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 www.molcyt.com

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 www.molcyt.org

2. Ensete ventricosum 2nd genus in Musaceae
enset, ensete, false banana

4. • Germplasm: Bizuayehu Tesfaye, Hawassa, Ethiopia

6. 6

7. 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

9. • 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.

10. Genomics changes study of
taxonomy, phylogeny, diversity
Revolutionizes crop genetics
and breeding
Exploits Musa as a reference

11. Diploid chromosomes in Musaceae (blue DAPI stain) with centromeric element labelled

12. 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

13. Analysis with RepeatExplorer
A978
Petunia
Ensete repetitive DNA distribution
Not huge abundance of repetitive sequences in Ensete – 25% of genome
Taraxacum

14. 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.

15. • 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

16. • 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

17. 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

18. 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)

19. Fingerroot ginger - Bosenbergia rotunda - Zingiberales

20. • Project on Boesenbergia lead by Norzulaani
Khalid & Jennifer Ann Harikrishna
Genome sequence
Secondary products
Tissue culture changes
Epigenetics – DNA and
chromatin modification

21. 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

22. 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

23. 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

24. Outputs
–CROPS
– Fixed energy
Inputs
–Light
–Heat
–Water
–Gasses
–NutrientsLand

25. Outputs
–CROPS
– Fixed energy
25
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients
– Light
– Heat
– Water
– Gasses
– Nutrients

26. Agricultural production
• Agronomy
• Genetics
• Genetics for production systems –
technological solutions for sustainable
agriculture

27. 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

28. • 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)

29. 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 www.molcyt.org

30. 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
www.molcyt.org

32. Molecular Cytogenetics Group
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