Tag Archives: genomics

Giant organisms, giant genomes…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

A deluge of plant genomes for you this month (what is the collective name for loads of genomes – an embarrassment?). First a brace of gymnosperm genomes: the ginormous 20 gigabases of Norway Spruce (Picea abies) announced by Björn Nystedt et al., and the similarly sized genome of white spruce (P. glauca) published by Inanc Birol et al. At a size 20 times larger than arabidopsis’ sequencing, these huge genomes presents ‘unique challenges’, according to Birol et al. However, now those challenges have been overcome it is hoped that these genomics resources will be useful for improved forest management of, and conservation efforts for, these trees, which, as major representatives of conifers, are of ‘huge ecological and economic importance’ (Nystedt et al.), globally. Hmm, Norwegian wood, isn’t it good? Hands up all those who aren’t singing the lyrics to The Beatles’ song of the same name. From the very big to the more compact now with Enrique Ibarra-Laclette et al. and the much more modest 82-megabase genome of the carnivorous bladderwort Utricularia gibba. One of the main interests in this plant’s genome is its tiny size, but which still ‘accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA’. Non-genic – or non-coding DNA, which doesn’t code for protein sequences – is often termed ‘junk DNA’. Humans have about 98 % of so-called junk DNA, bladderwort has 3 %, which makes plants much more DNA-efficient than humans: result! Finally, Ray Ming and co-workers have sequenced the genome of the sacred lotus, Nelumbo nucifera. I say ‘finally’ merely to indicate the pause for this quartet of genomes in this news item. But it may be that such reports have had their day if David Smith is correct in his thoughtful opinion article entitled ‘Death of the genome paper’. So, DNA RIP? I doubt it – those sequencers have to pay for themselves somehow! But it is important that behind the morass – however impressive it may appear! – of bases and sequence data we ‘don’t lose the organism in the excitement over its genes’.

[Interestingly, Robert Lanfear et al. have discovered that taller plants have lower rates of molecular evolution, which may explain why gymnosperms have been around for hundreds of millions of years (almost unchanged), whereas arabidopsis has undergone unprecedented amounts of genetic change and mutation in only the last 40 years(!). Well, that, the massive discrepancy in size of their respective genomes, and the intensive artificial-selection pressures foisted on thale cress by over-zealous molecular botanists. And, incidentally ‘tall’ is the Swedish word for … pine! – Ed.]

 

Techniques used to modify a plant genome also affect its epigenome

Rice Rice is one of the most important food crops and is estimated to provide more than a fifth of the calories consumed by the world’s population. For several decades, rice has been modified by conventional breeding methods to produce plants with increased yields and greater resistance to pests and harsh weather conditions. Efforts are also being made to create rice plants with superior yield traits and resistance to biotic and abiotic stresses using genetic engineering techniques.

Genetically modified plants are usually produced using tissue culture. New genes are introduced into plant cells that are growing in a dish, and each cell then replicates to form a mass of genetically identical cells. The application of plant hormones triggers the tissue to produce roots and shoots, giving rise to plantlet clones.

In addition to the genes that comprise its genome, the genetic make-up of an organism also includes its epigenome—a collection of chemical modifications that influence whether or not a given gene is expressed as a protein. The addition of methyl groups to specific sequences within the DNA, for example, acts as an epigenetic signal to reduce the transcription, and thus expression, of the genes concerned.

The techniques used to modify a plant’s genome—in particular, the process of tissue culture—also affect its epigenome. They prepared high-resolution maps of DNA methylation in several regenerated rice lines, and found that regenerated plants produced in culture showed less methylation than control plants. The changes were relatively over-represented around the promoter sequences of genes—regions of DNA that act as binding sites for the enzymes that transcribe DNA into RNA—and were accompanied by changes in gene expression. Crucially, the plants’ descendants frequently also inherited the changes in methylation status. These results are likely part of the explanation for a phenomenon called somaclonal variation, first observed before the era of modern biotechnology, in which plants regenerated from tissue culture sometimes show heritable alterations in the phenotype of the plant.

 

Plants regenerated from tissue culture contain stable epigenome changes in rice. (2013) Elife 2: e00354. doi: 10.7554/eLife.00354.
Abstract

Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.

 

Free paper — Genome size in Anthurium evaluated in the context of karyotypes and phenotypes

Little is known about the genome of Anthurium other than chromosome observations, which frequently indicate supernumerary (“B”) chromosomes. New genome size estimates for 34 species and nine cultivars presented here  provide insights into genome organization and evolution in this very large genus.

Free paper — Cytogenetic characterization and genome size of the medicinal plant Catharanthus roseus (L.) G. Don

The genome size and organization of the important medicinal plant Catharanthus roseus is shown to correspond to 1C = 0.76 pg (~738 Mbps) and 2n=16 chromosomes. The data  in this recently published paper provide a sound basis for future studies including cytogenetic mapping, genomics and breeding.

Free paper — Identification of Stylosanthes guianensis varieties using molecular genetic analysis

Molecular genetic diversity and population structure analysis were used to clarify the controversial botanical classification of Stylosanthes guianensis.  In this paper, the accessions were clustered in nine groups, each of which was mainly composed of only one of the four botanical varieties.

Faces of Plant Cell Biology: A series on PlantCellBiology.com from Anne Osterrieder

PlantCellBiology.com banner

PlantCellBiology.com banner

Anne Osterrieder has a new series on her blog called Faces of plant cell biologists, where we are asked a series of questions. So far, it has featured Charlotte Carroll (also an AoBBlog.com guest author here), Chris Hawes and Kentaro Tamura, who all answer Anne’s questions is surprisingly contrasting but  complementary ways. Today, I have been selected and my interview is on her blog via YouTube – as usual best viewed in 1080p if you have a fast internet. All the contributors so far have featured videos in their presentations, and perhaps because we study dynamic processes, this is very appropriate!

I think Anne’s concept of building up a library of these interviews is a great idea, and I know that she will welcome and encourage contributions from all plant cell biologists (in the broadest sense).

Is the earliest wine getting earlier and earlier?

There’s been a rash of stories about how new grape varieties will be needed to fight disease if wineries are to keep flowing. As far as I can tell, because I haven’t seen anyone link to the paper, it’s based on Genetic structure and domestication history of the grape and Open Access paper in PNAS (back-up link because the doi isn’t working). Sean Myles argues that there’s plenty of room to develop new varieties of grape by careful cross-breeding.

A surprising result (to me) is that the date for domestication is by 5,000 years ago. Meanwhile in related archaeological research, the earliest evidence of wine-making equipment has been found in Areni, Armenia dating from around 4100 BC. The two don’t necessarily contradict each other. For a start the Armenian winery could have been using grapes that were abandoned for superior varieties, but I don’t know how accurate the dating is on either side as I haven’t had chance to read the papers properly. If it’s the latest common ancestor then that’s close to a match.

Myles places the earliest domestication as a region of the South Caucasus between the Caspian and Black Seas. Here’s a map with the Areni winery marked.

View Areni and Grapes in a larger map

h/t BBC News.