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3 Posts tagged with the genomics tag
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Arthropod specimens and genome skimming: Extracting a large panel of diet, symbiotic and phylogenomic information

 

Benjamin Linard, Department of Life Sciences, NHM

 

Wednesday 15 October 1100

 

Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)

 

 

Genome skimming (GS) is the shallow sequencing of the DNA extracted from pooled specimens. This approach was successfully tested on plants to extract simultaneously chloroplast / mitochondria / rRNAs and nuclear markers for phylogenomics and ecological studies. We previously produced insect specimen pools, initially to generate hundreds of complete mitochondria but also skimming the nuclear genomes of the specimens and their gut content. We will describe here the promising potential of GS when applied to arthropods.

 

In particular, we will show: (1) how trophic interaction between aphid preys, ladybirds (Coccinellini specimens) and associated symbiont can be skimmed from gut contents; (2) why a large panel of DNA markers (mitochondria, coding regions, repeats) are systematically leachable from insect pools through GS; (3) why applying GS to field collected material could extend our knowledge of insect genome evolution and uncover several ecological messages.

 

ladybird small.jpg

 

More information on attending seminars at http://www.nhm.ac.uk/research-curation/news-events/seminars/

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Tom Richards from the Museum's Life Science department is an author on a paper in Nature that explores the genome of one of the most abundant species of planktonic plant - the coccolithophore Emiliania huxleyi.  Coccolithophores occur in great numbers in the ocean: the chalk cliffs at Dover are made up of the remains of their calcium carbonate skeletons.

 

The World's oceans are tremendously complex.  Currents move over thousands of kilometres, some descending as they are cooled by weather systems, or mixing at the surface with fresh waters, sediments and nutrients from continental rivers.  Life is immensely diverse, ranging from corals to the deep-sea vent faunas.  The highest biomass of life is in the shallow seas near to land, but the open ocean contains a constantly shifting system of tiny planktonic organisms ranging from bacteria to single-celled plants to grazing zooplankton and their predators. 

 

These planktonic ecosystems change with currents, seasons, nutrient availability and predation. Their growth, population explosions, deaths and decline interact with the planet's cycling of carbon and other nutrients.  These interactions are important in understanding ocean productivity and climate: there are links to carbon dioxide fluctuation, for example, as the plants absorb it during growth and release some at death.  Despite the tiny size of the organisms, their huge numbers over two-thirds of the planet's surface means that their role in planetary systems is very significant.

 

E. huxleyi experiences huge population explosions in the open ocean - planktonic blooms. Some species of phytoplankton bloom under very particular conditions of temperature and nutrient availability, but E. huxleyi thrives in a wide range of conditions, occuring from the warm waters of the equator to polar regions.

 

NaturalHistoryMuseum_PictureLibrary_033355_Comp.jpgEmiliania huxleyi, showing the distinctive calcium carbonate plates that cover its exterior. 

These may have important protective and light-reflecting qualities for the organism.

 

The paper finds that E. huxleyi strains from different areas share a core genome - this gives them a robust abilty to resist the inhibiting and damaging effects of intense sunlight, together with genes that allow effective growth in low phosphorus conditions.  There are genetic differences between the strains that lead to distinct abilities to thrive in different nitrogen, ammonia and metal conditions.  It seems that this, and other characteristics, give E. huxleyi the ability to bloom in very different oceanic environments - it is described as a species complex because of its genetic diversity.

 

This work will enable scientists to understand better the responses and influences of this very widespread species, and to investigate the complex processes and systems of the ocean that determine productivity and influence climate change.

 

Read, B.A. et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature doi:10.1038/nature12221

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Tapeworm genomics

Posted by John Jackson Dec 22, 2011

Genome data represent the largest and most diverse set of heritable characters for comparative evolutionary studies. In collaboration with the The Wellcome Trust Sanger Institute, we have recently characterised and assembled the complete genome of Hymenolepis microstoma, a classical tapeworm model with over 50 years of literature supporting it.

 

Together with colleagues from the University of Würzburg, Germany, Peter Olson and Magdalena Zarowiecki have recently published the first insights into the gene content and general characteristics of tapeworm genomes based on data from Hymenolepis and the medically important genera Echinococcus and Taenia. Findings show that tapeworms have small genomes at ~150 Mb, compared to ~350 Mb in flukes and over 700 Mb in free-living planarians.

 

Their genomes are compact, containing few repetitive or mobile elements, and appear to contain a majority of common gene families, albeit they may be missing ~10% of 'core' or universal metazoan genes found in free-living animals and typically show a reduction in the number of genes per family. A number of necessary biosynthesis components are missing, such as genes required to synthesise cholesterol, and hence these essential molecules must be taken directly from the host. Data are now publicly available via the Web and promise to accelerate the pace of research in the field by eliminating the need for time consuming and costly genetic manipulations at the bench.


PD Olson, M Zarowiecki, F Kiss and K Brehm (2011). Invited review: Cestode genomics--progress and prospects for understanding basic and applied aspects of flatworm biology. Parasite Immunology [doi: 10.1111/j.1365-3024.2011.01319.x]