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