EdwardsLab at Australasian Evolution Society #AUSEVO2021

Look out for some interesting talks by Edwards Lab members at this year’s Australasian Evolution Society 2021 conference, starting today:

Thursday 2nd December: 3-minute talks | 1130-1230

Kelton Cheung - Analysis of mitochondrial DNA reveals significant genetic diversity in invasive Australian cane toads

Kelton Cheung, Mark Richardson, Richard Edwards & Lee Ann Rollins

Mitochondrial DNA haplotype patterns across the native and invaded ranges can reveal the history and evolutionary trajectory of invasions. The invasion of Australia by the cane toad (Rhinella marina) has accelerated as it expanded westward. Despite this success, previous studies reported no mitochondrial genetic diversity in Australia. Here, we assembled a complete mitochondrial reference genome and haplotyped toads (N=119) from the native range and two introduced populations (Hawai’i and Australia), using whole genome and RNA-seq data. The complete R. marina mitochondrial genome consists of 18,152 base pairs with no significant gene arrangement as compared to other bufonid species. Although native range genetic diversity was much higher than that of the introduced ranges, we identified 29 haplotypes in Australia. While we did find evidence of founder effects following introduction, our results suggest there is significant genetic diversity within Australia, which may assist adaptation and invasion success in this species.

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Thursday 2nd December: Selection 1 | 1415-1430

Katarina Stuart - A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris)

Abstract coming soon…

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Thursday 2nd December: Biogeography and phylogenetics | 1530-1545

Richard Edwards - DepthKopy: copy number prediction using single-copy long-read depth profiles

Richard J Edwards, Stephanie H Chen, Katarina C Stuart, Mark M Tanaka & Jason G Bragg

Gene duplication, followed by functional divergence of gene copies, is a fundamental component of genetic adaption and the evolution of novelty. Increasingly, evolutionary studies make use of the ever-expanding number of high-quality genome assemblies to characterise patterns of gene gain and loss. However, even reference genomes of the highest quality can experience assembly errors at tandemly repeated gene loci, resulting in incorrect inference of gene duplication patterns. Here, we present DepthKopy (https://github.com/slimsuite/depthkopy), which estimates the copy number for a gene, region or sequence of interest, using an estimate of single-copy sequencing depth derived from complete BUSCO genes. This is useful for identifying haplotigs, and collapsed repeat regions during genome assembly curation. Critically, for evolutionary studies of gene families, DepthKopy can identify genes for which the number of genes in the assembly does not seem to match the genome.

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Friday 3rd December: Climate change and temperature | 1330-1345

Collin Ahrens - Genomic constraints of drought adaptation

Abstract coming soon…

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome

Watson-Lazowski A, Lin Y, Miglietta F, Edwards RJ, Chapman MA & Taylor G (2016): Plant adaptation or acclimation to rising CO₂? Insight from first multigenerational RNA-Seq transcriptome. Glob Chang Biol. Adv. access. doi: 10.1111/gcb.13322

Abstract

Atmospheric carbon dioxide (CO2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambient CO2 control site, we investigated multigenerational response to future, elevated atmospheric CO2 . Plants were grown in either ambient or elevated CO2 (700 μmol mol-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO2 likely to occur over coming decades.

PMID: 27539677

Fluorescent protein-mediated colour polymorphism in reef corals: Multi-copy genes extend the adaptation/acclimatization potential to variable light environments

Gittins JR, D’Angelo C, Oswald F, Edwards RJ & Wiedenmann J (2014): Fluorescent protein-mediated colour polymorphism in reef corals: Multi-copy genes extend the adaptation/acclimatization potential to variable light environments. Mol Ecol. doi: 10.1111/mec.13041

Abstract

The genomic framework that enables corals to adjust to unfavourable conditions is crucial for coral reef survival in a rapidly changing climate. We have explored the striking intraspecific variability in the expression of coral pigments from the green fluorescent protein (GFP) family to elucidate the genomic basis for the plasticity of stress responses among reef corals. We show that multi-copy genes can greatly increase the dynamic range over which corals can modulate transcript levels in response to the light environment. Using the red fluorescent protein amilFP597 in the coral Acropora millepora as a model, we demonstrate that its expression increases with light intensity, but both the minimal and maximal gene transcript levels vary markedly among colour morphs. The pigment concentration in the tissue of different morphs is strongly correlated with the number of gene copies with a particular promoter type. These findings indicate that colour polymorphism in reef corals can be caused by the environmentally regulated expression of multi-copy genes. High-level expression of amilFP597 is correlated with reduced photodamage of zooxanthellae under acute light stress, supporting a photoprotective function of this pigment. The cluster of light-regulated pigment genes can enable corals to invest either in expensive high-level pigmentation, offering benefits under light stress, or to rely on low tissue pigment concentrations and use the conserved resources for other purposes, which is preferable in less light-exposed environments. The genomic framework described here allows corals to pursue different strategies to succeed in habitats with highly variable light stress levels. In summary, our results suggest that the intraspecific plasticity of reef corals’ stress responses is larger than previously thought.

PMID: 25496144

iOES Poster: Using metagenomics to assess soil microbial diversity under future climate scenarios

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster CE-3.

Abstract:

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.

iOES Poster: Using Next Generation Sequencing to Understand Plant Acclimation and Adaptation to the Changing Environment

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster EcO-15.

Abstract:

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

1st International Environmental Omics Synthesis (iEOS) Conference

The lab has a couple of posters at the 1st International Environmental Omics Synthesis (iEOS) Conference conference in Cardiff this week (Sept 11-13), so come and say hello to Joe and/or Alex if you are in Cardiff.

Poster EcO-15:

UNDERSTANDING PLANT ADAPTATION TO THE CHANGING ENVIRONMENT USING NEXT GENERATION RNA TRANSCRIPTOME SEQUENCING

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor. Centre for Biological Sciences, University of Southampton.

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

Poster CE-3:

USING METAGENOMICS TO ASSESS SOIL MICROBIAL DIVERSITY UNDER FUTURE CLIMATE SCENARIOS

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards. University of Southampton, ExpeER, EuroChar.

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.