Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

AbstractThe genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to their ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, the most extremely cold-adapted Drosophila species. We describe the genome, which is similar in size and gene content to most Drosophila species. We look for evidence of accelerated divergence from a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana representing its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

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Cold adaptation drives population genomic divergence in the ecological specialist , Drosophila montana

Molecular Ecology ◽

10.1111/mec.16003 ◽

2021 ◽

Author(s):

R. A. W. Wiberg ◽

V. Tyukmaeva ◽

A. Hoikkala ◽

M. G. Ritchie ◽

M. Kankare

Keyword(s):

Cold Adaptation ◽

Population Genomic ◽

Genomic Divergence ◽

Drosophila Montana

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Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana

10.1101/2020.04.20.050450 ◽

2020 ◽

Author(s):

R. A. W. Wiberg ◽

V. Tyukmaeva ◽

A. Hoikkala ◽

M. G. Ritchie ◽

M. Kankare

Keyword(s):

Cold Tolerance ◽

Cold Adaptation ◽

Ecological Adaptation ◽

Climatic Variables ◽

Population Divergence ◽

Candidate Snps ◽

Clinal Variation ◽

Ecological Selection ◽

Genomic Divergence ◽

Drosophila Montana

ABSTRACTDetecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and searched for signatures of cold adaptation in populations’ genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the whole scale of environmental variation experienced by the species, and measure variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements. The top candidate SNPs were enriched on the X and 4th chromosomes, and they also lie near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and 4th chromosomes, which also showed highest interpopulation Fst. This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.

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Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

Genome Biology and Evolution ◽

10.1093/gbe/evy147 ◽

2018 ◽

Vol 10 (8) ◽

pp. 2086-2101 ◽

Cited By ~ 14

Author(s):

Darren J Parker ◽

R Axel W Wiberg ◽

Urmi Trivedi ◽

Venera I Tyukmaeva ◽

Karim Gharbi ◽

...

Keyword(s):

Cold Adaptation ◽

Genomic Divergence ◽

Drosophila Montana

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Increased ACTH response to corticotropin-releasing factor in cold-adapted rats in vivo

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.1989.257.3.e336 ◽

1989 ◽

Vol 257 (3) ◽

pp. E336-E339 ◽

Cited By ~ 1

Author(s):

A. Uehara ◽

Y. Habara ◽

A. Kuroshima ◽

C. Sekiya ◽

Y. Takasugi ◽

...

Keyword(s):

Stress Responses ◽

Cold Adaptation ◽

Corticotropin Releasing Factor ◽

Plasma Acth ◽

Cold Adapted ◽

Repeated Restraint Stress ◽

Cross Adaptation ◽

Freely Moving ◽

Increased Activity

We have recently reported that chronically repeated restraint stress results in improved cold tolerance in rats via an increased activity of nonshivering thermogenesis, a characteristic metabolic change observed during cold adaptation, suggesting the presence of cross-adaptation between cold and stress. It is well established that the hypothalamic-pituitary-adrenal (HPA) axis is activated in various stress responses. In the present study, therefore, we examined whether cold adaptation would alter the adrenocorticotropic hormone (ACTH)-releasing state in vivo using freely moving, conscious rats chronically implanted with intra-atrial cannulas. There was no difference in the basal levels of plasma ACTH between warm control and cold-adapted rats. On the other hand, the ACTH response to the intravenous administration of corticotropin-releasing factor (CRF; 2 micrograms/animal) was significantly elevated in cold-adapted rats. However, the injection of 10 micrograms of CRF, which was considered as a dose to elicit the maximal ACTH response, resulted in similar ACTH release patterns between the two groups. These changes in the responsiveness of ACTH secretion have been observed in rats chronically exposed to stressful conditions. The results demonstrated in the present study, therefore, provide further evidence for our hypothesis that there may exist cross-adaptation between cold and nonthermal stress.

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The Effects of Thyroxine and Isopropylnoradrenaline on Cytochrome Oxidase Activity in Brown Adipose Tissue

Canadian Journal of Physiology and Pharmacology ◽

10.1139/y73-114 ◽

1973 ◽

Vol 51 (10) ◽

pp. 751-758 ◽

Cited By ~ 26

Author(s):

H. M. C. Heick ◽

C. Vachon ◽

Mary Ann Kallai ◽

Nicole Bégin-Heick ◽

J. LeBlanc

Keyword(s):

Adipose Tissue ◽

Brown Adipose Tissue ◽

Protein Content ◽

Cytochrome Oxidase ◽

Cold Adaptation ◽

Metabolic Response ◽

Mitochondrial Enzymes ◽

Cold Adapted ◽

Brown Adipose ◽

Hormonal Treatments

Groups of animals were treated with injections of isopropylnoradrenaline, thyroxine, or both hormones together. The effects of these hormonal treatments on the size, protein content, and level of some mitochondrial enzymes, in particular the cytochrome oxidase, were determined and compared to the effect on these parameters produced by cold adaptation. The changes observed were correlated with the resistance of the animals to cold stress and with their metabolic response to injections of isopropylnoradrenaline. All treatments increased the size of the brown adipose tissue. Whereas thyroxine had little effect on the protein content and cytochrome oxidase, both isopropylnoradrenaline and cold adaptation produced increases in these parameters. It appears that the isopropylnoradrenaline-treated animals mimic more closely the cold-adapted animals than do those with thyroxine treatment. However, the isopropylnoradrenaline-treated animals are not as resistant to cold as the cold-adapted animals.

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Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab127 ◽

2021 ◽

Author(s):

Gilda Varliero ◽

Muhammad Rafiq ◽

Swati Singh ◽

Annabel Summerfield ◽

Fotis Sgouridis ◽

...

Keyword(s):

Active Layer ◽

Sequence Variation ◽

Gene Clusters ◽

Taxonomic Composition ◽

Sequence Information ◽

Biosynthetic Gene Clusters ◽

Medical Settings ◽

Cold Adapted ◽

Database Construction ◽

Medium Quality

Abstract Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.

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The effect of cold adaptation on kinetics of insulin and growth hormone in heifers

Canadian Journal of Animal Science ◽

10.4141/cjas93-003 ◽

1993 ◽

Vol 73 (1) ◽

pp. 33-47 ◽

Cited By ~ 4

Author(s):

S. L. Scott ◽

R. J. Christopherson

Keyword(s):

Growth Hormone ◽

Cold Adaptation ◽

Slow Component ◽

Plasma Concentrations ◽

Endocrine System ◽

Insulin Injection ◽

Metabolic Clearance ◽

Cold Environment ◽

Cold Adapted ◽

Total Turnover

Ten Holstein heifers 1 yr of age were housed in groups of five in temperature-controlled environmental chambers maintained at either 20 °C (warm environment) or − 17 °C (cold environment). Each heifer received an injection of insulin or growth hormone followed by frequent blood sampling. Plasma samples were analyzed for insulin, insulin-like growth factor I (IGF-1), growth hormone, glucagon, triiodothyronine, thyroxine and glucose. Basal plasma concentrations of all hormones except growth hormone and IGF-1 were elevated (P < 0.05) in the cold environment. Kinetic parameters for growth hormone and insulin were calculated using a two-pool model. Both the zero-time intercept and the rate constant for the slow component of growth hormone were lower (P < 0.05) in cold-adapted animals. The total turnover rate of growth hormone in both pools also tended to be reduced by cold adaptation (P < 0.07). The reduction in growth-hormone turnover may be related to the reduced average daily gains that were observed in the cold (P < 0.05). Plasma glucose concentration following both the insulin and growth-hormone injections was higher in the cold-adapted heifers (P < 0.001 and P < 0.05, respectively). The response of glucagon to insulin injection was greater in the cold (P < 0.05), as was the response of IGF-I to growth-hormone injection (P < 0.10). These cold-induced alterations in the endocrine system appear to be directed toward providing substrates, including glucose, for use in thermogenesis rather than growth. Key words: Cold adaptation, growth hormone, insulin, metabolic clearance rate, hormone kinetics, cattle

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Survival of halophilic Archaea in Earth's cold stratosphere

International Journal of Astrobiology ◽

10.1017/s1473550416000410 ◽

2016 ◽

Vol 16 (4) ◽

pp. 321-327 ◽

Cited By ~ 11

Author(s):

P. DasSarma ◽

V.J. Laye ◽

J. Harvey ◽

C. Reid ◽

J. Shultz ◽

...

Keyword(s):

Low Temperatures ◽

Cold Adaptation ◽

Halophilic Archaea ◽

Cold Temperature ◽

Freezing And Thawing ◽

Cold Adapted ◽

Liquid Cultures ◽

Genome Wide ◽

Temperature Exposure ◽

Genetic Responses

AbstractHalophilic Archaea are known to tolerate multiple extreme conditions on Earth and have been proposed as models for astrobiology. In order to assess the importance of cold-adaptation of these microorganisms in surviving stratospheric conditions, we launched live, liquid cultures of two species, the mesophilic model Halobacterium sp. NRC-1 and the cold-adapted Antarctic isolate Halorubrum lacusprofundi ATCC 49239, on helium balloons. After return to Earth, the cold-adapted species showed nearly complete survival while the mesophilic species exhibited slightly reduced viability. Parallel studies found that the cold-adapted species was also better able to survive freezing and thawing in the laboratory. Genome-wide transcriptomic analysis was used to compare the two haloarchaea at optimum growth temperatures versus low temperatures supporting growth. The cold-adapted species displayed perturbation of a majority of genes upon cold temperature exposure, divided evenly between up-regulated and down-regulated genes, while the mesophile exhibited perturbation of only a fifth of its genes, with nearly two-thirds being down-regulated. These results underscore the importance of genetic responses of H. lacusprofundi to cold temperature for enhanced survival in the stratosphere.

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Pathobiological and Genomic Characterization of a Cold-Adapted Infectious Bronchitis Virus (BP-caKII)

Viruses ◽

10.3390/v10110652 ◽

2018 ◽

Vol 10 (11) ◽

pp. 652

Author(s):

Seung-Min Hong ◽

Se-Hee An ◽

Chung-Young Lee ◽

Chang-Seon Song ◽

Kang-Seuk Choi ◽

...

Keyword(s):

Infectious Bronchitis Virus ◽

Cold Adaptation ◽

Reproductive Tract ◽

Genomic Sequence ◽

Live Attenuated Vaccine ◽

Genetic Changes ◽

Cold Adapted ◽

Infectious Bronchitis ◽

Field Virus ◽

Specific Pathogen

We established a cold-adapted infectious bronchitis virus (BP-caKII) by passaging a field virus through specific pathogen-free embryonated eggs 20 times at 32 °C. We characterized its growth kinetics and pathogenicity in embryonated eggs, and its tropism and persistence in different tissues from chickens; then, we evaluated pathogenicity by using a new premature reproductive tract pathogenicity model. Furthermore, we determined the complete genomic sequence of BP-caKII to understand the genetic changes related to cold adaptation. According to our results, BP-caKII clustered with the KII genotype viruses K2 and KM91, and showed less pathogenicity than K2, a live attenuated vaccine strain. BP-caKII showed delayed viremia, resulting in its delayed dissemination to the kidneys and cecal tonsils compared to K2 and KM91, the latter of which is a pathogenic field strain. A comparative genomics study revealed similar nucleotide sequences between BP-caKII, K2 and KM91 but clearly showed different mutations among them. BP-caKII shared several mutations with K2 (nsp13, 14, 15 and 16) following embryo adaptation but acquired multiple additional mutations in nonstructural proteins (nsp3, 4 and 12), spike proteins and nucleocapsid proteins following cold adaptation. Thus, the establishment of BP-caKII and the identified mutations in this study may provide insight into the genetic background of embryo and cold adaptations, and the attenuation of coronaviruses.

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