ORCID Profile
0000-0003-4706-7256
Current Organisation
King Abdullah University of Science and Technology
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Publisher: Frontiers Media SA
Date: 2016
Publisher: Wiley
Date: 10-2023
DOI: 10.1002/ECE3.10608
Publisher: Springer Science and Business Media LLC
Date: 10-02-2020
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-2018
Abstract: Changes in gene body methylation predict phenotypic acclimatization of the coral Stylophora pistillata to ocean acidification.
Publisher: Springer Science and Business Media LLC
Date: 04-08-2021
DOI: 10.1038/S41598-021-95357-0
Abstract: Brown hares ( Lepus europaeus Pallas) are able to hybridize with mountain hares ( L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic ersity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1 ), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare ex le where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
Publisher: Oxford University Press (OUP)
Date: 11-02-2016
DOI: 10.1093/GBE/EVW019
Publisher: Wiley
Date: 13-11-2022
DOI: 10.1111/MEC.16755
Abstract: Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare ( Lepus timidus Linnaeus) and the temperate steppe‐climate adapted brown hare ( Lepus europaeus Pallas). We discovered the existence of a species‐specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
Publisher: Frontiers Media SA
Date: 04-10-2018
Publisher: Public Library of Science (PLoS)
Date: 12-12-2018
Publisher: Wiley
Date: 23-12-2017
DOI: 10.1111/MEC.14452
Abstract: Reef-building corals and other cnidarians living in symbiotic relationships with intracellular, photosynthetic dinoflagellates in the genus Symbiodinium undergo transcriptomic changes during infection with the algae and maintenance of the endosymbiont population. However, the precise regulatory mechanisms modulating the host transcriptome are unknown. Here, we report apparent post-transcriptional gene regulation by miRNAs in the sea anemone Aiptasia, a model system for cnidarian-dinoflagellate endosymbiosis. Aiptasia encodes mainly species-specific miRNAs, and there appears to have been recent differentiation within the Aiptasia genome of miRNAs that are commonly conserved among anthozoan cnidarians. Analysis of miRNA expression showed that both conserved and species-specific miRNAs are differentially expressed in response to endosymbiont infection. Using cross-linking immunoprecipitation of Argonaute, the central protein of the miRNA-induced silencing complex, we identified miRNA binding sites on a transcriptome-wide scale and found that the targets of the miRNAs regulated in response to symbiosis include genes previously implicated in biological processes related to Symbiodinium infection. Our study shows that cnidarian miRNAs recognize their mRNA targets via high-complementarity target binding and suggests that miRNA-mediated modulations of genes and pathways are important during the onset and maintenance of cnidarian-dinoflagellate endosymbiosis.
Publisher: MDPI AG
Date: 30-04-2021
Abstract: Oxidative stress can be modeled using various different experimental approaches, such as exposing the cells or organisms to oxidative chemicals. However, the actual effects of these chemicals, outside of the immediate measured effect, have attracted relatively little attention. We show here that three commonly used oxidants, menadione, potassium bromate, and hydrogen peroxide, while known to function differently, also elicit different types of responses in HEK293T cells. Menadione and bromate exposure mainly trigger an integrated stress response, whereas hydrogen peroxide affects cellular processes more ersely. Interestingly, acute oxidative stress does not universally cause notable induction of DNA repair or antioxidant defense mechanisms. We also provide evidence that cells with previous experience of oxidative stress show adaptive changes in their responses when the stress is renewed. Our results urge caution when comparing studies where different sources of oxidative stress have been used or when generalizing the findings of these studies to other oxidant types or tissues.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-11-2017
Abstract: Deep-sea fishes evolved an unconventional visual system to optimize vision in twilight conditions.
Publisher: Elsevier BV
Date: 08-2021
Publisher: Wiley
Date: 21-08-2018
DOI: 10.1111/MEC.14810
Abstract: Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these erse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting lifiable total DNA from soft fungal s les of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the s le is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our s les-regardless of biomass or other properties-being successfully PCR- lified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities. Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these erse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting lifiable total DNA from soft fungal s les of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the s le is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our s les-regardless of biomass or other properties-being successfully PCR- lified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
Publisher: Proceedings of the National Academy of Sciences
Date: 31-08-2015
Abstract: Coral reefs form marine-bio ersity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences, including global warming, ocean acidification, and pollution, heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a system, and our analysis of its genome provides a foundation for research in this area and has revealed numerous features of interest in relation to the evolution and function of the symbiotic relationship.
Publisher: Oxford University Press (OUP)
Date: 31-03-2021
DOI: 10.1093/G3JOURNAL/JKAB094
Abstract: Hymenoptera is a hyper erse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environments, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance. There are 99 hymenopteran genomes in the NCBI database, yet only five are representative of the paraphyletic suborder Symphyta (sawflies, woodwasps, and horntails), while the rest represent the suborder Apocrita (bees, wasps, and ants). Here, using a combination of 10X Genomics linked-read sequencing, Oxford Nanopore long-read technology, and Illumina short-read data, we assembled the genomes of two willow-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae: Euurina): the bud-galling species Euura lappo and the leaf-galling species Eupontania aestiva. The final assembly for E. lappo is 259.85 Mbp in size, with a contig N50 of 209.0 kbp and a BUSCO score of 93.5%. The E. aestiva genome is 222.23 Mbp in size, with a contig N50 of 49.7 kbp and a 90.2% complete BUSCO score. De novo annotation of repetitive elements showed that 27.45% of the genome was composed of repetitive elements in E. lappo and 16.89% in E. aestiva, which is a marked increase compared to previously published hymenopteran genomes. The genomes presented here provide a resource for inferring phylogenetic relationships among basal hymenopterans, comparative studies on host-related genomic adaptation in plant-feeding insects, and research on the mechanisms of plant manipulation by gall-inducing insects.
Publisher: Springer Science and Business Media LLC
Date: 17-10-2016
DOI: 10.1038/SREP35461
Abstract: Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.
Publisher: American Society for Microbiology
Date: 28-08-2014
Abstract: Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we report on the whole-genome sequencing, assembly, and annotation of three Endozoicomonas type strains. These data will assist in exploring interactions between Endozoicomonas organisms and their hosts, and it will aid in the assembly of genomes from uncultivated Endozoicomonas spp.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-08-2018
Abstract: The epigenetic mechanism of DNA methylation optimizes gene expression in endosymbiosis between cnidarians and their microalgae.
Publisher: Cold Spring Harbor Laboratory
Date: 31-08-2023
DOI: 10.1101/2023.08.29.555262
Abstract: Here we present a high-quality genome assembly of the mountain hare (Lepus timidus L.), based on a fibroblast cell line of a male specimen from Ilomantsi, Eastern Finland. The mountain hare represents the first Finnish contribution to the European Reference Genome Atlas pilot effort to generate reference genomes for European bio ersity. The genome was assembled using 25X PacBio HiFi sequencing data and scaffolded utilizing a Hi-C chromosome structure capture approach. After manual curation, the assembled genome length was 2,930,972,003 bp with N50 125.8Mb. 93.16% of the assembly could be assigned to 25 identified chromosomes (23 autosomes plus X and Y), matching the published karyotype. The chromosomes were named according to size. The genome has a high degree of completeness based on the BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, and Missing 2.9%. The mitochondrial genome of the cell line was sequenced and assembled separately. Compared to the previous pseudoreference genome of L. timidus ssp. hibernicus Bell, assembled using the rabbit genome, this new reference genome represents the nominal subspecies and the species-specific chromosomal conformation. In addition to providing a useful comparison for population studies, the genome can offer insight into the chromosomal evolution among Glires in general and Lagomorpha in particular. The chromosomal assembly of the genome also demonstrates that the cell line has not gone through karyotypic changes during culture.
Publisher: Pemberley Books (Publishing)
Date: 28-04-2018
DOI: 10.31184/M00138908.1542.3919
Abstract: The first definite records of the willow species Salix herbacea L. as a host of the leaf-mining sawfly Scolioneura tirolensis (Enslin, 1914) are presented. This is currently the only leaf-mining sawfly species whose larvae are known to feed on this host.
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2021
DOI: 10.1101/2021.02.16.431512
Abstract: Oxidative stress can be modeled using various different experimental approaches, such as exposing the cells or organisms to oxidative chemicals. However, the actual effects of these chemicals, outside of the immediate measured effect, have attracted relatively little attention. We show here that three commonly used oxidants, menadione, potassium bromate and hydrogen peroxide, while known to function differently, also elicit different types of responses in cultured cells. While cells response to menadione and bromate exposure mainly by an integrated stress response, hydrogen peroxide has more indirect effects. Primary oxidative stress does not induce DNA repair or antioxidant defense mechanisms. However, cells with previous experience of oxidative stress show adaptive changes when the stress is renewed. Our results urge caution when comparing studies using different sources of oxidative stress or generalizing the findings of these studies to different tissue or oxidant types.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2017
DOI: 10.1038/NATURE21370
Abstract: Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other s les of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
Publisher: Wiley
Date: 15-10-2015
DOI: 10.1002/LNO.10212
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.MARPOLBUL.2016.10.050
Abstract: Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene licon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.
Publisher: Wiley
Date: 23-01-2023
DOI: 10.1111/MEC.16844
Abstract: Resource specialization and ecological speciation arising through host‐associated genetic differentiation (HAD) are frequently invoked as an explanation for the high ersity of plant‐feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous ex les of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome‐wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host‐plant use in population s les of leaf‐ and bud‐galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix ) host species. To infer the repeatability of long‐term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short‐ and long‐term host use and ecological ersification in plant‐feeding insects are dominated by stochasticity and/or lineage‐specific effects.
Publisher: Wiley
Date: 10-09-2018
Publisher: Springer Science and Business Media LLC
Date: 08-07-2016
Publisher: Public Library of Science (PLoS)
Date: 03-08-2017
Publisher: Springer Science and Business Media LLC
Date: 17-01-2017
DOI: 10.1038/SREP40579
Abstract: Endozoicomonas bacteria are globally distributed and often abundantly associated with erse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis . We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and ersification, including genes for the production of amino acids. Given this metabolic ersity of Endozoicomonas we propose that different genotypes play disparate roles and have ersified in concert with their hosts.
Publisher: Springer Science and Business Media LLC
Date: 25-07-2017
DOI: 10.1038/S41598-017-05572-X
Abstract: Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in s ling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula , and Rhizotrochus typus . Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
Publisher: Frontiers Media SA
Date: 11-09-2015
Location: Saudi Arabia
Location: No location found
No related grants have been discovered for Craig Michell.