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Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long‐term laboratory maintenanceстатья
- Авторы: Mikhail Zarubin, Alena Yakhnenko, Elena Kravchenko
- Журнал: Ecology and evolution
- Год издания: 2020
- Издательство: Blackwell Pub. Ltd.
- Местоположение издательства: [Oxford], England
- DOI: 10.1002/ece3.6410
- Аннотация: Different strains of the same species can show a wide range of phenotypic variation concerning all aspects of their life cycle. The study of the basis of this diversity is important for understanding metabolic pathways, longevity, and adaptive evolution and contributes to the improvement of various parameters of human health and life. For example, a few researches using different strains of classic molecular genetics object Drosophila melanogaster and recent genome‐wide association studies demonstrated interesting results in genetics of different complex traits (Ayroles et al., 2009), longevity (Moskalev et al., 2019), energy metabolism and respiration (Montooth, Marden, & Clark, 2003), body weight and metabolic rate (Jumbo‐Lucioni et al., 2010), and energy stores (Klepsatel, Wildridge, & Gáliková, 2019). In addition, examinations of variation in transcript abundance between populations provided information about evolutionary processes such as migration, selection, mutation accumulation (Hsieh, Passador‐Gurgel, Stone, & Gibson, 2007), and parallel evolution (Zhao & Begun, 2017; Zhao, Wit, Svetec, & Begun, 2015).According to some studies D. melanogaster expanded from sub‐Saharan Africa at the recession of the last ice age time from 12,000 till 19,000 years ago (David & Capy, 1988; Li & Stephan, 2006) assuming ten generations per year (Stephan & Li, 2007; Thornton & Andolfatto, 2006) with a subsequent colonization of North America has been occurring in the past 500 years (Stephan & Li, 2007). Most likely that there was a single “out‐of‐Africa” population bottleneck event (Henn, Cavalli‐Sforza, & Feldman, 2012), and the genome‐wide studies of D. melanogaster populations from Africa, North America, Europe, Asia, and the South Pacific confirmed these assumptions (Arguello, Laurent, Clark, & Gaut, 2019). In D. melanogaster, latitudinal clines were observed for a large number of traits, for instance, cell membrane plasticity (Cooper, Hammad, & Montooth, 2014), lifespan, lifetime fecundity, heat and cold resistance (Schmidt & Paaby, 2008), and ethanol tolerance (Cohan & Graf, 1985). It is also known that the frequency of certain alleles of genes increases (Adh‐F , Aldh‐Phe , Tpi‐F , Pgd‐F ) (Berry & Kreitman, 1993; Fry, Donlon, & Saweikis, 2008; Oakeshott et al., 1982; Oakeshott, McKechnie, & Chambers, 1984) and decreases (EstC3 , Odh‐S , LapD3 ) (Oakeshott, Gibson, Willcocks, & Chambers, 1983; Singh, Hickey, & David, 1982) with latitude. However, a significant part of alleles involved in latitude adaptation is not known.Several Drosophilidae strains of different geographical origin were previously compared at the DNA or RNA levels (USA (Fabian et al., 2012), USA–Australia (Reinhardt, Kolaczkowski, Jones, Begun, & Kern, 2014), USA–Panama (Zhao et al., 2015), and Western European (the Netherlands)–African (Zimbabwe) (Hutter, Saminadin‐Peter, Stephan, & Parsch, 2008) populations), and these studies demonstrated interesting patterns of local adaptation through gene expression differentiation, including sex‐biased gene expression. For instance, local adaptation between African and European populations of D. melanogaster mainly manifested increased expression of the gene Cyp6g1 , responsible for insecticide DDT protection for European populations, as well as genes involved in olfaction and the detection of chemical stimulus (Müller et al., 2011). However, there are data neither at the genomic nor transcriptomic levels obtained from Eastern European (Russia) strains of D. melanogaster .One of the main parameters for adaptation is temperature. In addition, one of the most significant things linked with the problem of global warming (IPCC, 2014) is the extinction of insect species that cannot acclimate to temperature increase (Sánchez‐Bayo & Wyckhuys, 2019). Since insects play critical role in many ecosystems for maintaining biodiversity and stable existence of other species of living organisms, the study of insect adaptations to warmer environments becomes increasingly more important. Understanding of adaptation mechanisms at the genetic and metabolic levels allows predicting the extinction of some insect species during global warming and probably preventing it. Therefore, it seems important to compare Russian (Domodedovo 18) and USA (Canton‐S) D. melanogaster strains that lived in different environmental conditions (for instance the average annual temperature in the Canton (Ohio, USA) is about 5,5°C higher than in Domodedovo (Moscow region, Russia)), to obtain new information about transcript abundance between them in case if the long‐term laboratory maintenance keeps the differences between these two lines. D18 (Domodedovo 18) strain of D. melanogaster was collected in 1957 by N. P. Dubinin and colleagues from the natural environment in Russia, Moscow region, Domodedovo. The Canton‐Special (Canton‐S) strain was established by C. B. Bridges from wild type flies from Canton region (Ohio, USA) in 1920s, and it is probably one of the most widely used D. melanogaster lines. Therefore, the comparison of transcriptome profiles between the two laboratory lines will also allow planning experiments with taking into account the differences in their gene expression levels.Both lines are highly inbred and under identical conditions any possible phenotypic and transcriptomic differences between them are caused by genetic backgrounds that were previously formed under influence of evolutionary factors and adaptations to dissimilar environment and to some extent during neutral evolution and random genetic drift. Additional moderate contributions can also be made by spontaneous mutations accumulated during maintenance with the point mutation rate 2.8 × 10−9 per site per generation and deletion mutation rate of 1.2 × 10–9 (Keightley, Ness, Halligan, & Haddrill, 2014).As shown in recent studies of H. J. Maclean et al. (Maclean, Kristensen, Sørensen, & Overgaard, 2018), laboratory populations of D. melanogaster are not fundamentally different from field populations in basic physiological and ecological traits (in particular, in fecundity and developmental time, life span, moving activity level, standard metabolic rate, tolerance to desiccation, starvation, and heat tolerance) and laboratory‐maintained D. melanogaster strains can be used in ecological, physiological, and evolutionary comparative experiments. Similar data were obtained by Griffiths, Schiffer, and Hoffmann (2005) suggested that adaptation to laboratory conditions does not interfere with detection of geographical patterns in fact.Moreover, the use of highly inbred laboratory lines allows to diminish the effects of genetic heterogeneity that observed in wild populations and amplify the impact of studied loci that exhibit different expression levels between strains (Wills, Phelps, & Ferguson, 1975).Therefore, the whole transcriptome analysis of various D. melanogaster laboratory lines can provide new information about local adaptation processes and makes it possible to compare them with the few data obtained from natural populations.Here, we report the microarray analyses on two laboratory D. melanogaster lines of different latitude origin to estimate number and functional affiliation of differentially expressed genes after decades of laboratory maintenance and try to find genes that could be important for adaptation to various environmental conditions and their expression levels can be used as molecular markers of low‐ and high‐latitude D. melanogaster populations.
- Добавил в систему: Зарубин Михаил Павлович