selection of Chinese natural philosophy 199
Kalevi Kull – Thinkers in the windings of evolutionary theory 215

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A case of plagiarism

Text by Ülo Niinemets

<A letter to the editors of BMC Plant Biology>

It has caught our attention that the paper of: Shi, J., Ma, C., Qi, D., Lv, H., Yang, T., Peng, Q., … & Lin, Z. (2015). Transcriptional responses and flavor volatiles biosynthesis in methyl jasmonate-treated tea leaves. BMC plant biology, 15(1), 233.

contains a significant overlap with two figures from our highly cited paper:

In particular, in the paper of Shi et al. Fig. 4 is copy-paste of Fig. 3 from our paper with the only modification being the photoshopping-out of the caterpillar cartoon and adding the text “exogenous MeJA” with different font.

Then Fig. S6, is the exact reproduction of Fig. 2 in our paper.

No credit is given to the original source in the paper of Shi et al.

I find it terribly regretful that authors have shamelessly copy-pasted material from a published study without providing appropriate credit, and I wonder what is the editorial action in this matter?

Looking forward to your response and all the best
Ülo Niinemets


Quantitative patterns between plant volatile emissions induced b

Fig 3 from Niinemets et al


Fig 4 from Shu et al

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New paper published – Disproportionate photosynthetic decline and inverse relationship between constitutive and induced volatile emissions upon feeding of Quercus robur leaves by large larvae of gypsy moth (Lymantria dispar)

Text by Lauri Laanisto

Another paper by Ülo´s former postdoc Lucian, who does a lot of small experiments, where they measure all sorts of factors that could affect organic volatile emissions in plants. This time the focus is on the interplay between an oak and a moth. The topic is actually pretty interesting, or more precisely – it is something that we need to study. Climate change and the loss of ecosystem services like pest control (whether due to climate change or not) will change the invertebrate herbivore dynamics on plants in forseeable future. How significantly will it change the things, especially on small scale. So far we have very little idea about that. And this study tries to take the first steps in this direction.

As a remark I have to say that studying gypsy moth feels very-very Romanian thing to do;) I´m sure that soon the common name will be changed (like blackboys in Australia are now known as grasstrees etc). Maybe the Romani representatives have not yet had time to deal with such racial taxonomy…

Citation: Copolovici, L., Pag, A., Kännaste, A., Bodescu, A., Tomescu, D., Copolovici, D., … & Niinemets, Ü. (2017). Disproportionate photosynthetic decline and inverse relationship between constitutive and induced volatile emissions upon feeding of Quercus robur leaves by large larvae of gypsy moth (Lymantria dispar). Environmental and Experimental Botany, 138: 184–192. (link to full text)


Progressive spread of the gypsy moth (L. dispar) across north east US from 1900–2007; compiled from county data by US Forest Service (pic from here)


Gypsy moth (Lymantria dispar L., Lymantriinae) is a major pest of pedunculate oak (Quercus robur) forests in Europe, but how its infections scale with foliage physiological characteristics, in particular with photosynthesis rates and emissions of volatile organic compounds has not been studied. Differently from the majority of insect herbivores, large larvae of L. dispar rapidly consume leaf area, and can also bite through tough tissues, including secondary and primary leaf veins. Given the rapid and devastating feeding responses, we hypothesized that infection of Q. robur leaves by L. dispar leads to disproportionate scaling of leaf photosynthesis and constitutive isoprene emissions with damaged leaf area, and to less prominent enhancements of induced volatile release. Leaves with 0% (control) to 50% of leaf area removed by larvae were studied. Across this range of infection severity, all physiological characteristics were quantitatively correlated with the degree of damage, but all these traits changed disproportionately with the degree of damage. The net assimilation rate was reduced by almost 10-fold and constitutive isoprene emissions by more than 7-fold, whereas the emissions of green leaf volatiles, monoterpenes, methyl salicylate and the homoterpene (3E)-4,8-dimethy-1,3,7-nonatriene scaled negatively and almost linearly with net assimilation rate through damage treatments. This study demonstrates that feeding by large insect herbivores disproportionately alters photosynthetic rate and constitutive isoprene emissions. Furthermore, the leaves have a surprisingly large capacity for enhancement of induced emissions even when foliage photosynthetic function is severely impaired.

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New paper accepted – Extremely thick cell walls and low mesophyll conductance: welcome to the world of ancient living!

Text and pics by Linda-Liisa Veromann-Jürgenson

I am overjoyed that I have my first article for my PhD accepted! It is now published in Journal of Experimental Botany.

a day in the lab

Linda-Liisa in the lab

As everyone in our group knows, mesophyll conductance is a key player in net assimilation rates in plants, but it’s not too well studied. Recent research, several from this department, has highlighted the importance of mesophyll structure in determining its conductance. Although several papers have been published on the mesophyll conductance of angiosperms and its underlying ultrastructural characteristics, only two studies had been conducted on gymnosperms that consider gas-exchange as well as mesophyll anatomy. We studied evolutionarily old plants including three divisions of gymnosperms, a whisk fern and a clubmoss to understand the role of mesophyll conductance on net assimilation rate as well as the impact of mesophyll anatomy on gas-exchange with an evolutionary perspective. Additionally, we examined the leaf economics spectrum (LES) correlations in these species as gymnosperms have been found to differ significantly from angiosperms in the LES parameters. We got several important results. Firstly, mesophyll conductance is a very important limiter of photosynthesis in gymnosperms and it depends on mesophyll anatomy. Secondly, the cell wall thickness as well as chloroplast area exposed to intercellular airspaces influence mesophyll conductance significantly and in opposite directions. Furthermore, chloroplast shape and size can play an important role in limiting CO2 diffusion in the liquid phase. Thirdly, although anatomy plays a key role, high leaf mass per area did not relate low net assimilation or high cell wall thickness. Interestingly, we measured extremely thick cell walls in several species, which may indicate a preservation of ancient traits through time due to some evolutionary constraints.

Citation: Veromann-Jürgenson, L. L., Tosens, T., Laanisto, L., & Niinemets, Ü. (2017) Extremely thick cell walls and low mesophyll conductance: welcome to the world of ancient living!. Journal of Experimental Botany, DOI: (link to full text)

Psilotum nudum TEM

Psilotum nudum transmission electron microscopy photograph


Mesophyll conductance is thought to be an important photosynthetic limitation in gymnosperms, but they currently constitute the most understudied plant group in regard to the extent to which photosynthesis and intrinsic water use efficiency are limited by mesophyll conductance. A comprehensive analysis of leaf gas exchange, photosynthetic limitations, mesophyll conductance (calculated by three methods previously used for across-species comparisons), and the underlying ultra-anatomical, morphological and chemical traits in 11 gymnosperm species varying in evolutionary history was performed to gain insight into the evolution of structural and physiological controls on photosynthesis at the lower return end of the leaf economics spectrum. Two primitive herbaceous species were included in order to provide greater evolutionary context. Low mesophyll conductance was the main limiting factor of photosynthesis in the majority of species. The strongest sources of limitation were extremely thick mesophyll cell walls, high chloroplast thickness and variation in chloroplast shape and size, and the low exposed surface area of chloroplasts per unit leaf area. In gymnosperms, the negative relationship between net assimilation per mass and leaf mass per area reflected an increased mesophyll cell wall thickness, whereas the easy-to-measure integrative trait of leaf mass per area failed to predict the underlying ultrastructural traits limiting mesophyll conductance.

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Plant physiologists defeating stress in 7 km run

Text by Kaia Kask, pics by Steffen Noe and Kaia Kask

On the 8th of April 2017 Ülo Niinemets’ lab members went to run 7 km in Parkmetsa running competition in Tartu, Estonia. Our crew members were: Ülo Niinemets, Steffen M. Noe, Tiina Tosens, Kaia Kask, Leila Pazouki, Arooran Kanagendran, Bin Liu, Valentina Zolotarjova, Chickodinaka Okereke and Evi Vaino. Main purpose was to have fun and not to stress about the time. Weather was sunny and team was ready to give 100%!

Next running competition is in August 2017. So we have time to prove our running results!


Kaia and Tiina (65) running


Ülo (64) finishing


Valentina (73), Tiina (65), Steffen (71) and Bin (69) after the run


Chika mitigating stress with water


Kaia (66), Bin (69), Eevi (74), Arooran (70), Ülo (64) and Steffen after finishing

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