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2. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), Kangasjärvi, J. (Jaakko), Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), and Kangasjärvi, J. (Jaakko)

Abstract

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.

Published
2017

6. Differential responses of Scots pine stilbene synthase and chalcone synthase genes to Heterobasidion annosum infection.

Author

Kovalchuk, A., Zhu, L., Keriö, S., Asiegbu, F. O., and Klopfenstein, N.B.

Subjects
PHENYL compounds, PLANT defenses, CONIFER diseases & pests, STILBENE synthase, CHALCONES
Abstract

Phenolic compounds are essential components of the defensive chemical arsenal of conifer trees. This chemically diverse group encompasses stilbenoids, flavonoids, isoflavonoids, proanthocyanidins and lignans. All of them are produced from the common precursors, CoA esters of the phenylpropanoids: p-coumaroyl-CoA, cinnamoyl-CoA, caffeoyl-CoA and feruloyl-CoA. Two classes of enzymes, stilbene synthases and chalcone synthases, play important roles in the biosynthesis of plant phenolics, such as the conversion of the phenylpropanoid-CoA esters into stilbenoids and flavonoids, respectively. In this study, we investigated the transcriptional responses of the Scots pine ( Pinus sylvestris) genes encoding stilbene and chalcone synthases to the infection by the fungal pathogen Heterobasidion annosum. The experiments were performed on pine seedlings and mature trees. Our results show that the stilbene synthase gene is strongly induced in both age groups, but the level of induction in adult trees varied considerably among individual trees. Systemic induction in needles and hypocotyl regions was documented in young seedlings following fungal inoculation in root region. Concurrent changes in the expression of the chalcone synthase gene in response to fungal infection were much less pronounced. Our data confirm previous observations on the differential regulation of these enzymes in Scots pine and emphasize the role of stilbene synthase in the induced response to fungal infection. [ABSTRACT FROM AUTHOR]

Published
2017
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7. Defence-related gene expression of Hevea brasiliensis clones in response to the white rot pathogen, Rigidoporus microporus.

Author

Oghenekaro, A. O., Omorusi, V. I., Asiegbu, F. O., and Fossdal, C. G.

Subjects
GENE expression, HEVEA, WHITE rot (Grapes), RIGIDOPORUS, JASMONIC acid
Abstract

Gene expression levels of pathogenesis-related proteins ( PR1, PR3, PR5, PR8 and PR9), cell wall modification genes ( PAL and expansin), signal transduction genes ( ACC oxidase, AOC, MAPK) and a Myb transcription factor were compared in two Hevea brasiliensis budded clones ( RRIM612 and PR107) 5 weeks after wounding and artificial inoculation with the white rot fungus, Rigidoporus microporus. PR3 class I chitinase was upregulated in RRIM612 in response to the pathogen when compared with the wounded control. PR9 class IV peroxidase was highly upregulated in PR107. PR1 and PR8 were expressed more in wounded than in inoculated clones. Genes involved in ethylene and jasmonic acid signalling pathways and phenylalanine ammonia-lyase ( PAL) were upregulated almost equally in both clones. The Myb transcription factor was upregulated in RRIM612, while MAPK was upregulated in PR107 when compared to the wounded control. The predicted expansin-like protein was upregulated 40-fold in RRIM612 when compared to the wounded control. The results demonstrate the variability in defence responses in different clones and provide the first set of defence genes expression profiles in the host-pathogen interaction of the white rot disease of rubber trees. [ABSTRACT FROM AUTHOR]

Published
2016
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8. A simple phenol-free isolation method for high-quality RNA from bilberry.

Author

Wang K, Liu M, Cui F, and Asiegbu F

Abstract

High-quality RNA is required for accurate gene expression and transcriptome analysis. The current methods of RNA extraction from berry fruits are either time-consuming or expensive. To simplify the conventional phenol-chloroform based RNA extraction method, we modified the protocol with less steps as well as the removal of the use of phenol. In this protocol, the extraction buffer is composed of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and Dithiothreitol (DTT). The method facilitates efficient removal of polysaccharides and phenolic compounds from both fruit pulp and fruit peel. Additionally, the protocol is phenol-free and less toxic than traditional phenol-containing method. High-quality RNA, with RNA Integrity Number value > 8, isolated by this method is applicable for RNA sequencing and qPCR. Only 3-4 working hours are required for one batch of RNA isolation.•Our method replaces the use of phenol-chloroform with chloroform, making the extraction less toxic.•The bilberry friut RNA is of high-quality and purity with less time input., (© 2021 The Authors. Published by Elsevier B.V.)

Published
2021
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