Tag Archives: genomics

Plant molecular cytogenetics in the genomic and postgenomic era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

The way that we can address questions in genome evolution and expression has changed enormously in the last five years. We can get huge amounts of DNA sequence for any species for a budget within that of most labs. As importantly perhaps, the web and PC-based analytical tools now enable researcher to do something with all those giga-bases of sequence within your own lab. Linking DNA sequence to the physical chromosomes has been a continuing challenge though, despite the widespread use of in situ hybridization. The huge number of whole genome and whole-chromosome evolution processes are not amenable to whole genome sequencing, but chromosome analysis can use the information to understand real biological problems. So this week, I’m thinking about Plant Molecular Cytogenetics in the Genomic and Postgenomic Era at a meeting in Poland. Although my tweets from the conference gained quite some following (thank you for letting me know, Twitter analytics) under the @ChrConf user and #PMC tag, I didn’t have a partner on social media so impressions are a little one-sided. However, I hope the collation below will give some flavour of the range of topics addressed during the meeting – but as usual the posters and social events provided the source of new inspiration. Skype will never replace personal meetings with old friends nor give the opportunity for making new links!

This conference in Katowice, Poland, is bringing together about 150 people, mostly from Europe with a substantial addition from that hive of cytogenetic activity, Brazil. It is organized by Robert Hasterok, a leader in use of the grass Brachypodium as a model species (http://aob.oxfordjournals.org/content/104/5/873.short) and understanding its evolution (http://aob.oxfordjournals.org/content/109/2/385.short). The meeting honours Jola Maluszynska, one of the earliest people to use molecular cytogenetics and who I have been privileged to work with – not least with that other model species, Arabidopsis (some published in Annals of Botany long ago http://aob.oxfordjournals.org/content/71/6/479.short).

The programme includes good time to look at the impressive array of posters showing the vibrancy of the post-genomic research. These are described in the abstract book, but here I will overview a selection of highlights from the talks. Although speaking near the end of the programme, it is only fair to start with Robert Hasterok – it is always a challenge both to talk and organize a meeting in your home town. In a wide-ranging talk about Brachypodium, he presented a diverse range of cytomolecular work going on in his lab, drawing out broader points from the posters we had studied on the first day. He defined a model species as an organism that possesses certain features that make it more amenable to scientific investigation compared with other less tractable members of the group it represents. It is also helpful when it possesses well-developed research resources and infrastructure (including how to grow the plant) that enable efficient work. The Brachypodium genome project was established in 2006 and the Brachypodium distacyhon genomic sequence completed in 2010. At that time, even the definition of key species in the genus was not clear, and it was only in 2012 that use of in situ hybridization clearly showed that there were three species

http://aob.oxfordjournals.org/content/109/2/385.short , now named Brachypodium distachyon (2n=10), B. stacei (2n=20), and the hybrid B. hybridum (2n=30). Robert then addressed the question of “What is known about grass genome evolution at the level of the chromosome?” “How is the development of compound chromosomes from a grass ancestral karyotype?” Cytomolecular work is showing chromosome remodelling and compound chromosomes in Brachy and its nearer and more distant ancestors in work published earlier this year ( http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093503 _). The next section of his talk looked at nuclear organization. At interphase, there are clear chromosome territories, but for individual pairs of homologous chromosomes, all four possibilities of organization are seen with association of top arms of chromosomes, association of bottom arms, association of two homologous, or no association at all – the four being in very roughly equal proportions (perhaps the first a bit more frequent). A second group of experiments was looking at arrangements of centromeric and telomeric domains at interphase in various Brachypodium species: remarkably, there was a Rabl configuration with centromeres at one pole and telomeres at the opposite end of diploid interphase nuclei, while no such pattern was seen in the tetraploid 4x. This led to discussion of epigenetic effects, where nucleolar dominance is seen B. hybridum: the B. distachyon-origin rDNA genes are dominant over those of B. stacei. As with all good talks we were given insight into the brick walls of research: Brachypodium is nearly an anti-model for studying meiosis, while the obvious question about behaviour of resynthesized B. hybridum compared to the million-year old species is stymied by the lack of viability of the new hybrid.

So back then to the start of the programme with Dieter Schweizer giving insight into structural maintenance of chromosomes and epigenetics effects. The DMS3 structural protein interacts with DME Demeter, a DNA glycosylase domain protein and transcriptional activator, which has a function in directly excising 5 methyl cytosine from DNA and initiating replacement by unmethylated cytosine. In a lecture of two parts, Dieter’s second theme was cytogenetics and immunocytochemistry of triploid endosperm, where, there is parental genome separation and somatic pairing.

I’ll include a discussion of aspects of my talk (particularly one slide on crop production and the contribution of genetics) in a later post  – meanwhile my talk is posted here although with little supporting text. Hans De Jong followed with discussing plant cytogenetics in the era of modern genomics where I wasn’t sure if he was happy or sad that the Dutch contribution to the tomato genome sequence project, chromosome 6, proved to be one of the most rearranged or variable and hence tricky to analyse. Amazing 6-colour in situ hybridization sorted out many complex problems in ordering contigs of continuous blocks of sequence, and then linked orders between tomato and potato. Hans concluded that assembly algorithms placed about 33% of all assembled contigs were in the wrong position or wrong order in tomato. I was also interested to hear his final discussion about wide comparisons at the sequence level now being made between different species and even genera in Solanaceae, although I look forward to seeing how these cope with the proportion of highly variable repeats between the species.

After our first break, Ingo Schubert and collaborator Giang TH Vu talked about break repair – double-strand breaks (DSBs) at meiosis of in somatic cells, linking the molecular with the microscopic level in the monocot crop barley. DSB are ubiquitous, frequent and hazardous to the genome, and if unrepaired are lethal for dividing cells. Ingo could distinguish by molecular constructs and microscopy between the different DSB repair pathways involving homologous recombination or non-homologous end-joining. The latter NHEJ was seen to be the dominant DSBs repair pathway in barley with the consequent small deletions and/or insertions with or without microhomology. In asking my question about the role of enzymes and differences between species, I felt like the notorious “third referee” of important manuscripts wanting even more work for what is the first demonstration of the relationships of the different DSB repair mechanisms!

Andreas Houben, one of a large delegation from IPK in Gatersleben, then discussed centromeres with his interests in haploid technology and doubled haploids. CENH3 is an essential centromere component in almost all eukaryotes as modified histone H3. Andreas showed another hybrid species, Arabidopsis suecica (were natural and this time artificial hybrids can be made), making specific antibodies specific to the CENH3 in the two ancestors. In stable hybrids, both CENH3 sequences immune-hybridized to both centromeres – not like the species-specific centromeric sequences (http://www.le.ac.uk/bl/phh4/openpubs/openpubs/Kamm_Arenosa.pdf ) – but with high-resolution microscopy, his lab could see CENH3 variants are differentially loaded into distinct centromeric subdomains. Used some barley tilling mutation sets of lines, a mutated betaCENH3 was found which was not loaded onto the centromeres which had a normal phenotype except it was rather sterile: 56% univalents and 24% lagging at meiosis. Moving back to Arabidopsis, a mutant CENH3 that generates a haploid induce line (with a single amino acid change) was demonstrated, with the important consequence that hybrids using this could loose the maternal genome, enabling plant breeders to replace the cytoplasm in one generation.

Paul Fransz moved forward our understanding of a major paracentric inversion from 10000 yrs ago seen in Arabidopsis. His sequencing and cytogenetic work allowed detection of the inversion borders and hence the molecular mechanism of the inversion, work with (epi)genetic and phylogenetic consequences. Remarkable genome wide association analyses (GWAS) showed increased fitness under abiotic drought stress – the trait of fruit length and fecundity – was associated with the genes in the low recombination zone around the inversion.

Hanna Weiss-Schneeweiss showed the way modern cytogenetic approaches reveal “More than meets the eye: contrasting evolutionary trajectories in polyploids of the Prospero complex” and she was able to sort out the complex relationships in these species.

Our second day started with display of the wonderful timelapse films of the Polish botanists Bajer & Mole-Bajer, made in 1956, showing mitosis in Haemanthus endosperm. I knew these from my undergraduate days, and in the 1990s was given a 16mm film version by Professor Rachel Leech from York. I had them converted to VHS video tape, but happily we can now all access them freely on the web – whether downloadable from http://www.cellimagelibrary.org/images/11952 or several posts on YouTube such as https://www.youtube.com/watch?v=s1ylUTbXyWU .

An important practical question for breeding and selection, building from several talks on the first day, relate to Glyn Jenkins’ key question: Can we change sites of recombination to release novel recombination, new genetic variation and useful phenotypes? Then we are well on the way to  ‘optimising’ the germplasm of barley by manipulating recombination. The range of meiotic antibodies –  ASY1, ZYP1 and HvMLH3  – allowed study of recombination processes and give a recombination nodule map. Reconstructions of individual bivalents with meiosis antibodies shows distal bias of chiasmata (http://jxb.oxfordjournals.org/content/64/8/2139.short). Remarkably, a substantial but not extreme (15 C to 25 C) increase in temperature of growth for barley altered the genetic length, becoming much longer (more recombination) at high temperatures in male meiosis, although not on the female side. The map expansion was in pericentromeric regions, and significantly shifted HvMLH3 foci locations but not numbers.

AoB Editor Martin Lysak with Terezie Mandakova discussed very extensive work on Brassicaceae chromosome evolution under the title ‘More than the cabbage: chromosome and genome evolution in crucifers’ (eg http://www.plantcell.org/content/25/5/1541.short). The simplicity of the models of evolution of crucifer genomes that Martin showed belie the huge amount of underpinning data on comparative cytogenetics, sequenced genomes, genetic maps and phylogenetics, as well as the number of ‘envelopes’ that must have been used to sketch out models (although I’m not sure what replaces envelopes in the day of e-mails). Basically, the ancestral crucifer karyotype (ACK) in ‘diploids’ (themselves often of polyploid or hybrid origin) and polyploids can be divided into 24 ancestral genomic blocks. One of the most simple situations, in Capsella rubella (Slotte et al. 2013) the ACK  remained largely conserved, while there can be diversification without large scale rearrangements in Cardamine. Arabis alpina is more complex, with seven of 8 ancestral chromosome reshuffled, probably involving  five reciprocal translocations, four pericentric inversions, three centromere repositionings , one centromere loss and one new centromere. Wow! Martin treated us to consideration of all the major lineages in the group, from the extreme of chromosome number reduction to n=5 in Arabidopsis thaliana, through to the most remarkable 72 genome duplication events in oilseed rape/Brassica napus since origin of angiosperms! Clearly, a whole genome triplication spurred genome and taxonomic diversity in Brassica and the tribe Brassiceae and I will need to follow his next publications, with many colleagues but particularly talk co-author Terezie Mandakova, to understand the consequences of descending dysploidy from the ACK ancestral crucifer karyotype and PCK (Proto-Calepineae karyotype), with range of mechanisms involving translocations, loss of minichromosomes, end to end fusions, inversions, and centromere shifts.

The last talks before posting these notes came from Kesara Anamthawat-Jonsson – my first PhD student – addressing Where did birch in Iceland come from? Betula is another genus with lots of hybrids, even though the history of birch in Iceland only extends for the 10000 years of the holocene since Iceland came out from under the ice. Kesara builds on her Annals of Botany paper http://aob.oxfordjournals.org/content/99/6/1183.short showing that 10% of Icelandic birches are 2n=3x=42 hybrids, but only half of these can be seen from their morphology. Kesara has now looked at chloroplast DNA haplotypes across Iceland as well as evidence for extensive introgression between the species via 3x hybrids involving whole genomes of both Betula nana and B. pubescens.

There are still a few more talks, and then I am off for some lab visits – I’m sorry I can’t cover everything but I hope this flavour of the exciting meeting will be useful to a few. It is clear that we are really in a post-genomic era, and cytogenetic approaches are making major advances in this new landscape.

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.