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Good model for comparative genomics in relation to temperature adaptation

Good model for comparative genomics in relation to temperature adaptation


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Can anyone suggest any highly related bacterial or parasitic species which live at very distinct temperatures, which might be a good model for comparison of genomes in regard to temperature adaptation. For example, related pathogens of which one species infects warm blooded animals, and the other infected cold blooded animals? So far I have come up with one possible example: Salmonella enterica is a pathogen which infects warm blooded animals, whilst Salmonella bongori infects mainly reptiles.

Examples for which there are publicly available genomes, and which have been used in previous studies would be preferable.


As a starting point I would suggest you look at genomes of thermophiles and hyperthermophiles (organisms that thrive at upwards of 40 °C and 60 °C respectively), which are often found near underwater volcanos or hot springs.

For instance, one could do a genomic analysis of the archaean Methanocaldococcus jannaschii, comparing it to mesophilic species of Methanocaldococcus or Methanococcus. This organism is well studied, and genomic information for this organism is readily accessible.

Some studies have been done comparing the genomes of mesophiles and thermophiles. For example, Zheng and Wu (2010) found a correlation between GC content in coding/noncoding regions and temperature conditions.

At the other end of the spectrum you could examine psychrophiles (organisms that grow at low temperatures, −20 °C to +10 °C). However, few of these organisms are obligate psychrophiles, meaning many can thrive at higher temperatures as well and thus may not be suitable for your purpose.


Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.

Results

By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177).

Conclusion

After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.


Systems Biology and Synthetic Biology in Relation to Drought Tolerance or Avoidance in Plants

The dwindling supply of blue water (surface and ground) resources resulting from urbanization, increasing human population and changes in global temperature and precipitation is a major challenge for sustainable crop production for food, feed, fiber, and bioenergy in this century. Plants employ two main .

The dwindling supply of blue water (surface and ground) resources resulting from urbanization, increasing human population and changes in global temperature and precipitation is a major challenge for sustainable crop production for food, feed, fiber, and bioenergy in this century. Plants employ two main strategies for overcoming drought: drought tolerance (e.g., maintaining cell turgor through osmotic adjustments or cell wall elasticity) and drought avoidance (e.g., changing in stomatal patterning, stomatal physiology, root and leaf anatomy, root physiology). Engineering improved drought resistance requires deep understanding of molecular mechanisms underlying drought tolerance or avoidance in model crop and non-crop species and in plants adapted to water-limited habitats. Systems Biology research, empowered by high-throughput omics (e.g., transcriptomics, proteomics, metabolomics) and genome-editing technologies, enables unprecedented insights into gene function, regulatory networks and signaling pathways relevant to plant drought tolerance or avoidance. The knowledge gained through Systems Biology research lays a solid foundation for redesigning the gene modules or pathways to accelerate the adaptation of plants to water-limited environments using synthetic biology approaches, which is a relatively new discipline aiming at redesigning existing biological systems using completely new parts and devices through iterative Design-Build-Test-Learn cycles. There is a resurgence of interest in crassulacean acid metabolism (CAM), a drought avoidance strategy and potential biological solution to the challenges in crop production caused by water limitation. Derived from C3 photosynthesis, CAM is a water-use efficient photosynthetic pathway that has been evolved independently in diverse lineages of plants. New genomics resources have been established in multiple CAM species and international efforts are being made to engineer CAM machinery into C3 photosynthesis plants for sustainable crop production in water-limited environments.

This Research Topic features system biology research for unravelling the molecular basis of plant adaptation to water-limited conditions and utilization of synthetic biology technology for engineering of drought tolerance or avoidance traits. All types of articles are welcome, with a preference for Original Research, Reviews, and Perspectives focusing on the following aspects:
• Discovery of genes and/or gene networks associated with plant response to drought stress through analysis of transcriptome, proteome, and/or metabolome.
• Functional characterization of genes involved in drought tolerance or avoidance in C3, C4 and CAM photosynthesis plants through loss- and/or gain-of-function mutagenesis generated by genome editing technologies (e.g., CRISPR-Cas9 or CRISPR- Cpf1).
• Discovery and characterization of genes involved in stomatal development and movement.
• Molecular basis of leaf succulence in relation to drought avoidance.
• Comparative genomics analysis of CAM and non-CAM plants to identify candidate genes for CAM-into-C3 photosynthesis engineering.
• Engineering of CAM plant genes into C3 photosynthesis plants to increase water-use efficiency.

Keywords: Drought stress, systems biology, synthetic biology, crassulacean acid metabolism, water-use efficiency

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.


Structural changes and evolutionary forces

Structural genomic comparisons show that, despite significant differences in genome sizes, large regions of co-linearity are present between the four species [2, 4, 5]. Differences in genome size could be explained mainly by differences in the intergenic regions, where repeated sequences and transposable elements are commonly found. While in A. thaliana large numbers of microdeletions in these areas are suspected, resulting in a reduction of genome size [2], recent activity of transposable elements is thought to be one of the main reasons for the expansion of the T. salsuginea [4] and A. lyrata [2] genomes. The latter elements are also thought to be one of the factors at the origin of so-called taxonomically restricted, or orphan, genes and gene families, which are new genes that have recently arisen in a taxon. Wu et al. [4] show the T. salsuginea genome to contain 984 families of such genes, the functions of which still remain to be explored. Finally, tandem duplication, segmental duplication and retrotransposon-related gene duplication may act on genome structure, and also may be related to functional adaptation, both via modifying gene expression and by providing an opportunity for functional diversification. Retrotransposition as a source of gene duplication is found to be especially common in the extremophile T. salsuginea, relative to A. thaliana [4].


B-4. Assessment of genetic structure within and among Normandie (Northern France) populations of wild beet (Beta vulgaris sps. maritima Arcang.)

Tran HT XE "Tran HT" (1,*), Cuguen J XE "Cuguen J" (2), Touzet P XE "Touzet P" (2), Saumitou-Maprade P XE "Saumitou-Maprade P" (2)

The examination of coastal northern France (Normandie) beet populations is of particular concern for competent authorities for the regulation of transgenic organisms (GMO) due to the close proximity of wild beet to sugar beet fields. Gene flow from cultivated beets in this area is theoretically possible, if fields near wild beet habitats contain vernalized sugar beets or annual weed types. For purpose of in situ conservation of this genetic resource . For crop improvement, it is very important to examine genetic diversity of sea beet population in Normandie where still is a little information about this.

Materials and Methods

Young leafs gathered from from 396 plants in 9 populations coastal northern France. Nuclear microsatellite loci (codominant marker)used to analysis genetic variations.

Results

The global inbreeding coefficient Fit is 0.3336 , meaning that overall there is evidence for quite substantial inbreeding. We see that 17% of genetic variation is found among populations and 83% within popupulations. The Fst/(1-Fst) ratio for pairs of populations increased no linearly with the natural logarithm of the geographical distance. (Mantel test: P = 0.0005, R 2 = 0.0099), showing a pattern of no isolation by distance (Rousset 1997). There are two groups of populations widely separated: one group of three populations, fec4, veu5 and val6 the other with all 6 other populations. Within the latter group, mars-08 and pou9 are very closely related to each other.

Discussion

Information of biological characteristics from this study is usseful for consevation management such as the level of inbreeding, the population bottlenecks and the variance of gene dispersal distances.

Institute of Agricultural Genetics

Author Affiliations

1*.Institute of Agricultural Genetics, Laboratory for Forest Genetics and Conservation, Hanoi 10000, Vietnam 2.Université des Sciences et Technologies de Lille I, Laboratoire de Génétique et Evolution des Populations Végétales, UPRESA 8016 du CNRS, Bâtiment SN2, 59655 Villeneuve d'Ascq Cedex, France

Acknowledgements

AUPEL-UREF- Bourses d’excellence


Discussion

In evolutionary biology, comparative genomic analysis had been widely applied in understanding the genetic basis of organisms’ speciation [39,40,41] and adaptation [2, 4, 8, 11, 29, 35]. Although whole genome sequencing data of nonmodel organisms have increasingly become available, most organisms still lack genomic resource. Transcriptome sequencing is an effective and accessible approach to initiate comparative genomic analysis on nonmodel organisms, because it could also contain a large number of protein-coding genes likely enriched for targets of natural selection. In this study, we sequenced and annotated the transcriptome of the Schizothoracine fish, G. p. ganzihonensis [9, 18], and identified more than 6000 pairwise orthologs among five fish genomes. Then, we performed comparative genomic analysis on this Schizothoracine fish using its de novo assembly transcriptome dataset and other four fish genomes. Finally, this transcriptome resource could develop our understanding of genetic makeup of highland fishes and provide a foundation for further studies to identify candidate genes underlying adaptation to the Tibetan Plateau of Schizothoracine fishes.

How an organism adapts to environment change is an important issue in evolutionary biology [42]. Adaptive evolution may prefer to proceed at molecular level, expressed by an increase in ratio of nonsynonymous substitutions to synonymous substitutions [43]. Previous studies revealed that terrestrial organisms adapted to life at high altitude by gene family expansion, accelerated evolutionary rate and underwent positive selection on genes associated with specific function [2, 4, 7, 8]. Convergence is an independent evolution of similar physiological or morphological features in different species [44]. Its occurrence could support the hypothesis that specific ecological environment challenges can induce species to evolve in predictable and repeatable ways [45]. Our current analysis results suggested that Schizothoracine fish lineage trends to genome-wide accelerated evolution relative to other fish lineages. Past evidence indicated that accelerated evolution is usually driven by positive selection [32], we therefore speculated that Schizothoracine fish may adaptively speed up its evolutionary rate of genes for better adaptation to extreme environment of the TP. The relaxation of function constraint could possibly trigger accelerated evolution, which the hypothesis should need more cases based on population genomic analyses to support. Furthermore, compared with the ancestral branch, the terminal branch of Schizothoracine fish had underwent an elevated dN/dS ratio, implying that accelerated evolution only in the Schizothoracine fish lineage after diverged from zebrafish (also belonged to Cyprinidae). Previous studies had identified various adaptive processes that may be responsible for highland adaptation in terrestrial animal, including energy metabolism and hypoxia response [2, 4, 46]. Therefore it is not surprising that many GO categories related to energy metabolism and stress response in aquatic animal, Schizothoracine fish. A striking finding of the present study is that “transport function” genes may undergo accelerated evolution, this is consisted of the finding in recent study on the extremely alkaline environment adaptation mechanism in Amur ide, Leuciscus waleckii [47]. This finding implied that the adaptive evolution might play important role in this recent split Schizothoracine fish, G. p. ganzihonesis in transition of salt water to fresh water.

The functions of candidate PSGs were consistent with above identified functional groups of GO categories exhibiting accelerated evolution. Recent studies revealed the genetic basis of terrestrial animal adaptation to low oxygen and low temperature environment at high altitude [1, 2, 4, 7, 12, 13, 29]. In G. p. ganzihonesis, we failed to identify any PSG involved in hypoxia response. This may because the oxygen condition in Tibetan Plateau aquatic environment is different with ground. Previous evidence indicated that abundant and diverse of hydrophyte species in Ganzi River [18], these factors could have positive impacts on the dissolved oxygen content as the plant photosynthesis, which may help to explain the absence of PSGs related to response to hypoxia function. Low temperature is a typical feature of lake and river environment on the TP, which faced up this challenge for all aquatic animals. Accord to previous findings [2, 4], several candidate PSGs involved in energy metabolism were identified. For example, the ATP13a gene that encodes an accessory protein for ATP synthesis and decomposition, suggesting an important role in energy metabolism to adaptation to this low temperature water environment. In addition, SLC family play vital roles in transport function contribute to organism response to dynamic aquatic environment [48]. We also identified several SLC family members shown positive selection in Schizothoracine fish lineage, such as SLC12A1, SLC7A2, SLC38A4. This finding were similar to previous genome-wide study on the Amur ide in extremely alkaline environment [47], which indicated that adaptive evolution within genes involved in transport function contribute to provide novel insight into adaptation to extreme aquatic environment on the Tibetan Plateau. Remarkably, here we provide another novel insight to understand the genetic mechanism of highland adaptation in Schizothoracine fish, the adaptive evolution of innate immunity. Recent evidence showed that Schizothoracine fish is susceptible to infectious diseases and triggered high mortality rate in non-native environment [49,50,51,52]. In addition, recent genome-wide study reveal that adaptive evolution of innate immunity contributed to fish well response to pathogen invasion [53]. Intriguingly, we identified significant positive selection signs in TLR3, IRF8, IL10 and TNFRSF1b involved in innate immunity. This finding is similar with our previous reports on the PSGs and neofunctionalization in TLR signaling pathway genes [49, 51, 52], suggesting that adaptive evolution of innate immunity may play important roles in Schizothoracine fish adaptation to high attitude aquatic life.


Introduction

The switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers) is an important developmental step in the life cycle of plants. Flowering needs to occur when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year. They commonly achieve this by using reliable environmental cues such as day length (photoperiod) and temperature. In addition, nutrient and water availability and plant size can be important.

The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot Arabidopsis thaliana, subsequently Arabidopsis (reviewed by [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]). As part of this study the Arabidopsis flowering pathways were curated in Arabidopsis Reactome (http://www.arabidopsisreactome.org [15]) to provide an electronic knowledge resource allowing for further developments such as integration with protein-protein interaction datasets, overlaying with microarray data and electronic projection into all newly sequenced plant genomes. Using this we compiled a list of genes and gene families with a known role in flowering time in Arabidopsis.

Flowering time has also been extensively studied in crop species (reviewed by [5], [6], [9], [11], [12], [13], [16], [17], [18], [19]). Flowering time is important for adaptation to specific environments and the world's major crop species provide a particularly interesting opportunity for study because they are grown in areas outside the ecogeographical limits of their wild ancestors. In addition, they are adapted to different farming practices such as fall (autumn) sowing or spring sowing in temperate regions. Adaptation to different environments and practices has been achieved by manipulation of flowering time responses and this makes flowering pathways an excellent system for comparison between and within domestic and wild species.

Comparative studies between Arabidopsis and the tropical cereal rice (Oryza sativa) have shown that rice has homologues of many flowering-time genes and that aspects of the photoperiod and autonomous pathway are well conserved (reviewed by [6], [9], [11], [12], [13], [16], [17], [19] Experimental studies have also shown that a gene may retain a role in flowering but with important changes of action. For example the CONSTANS (CO) gene of Arabidopsis promotes flowering in long days while the equivalent gene in rice (Hd1 [20]) promotes flowering in short days but represses flowering in long days [9]. In addition, novel flowering-time genes have been found in rice, showing that different plant lineages have evolved new flowering controls. Examples are the rice Ghd7, OsID1, Ehd1 and OsMADS51 genes that are discussed individually in the results section.

Vernalization pathways are significantly different between Arabidopsis and the grasses as the key flowering repressors (FLC in Arabidopsis and VRN2 in cereals) are not conserved (reviewed by [5], [11], [12], [13], [16], [17], [18], [19]). Understanding the control of flowering time in a range of plant species therefore gives us insights into the ancestral control of flowering time and the evolution of alternative mechanisms in different plant lineages.

The wild grass Brachypodium distachyon (subsequently Brachypodium) has emerged as an important model for temperate species which include important grain crops such as wheat (Triticum monococcum, T. durum and T. aestivum), barley (Hordeum vulgare) and oats (Avena sativa) and forage grasses such as Lolium and Festuca species. The availability of a complete genome sequence for Brachypodium enables the evolutionary relationships of chromosomes to be revealed [21], [22] and is a powerful method for identifying candidates for QTLs identified in individual crop species.

In this paper we used the complete genome sequences of Arabidopsis, rice and Brachypodium to find homologues of genes known to have a role in flowering time in Arabidopsis or other species. For our purposes the genes of interest were those known to affect flowering time measured as leaf number or days to bolting or flowering in Arabidopsis, or as days to panicle emergence, ear emergence or anthesis in cereals. Genes may have been identified from mutation screens or from studies of natural variation. Our aim was to analyse a range of genes involved in known pathways rather than to complete an exhaustive study of all possible flowering-time genes. From this basis phylogenetic analyses of gene families were used to investigate the evolutionary relationships of genes and the impact of segmental duplications on the number of genes in families. Segmental duplications are collinear regions containing paralogous genes that derive from likely whole genome duplication events that occurred in the ancestors of modern species (recently reviewed by [23]). Tandem duplications are instances in which paralogous genes reside side by side along a chromosome and these are likely to result from evolutionarily recent amplification events. The results give us an insight into the evolution of flowering-time genes at the monocot/dicot divide and the relationship between temperate cereals (long-day plants with a vernalization requirement) and tropical cereals (short-day plants with no vernalization requirement).


ACKNOWLEDGEMENTS

We thank Filip Kolár for helpful discussions. The main work was funded by grant 240223/F20 to CB from the Research Council of Norway additional support was obtained from the Czech Science Foundation (grant 15-18545S) and the CEITEC 2020 project (grant LQ1601). Computational analyses were performed on resources provided by UNINETT Sigma2 - the National Infrastructure for High Performance Computing and Data Storage in Norway, and on the Abel Cluster, owned by the University of Oslo and UNINETT Sigma2, and operated by the Department for Research Computing at USIT, the University of Oslo IT-department (http://www.hpc.uio.no/).


Acknowledgements

We thank Dr. Kate Teeter and Dr. Kurt Galbreath for assistance with bioinformatic and phylogenetic analyses. Thanks also to computer science students Nolan Earl and Justin Syria for scripting and coding assistance. We thank Torsten Schöneberg for valuable input on evolutionary analyses.

Funding

This work was funded by an NMU Faculty Grant to ARL.

Availability of data and materials

Data resulting from this project are included as supplementary materials. Additional scripts are available on request from the corresponding author.


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Department of Biology, 433 South University Avenue, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA

CCMAR, University of the Algarve, Faro, Portugal

CCMAR, University of the Algarve, Faro, Portugal

School of Integrative Biology, University of Queensland, St. Lucia QLD 4072 Australia

School of Marine Sciences, University of Maine, Orono, Maine 04469-5706 USA

Department of Biological Science, University of South Carolina, Columbia, South Carolina 29208 USA

School of Marine Sciences, University of Maine, Orono, Maine 04469-5706 USA

Marine Science Center, Northeastern University, Nahant, Massachusetts 01908 USA

Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250 USA

Department of Biological Science, University of South Carolina, Columbia, South Carolina 29208 USA

Institute of Integrative and Comparative Biology, University of Leeds, Leeds LS2 9JT United Kingdom

Institut des Sciences de l'Evolution, CNRS UMR 5554, U. Montpellier, Montpellier, France

Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island 02912 USA

Department of Biology, 433 South University Avenue, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA

CCMAR, University of the Algarve, Faro, Portugal

CCMAR, University of the Algarve, Faro, Portugal

School of Integrative Biology, University of Queensland, St. Lucia QLD 4072 Australia

School of Marine Sciences, University of Maine, Orono, Maine 04469-5706 USA

Department of Biological Science, University of South Carolina, Columbia, South Carolina 29208 USA

School of Marine Sciences, University of Maine, Orono, Maine 04469-5706 USA

Marine Science Center, Northeastern University, Nahant, Massachusetts 01908 USA

Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250 USA

Department of Biological Science, University of South Carolina, Columbia, South Carolina 29208 USA

Institute of Integrative and Comparative Biology, University of Leeds, Leeds LS2 9JT United Kingdom

Institut des Sciences de l'Evolution, CNRS UMR 5554, U. Montpellier, Montpellier, France

Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island 02912 USA

Corresponding Editor (ad hoc): C. W. Cunningham.

Abstract

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.


Watch the video: What is Comparative Genomics? (July 2022).


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