Chloroplast genomes from apomictic Taraxacum – identity and variation between microspecies

Taraxacum or dandelion chloroplast sequence diversity. Salih et al. PLoS One 2017.

Taraxacum or dandelion chloroplast sequence diversity. Salih et al. PLoS One 2017.

333. Salih RHM, Majeský L, Schwarzacher T, Gornall R, Heslop-Harrison P. 2017.  Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. PLoS ONE 12(2): e0168008.
doi:10.1371/journal.pone.0168008.

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnFGGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

http://dx.doi.org/10.1371/journal.pone.0168008

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The agriculture-nutrition-health nexus at the cost of water availability – conference paper

Terraces conserving water, maize and deserts: the agriculture-nutrition-health nexus. Noorka et al. 2016. ICWRAE 7 proceedings.

Terraces conserving water, maize and deserts: the agriculture-nutrition-health nexus. Noorka et al. 2016. ICWRAE 7 proceedings.

332. Noorka IR, Taufiqullah, Heslop-Harrison JS, Schwarzacher T. 2016. The agriculture-nutrition-health nexus at the cost of water availability in maize diverse genotypes to ensure food security. Proceedings of the 7th International Conference on Water Resources and the Arid Environments (ICWRAE 7): 569-578.

Link to manuscript: noorka_agriculture_nutrition_health_nexus_water_saudi.

A presentation by Dr Ijaz Rasool Nooka, University of Sargodha, Pakistan, at the 7th International Conference on Water Resources and the Arid Environments (ICWRAE 7) http://icwrae-psipw.org/ 4-6 December 2016, Riyadh, Saudi Arabia

A study is made of the use and conservation of important crop plant biodiversity under limited water supply to combat water stress conditions prevailing now throughout the world, creating food shortages and reducing agricultural sustainability. The main objective here is to find suitable plant material which can be grown in arid environments by using crosses and checking the combining abilities, to bear water stress in their life cycles. The most versatile plant, maize, is used by line × tester mating fashion to estimate general and specific combing ability in self and cross combinations of diverse maize genotypes under different water stress environments in Pakistan. Twelve parental genotypes, comprising eight lines and four testers, were crossed to produce 32 F1 hybrids. In next crop season the parents along with their hybrids were evaluated with three water treatments in two seasons. Results showed the nature and magnitude of general and specific combining ability for grain yield and yield related traits like plant height, leaf area, number of kernels per row, ear length, ear diameter, grain yield per plant and harvest index. The significant estimates of GCA and SCA suggested the importance of both additive and non-additive gene actions for the expression of the traits which can help for the selection of parents to be used for the development of useful synthetics and hybrids resilient to contrasting water regimes.

 

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Banana, Ensete and Boesenbergia Genomics talk by Schwarzacher, Heslop-Harrison, Harikrishna

Comparative genomic analysis in Zingiberales: what can we learn from banana to enable Ensete and Boesenbergia to reach their potential?
Talk for Plant and Animal Genomics #PAGXXV

Molecular cytogenetics can address challenges in crops with relatively little background knowledge. This talk shows some work around Ensete ventricosum, known as enset, ensete, False banana, Abyssynian or Ethiopian banana, and also with fingerroot ginger, Boesenbergia rotunda.

Slides are on Slideshare at http://www.slideshare.net/PatHeslopHarrison/banana-ensete-and-boesenbergia-genomics-schwarzacher-heslopharrison-harikrishna

A ten minute talk on Ensete prepared for an audience knowledgeable about Ensete but with less background in genomics is also embedded below from YouTube.

Abstract and text from slides pasted below YouTube video. (https://youtu.be/RZJCDQVedVU – the embed does not work in the conference centre).

Comparative genomic analysis in Zingiberales: what can we learn from banana to enable Ensete and Boesenbergia to reach their potential?
Talk for Plant and Animal Genomics XXV 25 – San Diego January 2017
Trude Schwarzacher, Jennifer A. Harikrishna and Pat Heslop-Harrison, University of Leicester and University of Malaya
phh(a)molcyt.com
Within the Zingiberales there are many orphan crops that are grown in Africa and Asia where recently started genomic efforts will have an impact for the future understanding and breeding of these crops. Advanced genomics and genome knowledge of the taxonomically closely related genus Musa will help identify genes and their function. We will discuss relevant recent work with Musa and results from DNA sequencing, examinations of diversity and studies of genome structure, gene expression and epigenetic control in Boesenbergia and ensete. Ensete is an important starch staple food in Ethiopia. It is harvested just as the monocarpic plant starts to flower, a few years after planting, and the stored starch extracted from the pseudo-stem and corm. A genome sequence has been published, but there is little genomics. Characterization of the diversity in the species and understanding of the differences to Musa will enable selection and breeding for crop improvement to meet the requirements of increasing populations, climate change and environmental sustainability. Boesenbergia rotunda is widely used in traditional medicine in Asia and has been shown to produce secondary metabolites with antiviral activity. For high throughput propagation and metabolite production in vitro culture is employed; embryogenic calli of B. rotunda in vitro are able to regenerate into plants but lose this ability after prolonged periods in cell suspension media. Epigenetic factors, including histone modifications and DNA methylation are likely to play crucial roles in the regulation of genes involved in totipotency and plant regeneration. These findings are also relevant to other crops within the Zingiberales. Further details will be given at http://www.molcyt.com

Banana, Ensete and Boesenbergia Genomics – Schwarzacher, Heslop-Harrison, Harikrishna

  1. 1. Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential Banana Genomics – Tue 17 Jan 2017 10.30 PACIFIC SALON 6-7 Mathieu Rouard & Angelique D’Hont Trude Schwarzacher and Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  2. 2. Ensete ventricosum 2nd genus in Musaceae enset, ensete, false banana
  3. 3. • Germplasm: Bizuayehu Tesfaye, Hawassa, Ethiopia
  4. 4. 6
  5. 5. The Global Musa Genomics Consortium • To assure the sustainability of banana as a staple food crop by developing an integrated genetic and genomic understanding, allowing targeted breeding, transformation and more efficient use of Musa biodiversity
  6. 6. • Vision: Musa genetic diversity is secured, valued and used to support livelihoods through sustainable production and improved food and nutrition security. • Actions aim to i) assess Musa genetic diversity, ii) conserve the entire Musa gene pool, iii) maximize use of genetic diversity, iv) apply genomics tools to banana to better support breeding and v) document and make information accessible.
  7. 7. Genomics changes study of taxonomy, phylogeny, diversity Revolutionizes crop genetics and breeding Exploits Musa as a reference
  8. 8. Diploid chromosomes in Musaceae (blue DAPI stain) with centromeric element labelled
  9. 9. Ty1-Copia element Rather few in Ensete RepeatExplorer: Graph-based clustering of related sequences, program/approach by Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3. Ensete has a published genome sequence: Harrison J, Moore KA, Paszkiewicz K, Jones T, Grant MR, Ambacheew D, Muzemil S, Studholme DJ. A draft genome sequence for Ensete ventricosum, the drought-tolerant “tree against hunger”. Agronomy. 2014 Jan 17;4(1):13-33. Some abundant tandem repeats in Ensete genome
  10. 10. Analysis with RepeatExplorer A978 Petunia Ensete repetitive DNA distribution Not huge abundance of repetitive sequences in Ensete – 25% of genome Taraxacum
  11. 11. 1000 bp 800 bp Azhar M, Heslop-Harrison JS. Genomes, diversity and resistance gene analogues in Musa species. Cytogenetic and genome research. 2008 May 7;121(1):59-66.
  12. 12. • Abiotic stresses – water, wind, nitrogen, plant nutrition • Biotic stresses – disease – competition, nematodes, fungi, bacteria, viruses, rodents • Environmental challenges – Soil, water, climate change, sustainability • Social challenges – Urbanization, population growth, mobility of people, under-/un-employment – Farming is hard, long work – increased standard of living
  13. 13. • Lee Wan Sin, Gudimella Ranganath, Norzulaani Khalid & Jennifer Ann Harikrishna • Centre for Research In Biotechnology for Agriculture (CEBAR) University of Malaya, Malaysia • Abiotic stress causes >50% of crop losses & is expected to worsen: • Urbanisation & population growth lead to reduction in arable land and fresh water for irrigation • Climate change models predict more extremes of drought and floods (including for Malaysia and other SE Asian countries) • Drought  irrigation  increased salinity  flooding in coastal regions
  14. 14. Transcriptome alignment to banana *genome Use assembled transcriptome to indicate transcript identity and abundance Distribution of transcriptome (31,390 non-redundant unigenes) >99.5% unigenes mapped Coverage >40X 2,000 to 3,200 (6 to 10% of the unigenes) map to each chromorosme Bar lengths reflect numbers of non redundant reads ~5% up-reg ~4% down in NaCl
  15. 15. Transcriptome: Differential expression Gene Ontology (GO) assignments of transcripts (unigenes) non-differentially-expressed / differentially-expressed Binding Transporter activity Cellular & metabolic processes Catalytic activity Response to stimulus 2,993 (9.5%) of the de novo assembled unigenes observed to be differently expressed in salt-stressed banana root (~5% up-reg ~4% down-regulated)
  16. 16. Fingerroot ginger – Bosenbergia rotunda – Zingiberales
  17. 17. • Project on Boesenbergia lead by Norzulaani Khalid & Jennifer Ann Harikrishna Genome sequence Secondary products Tissue culture changes Epigenetics – DNA and chromatin modification
  18. 18. Boesenbergia rotunda PRO-METAPHASE histone H3 dimethylated lysine K4 (49-1004) euchromatin mark at the end of the chromosomes centromeric heterochromatin not stained DAPI H3K4me2 Harikrishna, Khalid, Bailey, Schwarzacher B1-1-O2
  19. 19. Boesenbergia rotunda INTERPHASE histone H3 mono- methylated lysine K9 (49- 1006) hetero- chromatin mark DAPI H3K9me1 Harikrishna, Khalid, Bailey, Schwarzacher overlaps most of the strongly DAPI stained chromocentres (the large DAPI strong area in the middle of the nucleus is due to being the thickest part of the squashed nucleus) B1-3-A
  20. 20. Boesenbergia rotunda METAPHASE histone H3 di- methylated lysine K9 (49- 1007) hetero- chromatin mark DAPI H3K9me2 Harikrishna, Khalid, Bailey, Schwarzacher Mainly stains centre of chromosomses where we assume the location of centromeric heterochromatin to be B1-5-O12
  21. 21. Outputs –CROPS – Fixed energy Inputs –Light –Heat –Water –Gasses –NutrientsLand
  22. 22. Outputs –CROPS – Fixed energy 25 Inputs –Light –Heat –Water –Gasses –Nutrients – Light – Heat – Water – Gasses – Nutrients
  23. 23. Agricultural production • Agronomy • Genetics • Genetics for production systems – technological solutions for sustainable agriculture
  24. 24. Dr Adugna Wakjira, DDG, Ethiopian Institute of Agricultural Research (and co- author/colleague) “Our government recognizes biotechnology as one of the transformative tools to accelerate agricultural development … exemplified by Parliament’s amendment to a more progressive and permissive legislation of biotechnology” But needed quickly: training of new scientists to deliver local solutions. Certainty needed
  25. 25. • United Nation’s Sustainable Development Goal (SDG) targets for 2030, namely Target 15 (Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss), with implications for Target 2 (End hunger, achieve food security and improved nutrition and promote sustainable agriculture)
  26. 26. Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential Trude Schwarzacher and Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  27. 27. The genome and genomics of Enset Workshop on Enset (Ensete ventricosum) for Sustainable Development: Current research trends, gaps and future direction for a coordinated multidisciplinary approach in Ethiopia Organizer Sebsebe Demissew – October 2016 Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  28. 28. Molecular Cytogenetics Group http://www.molcyt.com Pat Heslop-Harrison Trude Schwarzacher and colleagues Impacts outside academia Legislation: European Parliament & Commission Breeding new, sustainable crop varieties Sequencing of whole genomes Discussing risk assessment and scientific advice with EU Health Commissioner Dr Vytenis Adriukaitis We study genomes and evolution mechanisms to find, measure and exploit genetic variation in crops, farm animals, and their wild relatives Developing superdomestication strategies to exploit biodiversity for sustainable agriculture Work on hybrids and alien introgression with novel quality / disease resistance characters Wheat with virus resistance identified in the group in breeding trials Diversity, wild genes and recombination in species and landraces DNA sequences we find confer stress resistance in crops New methods for biotechnology Food fraud and safety detection Reviewing research programmes Editing Journals

 

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Domestication, polyploidy and genomics of crops and weeds PAGXXV

Plant and Animal Genome Conference in San Diego #PAGXXV each January is the chance to join 3500 people working in genomics. I presented a talk on the molecular cytogenetics group’s work, starting with consideration of early stages of crop domestication, and then thinking about how we can make agriculture more sustainable. I also considered weeds, noting that they have been co-domesticated with crops by people, being under strong selection pressure and exploiting ecological niches coming from the activity of people.

Here are the slides for my talk which are on slideshare at http://www.slideshare.net/PatHeslopHarrison/domestication-polyploidy-and-genomics-of-crops-pagxxv-heslopharrison

Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison from Pat (JS) Heslop-Harrison

Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison from Pat (JS) Heslop-Harrison

This is the text on the slides:

  1. 1. Domestication, polyploidy and genomics of crops (and weeds) Pat Heslop-Harrison & Trude Schwarzacher Leicester, UK phh@molcyt.com http://www.molcyt.com http://www.molcyt.org Twitter Pathh1 . Crop Evolution Genomics & Future Agricultural Productivity PAGXXV 14 January 2017 20 min talk
  2. 2. Outputs –Crops (Chemical energy) – Food – Feed – Fuel – Fibre – Flowers – Pharmaceuticals – Fun2
  3. 3. Inputs –Light –Heat –Water –Gasses –Nutrients –Light –Heat –Water –Gasses –Nutrients (Ecosystem services) Outputs –CROPS – Chemical energy
  4. 4. Domestication, Polyploidy and Genomics of Crops • CROPS: where one species controls the growth and reproduction of another
  5. 5. Domestication, Polyploidy and Genomics of Crops • Most species domesticated 10,000 years ago (cereals, legumes/pulses, brassicas, fruits, cows/sheep/pigs, silkworm/bees) • Few species more recently (rabbits, fish, trees, biofuel crops) • A few dropped out of production • First steps: productive, reproduce easily, disease- free, edible/tasty, harvestable … • With critical technology of people: not obvious Heslop-Harrison & Schwarzacher Domestication genomics in Arie Altman http://www.tinyurl.com/domest and review of rabbits http://www.tinyurl.com/rabdom
  6. 6. Pinus sylvestris Scots pine
  7. 7. Argemone mexicana
  8. 8. Japanese knotweed – invasive in Europe Fallopia (and Fallopia x Muehlenbeckia hybrids)
  9. 9. Larrea tridenta Creosote bush
  10. 10. Domestication, polyploidy and genomics of crops and weeds • CROPS: where one species controls the growth and reproduction of another • WEEDS • Many animals collect food to see them through the winter, build nests in anticipation of reproduction • A few plants kill off all others nearby • Ants (Formicidae) farm plants, animals and fungi • Humans only for 20% of their history – and still exploiting environment unsustainably!
  11. 11. Organelle sequences from chloroplasts or mitochondria Sequences from viruses Transgenes introduced with molecular biology methods Genes, regulatory and non- coding low-copy sequences Dispersed repeats Repetitive DNA sequences Nuclear Genome Tandem repeats Satellite sequences DNA transposonsRetrotransposons Centromeric repeats Structural components of chromosomes Telomeric repeats Simple sequence repeats or microsatellites Repeated genes Subtelomeric repeats 45S and 5S rRNA genes Blocks of tandem repeats at discrete chromosomal loci DNA sequence components of the nuclear genome After Biscotti et al. Chromosome Research 2015 Other genes Transposable elements Autonomous/ non-autonomous Dispersed repeats that we don’t know about – except each is significant proportion of genome
  12. 12. Genomic Components: properties • Tandem Repeats • Simple Sequence Repeats • Dispersed Repeats • Functional Repeats • Retroelements • Genes Typical Fraction 10% 5% 10% 15% 50% 10%
  13. 13. Domestication, polyploidy and genomics of crops and weeds • Genome size • Critical parameter for genome studies – first sequenced genomes chosen to be small … Large genomes only tackled 25 years on • But is it critical for species … • No: you can’t ‘look’ at a species and make any suggestion about it’s genome size …
  14. 14. Nothing special about crop genomes? Crop Genome size 2n Ploidy Food Rice 400 Mb 24 2 Triploid endosperm Wheat 17,000 Mbp 42 6 Triploid endosperm Maize 950 Mbp 10 4 (palaeo-tetraploid) Triploid endosperm Rapeseed B. napus 1125 Mbp 38 4 Cotyledon oil/protein Sugar beet 758 Mbp 18 2 Modified root Cassava 770 Mbp 36 2 Tuber Soybean 1,100 Mbp 40 4 Seed cotyledon Oil palm 3,400 Mbp 32 2 Fruit mesocarp Banana 500 Mbp 33 3 Fruit mesocarp Heslop-Harrison & Schwarzacher 2012. Tinyurl.com/domest
  15. 15. Domestication, polyploidy and genomics of crops and weeds • Polyploidy is also critical part of genomes … • No: you can’t ‘look’ at a species and make any suggestion about it’s ploidy …
  16. 16. D’Hont et al. Nature 2012 doi:10.1038/nature11241
  17. 17. D’Hont et al. Nature 2012 doi:10.1038/na ture11241 Whole-genome duplication events.
  18. 18. Domestication, polyploidy and genomics of crops and weeds • Ancient polyploidy (detected by sequencing) • Modern polyploidy (detected by cytogenetics) • Advantages: more control, genes free to mutate, ?larger cells/organs • Disadvantages: meiosis challenging, buffering of changes, more DNA to replicate
  19. 19. Repetitive DNA in dandelion 3 microspecies 22, 12 & 12 Gb 2n=3x=24 apomictic Rubar Salih & Lubos Majesky
  20. 20. k-mer analysis For a 16-mer length, there are 2 billion canonical 16-mers (416/2), and the average 16-mer occurs 10 times in the 22Gb of sequence data. The overall distribution of these informs us about how repetitive the genome is, and the frequency of different repetitive elements.
  21. 21. k-mer analysis The most abundant 16-mers in the 150bp genome reads: 7bp telomere sequence (TTTAGGG/CCCTAAA) added ends of each chromosome occurs a total of 7M times, much higher than the expectation of 140. From 128-mer GT10kb Coverage Depth = 7 AF(11)_S983_009 Blue: DAPI fluorescence. Green: telomere primer HC_89bp Red: 5S rDNA
  22. 22. In asexual dandelion microspecies Rubar M. Salih Genome evolution and biodiversity •Actively evolving repetitive sequences in the genome •Differences seen between microspecies in repeats •Structural and mobile components of genome identified •Chloroplast sequence gives phylogeny and robust markers for diversity (PLoS One in press Dec 2016)
  23. 23. So questions are 1) where is this sequence located in the genome? and 2) are there any differences between the microspecies in its abundance? We can see this is a Ty1-Copia element because the retroelements coding domains are in the order RNaseH Reverse Transcriptase Integrase LTRs divergent More (solo LTRs) RepeatExplorer: Graph-based clustering of related sequences, program/approach by Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3.
  24. 24. Widely dispersed distribution of a copia retroelement family over all chromosomes of Taraxacum Retrotransposons in Taraxacum 2n=3x=24 NOR sats shown
  25. 25. Distribution from RepeatExplorer O978 the top 10 in terms of genome% and nature of sequence – for each of the three spp. # TxS3 TxA978 TxO978 Repeat masker Genome % Repeat masker Genome % Repeat masker Genome % 1 Low complexity 1.60 Low complexity 0.965 Simple repeat 1.400 2 Low complexity 1.26 Low complexity 0.818 LTR.Gypsy 1.250 3 LTR.Gypsy 1.22 LTR.Gypsy 0.807 Simple repeat 1.200 4 LTR.Gypsy 1.17 Low complexity 0.796 Low complexity 0.963 5 Low_complexity 1.09 Low complexity 0.788 LTR.Gypsy 0.845 6 LTR.Copia 1.04 Low complexity 0.771 Low complexity 0.820 7 LTR.Gypsy 0.995 LTR.Gypsy 0.730 LTR.Gypsy 0.793 8 Low_complexity 0.982 Low complexity 0.713 Low complexity 0.781 9 LTR.Gypsy 0.940 LTR.Gypsy 0.682 LTR.Gypsy 0.741 10 LTR.Copia 0.841 Low complexity 0.671 Low complexity 0.724 S3 A978 Petunia
  26. 26. Relative counts of various k- mers in three Taraxacum microspecies Rubar Salih et al. in prep
  27. 27. Dispersed on chromosomes in all microspecies: but differences AA1_AK07_171D_45S B_010 AC1_O996_171 D_KsHC B_003AC11_S933_171 D_KsHC B_004 0.075% Low complexity Assembled to genome of: A: S: O:
  28. 28. Sequence CL80 double-dots on 14 chromosomes (not 16 – not 2 genomes worth) – is it a centromeric repeat? LTR.Copia (2hits, 0.103%) Low complexity (5hits, 0.0895%) Genome proportion = 0.2480% Assembled to genome: A = S = O = AE (3)_A978_A dig_pta794_001 AE (4)_O976_A dig_pta794_002 AE (2)_S3_A dig_Pta794 bio_002
  29. 29. Unknown or Chloroplast Low Complexity Mixed Repeat LTR Degenerate LTR Gypsy LTR Copia DNA Transposons LINES LTR Caulimovirus Simple Repeat rRNA Tandem Repeat Telomere Genomeproportion(%) Cluster (number) I I I I I I I I 1 50 100 150 200 250 300 351 Telomere Tandem Repeat rRNA Simple Repeat LTR Caulimovirus LINES DNA Transposons LTR Copia LTR Gypsy LTR Degenerate Mixed Repeat Low Complexity Unknown or Chloroplast Retroelements and tandem repeats in Petunia Supplementary Ms 2. Bombarely et al. Petunia genome sequence Nature Plants 2: article number 16074. Telomere Tandem Repeat rRNA Simple Repeat LTR Caulimovirus LINES DNA Transposons LTR Copia LTR Gypsy LTR Degenerate Mixed Repeat Low Complexity Unknown or Chloroplast
  30. 30. Organelle sequences from chloroplasts or mitochondria Sequences from viruses Transgenes introduced with molecular biology methods Genes, regulatory and non- coding low-copy sequences Dispersed repeats Repetitive DNA sequences Nuclear Genome Tandem repeats Satellite sequences DNA transposonsRetrotransposons Centromeric repeats Structural components of chromosomes Telomeric repeats Simple sequence repeats or microsatellites Repeated genes Subtelomeric repeats 45S and 5S rRNA genes Blocks of tandem repeats at discrete chromosomal loci DNA sequence components of the nuclear genome After Biscotti et al. Chromosome Research 2015 Other genes Transposable elements Autonomous/ non-autonomous Dispersed repeats that we don’t know about – except each is significant proportion of genome
  31. 31. Japanese knotweed – invasive in watercourses in Europe Fallopia (and Fallopia x Muehlenbeckia hybrids)
  32. 32. Repeat Explorer analysis raw reads of F. japonica and M. australis. Top clusters represented 50% of the reads in F. japonica and 39.5% of reads in M. australis. F. japonica has a higher proportion of dispersed repeats than M. australis.
  33. 33. Fallopia x Muehlenbeckia hybrid : Differential probes identified by k-mer and RepeatExplorer Green is Fallopia-specific; Red is equal in both genomes Desjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep
  34. 34. Desjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep.
  35. 35. Panicum sensu stricto c. 100 species; x=9 Evolution of Panicum miliaceum Proso millet P. miliaceum 2n=4x=36 P. capillare 2n=2x=18 P. repens 2n=4x=36 also 2n=18 to 54 P. sumatrense 2n=2x=18 or 4x=36 Global North-temperate Low genetic diverstiy Weedy forms P. virgatum 2n=4x=36 or 2x=18 ? ? ? ? ?? • Hunt , HH et al. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot. 2014
  36. 36. Chromosome and genome engineering Cell fusion hybrid of two 4x tetraploid tobacco species Patel, Badakshi, HH, Davey et al 2011 Annals of Botany
  37. 37. Nicotiana hybrid 4x + 4x cell fusions Each of 4 chromosome sets has distinctive repetitive DNA when probed with genomic DNA Patel et al Ann Bot 2011 Cell fusion hybrid of two 4x tetraploid tobacco species Four genomes differentially labelled Patel, Badakshi, HH, Davey et al 2011 Annals Botany
  38. 38. Wheat evolution and hybrids Triticum uratu 2n=2x=14 AA Einkorn Triticum monococcum 2n=2x=14 AA Bread wheat Triticum aestivum 2n=6x=42 AABBDD Durum/Spaghetti Triticum turgidum ssp durum 2n=4x=28 AABB Triticum dicoccoides 2n=4x=28 AABB Aegilops speltoides relative 2n=2x=14 BB Triticum tauschii (Aegilops squarrosa) 2n=2x=14 DD Triticale xTriticosecale 2n=6x=42 AABBRR Rye Secale cereale 2n=2x=14 RR
  39. 39. Centromere dynamics and timing of chromosome synapsis (6x wheat) Adel Sepsi, Higgins, Heslop‐Harrison, Schwarzacher. CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat. Plant Journal. 2016 Sep 1. Sepsi et al. Plant Journal 2016
  40. 40. (b) Centromere depolarisation and SC formation during Zygotene Interphase Leptotene Zygotene Late ZygoteneTelomere bouquet Homologue chromosome pairs Centromeres ZYP1 Early Zygotene 1 2 3 Subtelomeric synapsis Interstitial alignment Interstitial elongation (a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I. Sepsi et al. Plant Journal 2016
  41. 41. How do genomes evolve? –Gene mutation very rarely • (human: 10−8 /site/generation) –Chromosome evolution –Polyploidy and genome duplication –Repetitive sequences: mobility & copy number • (10−4 /generation in µsat) –Recombination –Epigenetic aspects: centromeres & expression
  42. 42. Repetitive sequences • Many families and various types • Abundant • Rapidly evolving … or conserved – Copy number and sequence • May be near-genome specific, even chromosome-specific • Various genome/chromosomal locations
  43. 43. Organelle sequences from chloroplasts or mitochondria Sequences from viruses Transgenes introduced with molecular biology methods Genes, regulatory and non- coding low-copy sequences Dispersed repeats Repetitive DNA sequences Nuclear Genome Tandem repeats Satellite sequences DNA transposonsRetrotransposons Centromeric repeats Structural components of chromosomes Telomeric repeats Simple sequence repeats or microsatellites Repeated genes Subtelomeric repeats 45S and 5S rRNA genes Blocks of tandem repeats at discrete chromosomal loci DNA sequence components of the nuclear genome After Biscotti et al. Chromosome Research 2015 Other genes Transposable elements Autonomous/ non-autonomous Dispersed repeats that we don’t know about – except each is significant proportion of genome
  44. 44. Sequences from viruses Transgenes introduced with molecular biology methods Genes, regulatory and non- coding low-copy sequences Dispersed repeats Repetitive DNA sequences Nuclear Genome Tandem repeats Satellite sequences DNA transposonsRetrotransposons Centromeric repeats Structural components of chromosomes Telomeric repeats Simple sequence repeats or microsatellites Repeated genes Subtelomeric repeats 45S and 5S rRNA genes Blocks of tandem repeats at discrete chromosomal loci Real? Passively Amplified DNA sequences: PADs Or: Transposable element derivatives (LTRs etc)? Other genes Transposable elements Autonomous/ non-autonomous Dispersed repeats that we don’t know about – except each is significant proportion of genome
  45. 45. Domestication, polyploidy and genomics of crops (and weeds) Pat Heslop-Harrison & Trude Schwarzacher and collaborators Leicester, UK phh@molcyt.com http://www.molcyt.com http://www.molcyt.org Twitter Pathh1 .
  46. 46. From Chromosome to Nucleus Pat Heslop-Harrison phh4@le.ac.uk http://www.molcyt.com
  47. 47. • About half of all higher plant species are recognizable as polyploids, a major feature of genome architecture where there are more than two sets of chromosomes. Advantages include multiple copies of each gene with different regulation, so essentially fixing heterosis; larger cell size; and the opportunity for mutation without lethality. Disadvantages include twice as much DNA to replicate; incorrect control of multiple gene copies in interacting genomes; chromosome instability at mitosis; and the challenges of ensuring chromosome pairing and regular meiotic segregation in seed crops, in breeding hybrid materials, or else combining sterility with parthenocarpy in fruit crops. Given these substantial contrasts, it is perhaps surprising that the top three cereal crops are wheat (a modern hexaploid 2n=6x=42), rice (diploid, 2n=2x=14), and maize (palaeotetraploid, 2n= 2 or 4 x =20), suggesting neither advantages nor disadvantages are overwhelming. I will consider the balance of positives and negatives over evolutionary and crop-breeding timescales. In the second part of my talk, I will consider how knowledge of polyploid behaviour and knowledge of ancestors can be exploited, discussing our work with polyploids, both well-known (wheat, Brassica, banana) and less known (proso millet, ornamentals and saffron crocus). Further details and references will be at http://www.molcyt.com. Email phh(a)molcyt.com

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