banana, ensete and boesenbergia genomics - schwarzacher, heslop-harrison, harikrishna

Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential

Banana Genomics – Tue 17 Jan 2017 10.30PACIFIC SALON 6-7Mathieu Rouard & Angelique D'Hont

Trude Schwarzacher and Pat Heslop-Harrison [email protected] www.molcyt.org

Ensete ventricosum 2nd genus in Musaceaeenset, ensete, false banana

• Germplasm: Bizuayehu Tesfaye, Hawassa, Ethiopia

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

• 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.

Genomics changes study of taxonomy, phylogeny, diversityRevolutionizes crop genetics and breedingExploits Musa as a reference

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

Ty1-Copia elementRather few in Ensete

RepeatExplorer: Graph-based clustering of related sequences, program/approach byNovák 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 abundanttandem repeats in Ensete genome

Analysis with RepeatExplorer

A978

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TelomereTandem repeatrRNASimple repeatLTR CaulimovirusLINESDNA transposonsLTR copiaLTR GypsyLTR degenerateMixed repeatLow complexityunknown

Petunia

Ensete repetitive DNA distribution

Not huge abundance of repetitive sequences in Ensete – 25% of genome

Taraxacum

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.

• 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

• 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

Transcriptome alignment to banana *genomeUse 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

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)

• Fingerroot ginger - Bosenbergia rotunda - Zingiberales

• Project on Boesenbergia lead by Norzulaani Khalid & Jennifer Ann Harikrishna

Genome sequenceSecondary productsTissue culture changes

Epigenetics – DNA and chromatin modification

Boesenbergia rotunda

PRO-METAPHASE

histone H3 dimethylated lysine K4 (49-1004)

euchromatin mark

at the end of the chromosomescentromeric heterochromatin not stained

DAPI H3K4me2

Harikrishna, Khalid, Bailey, Schwarzacher

B1-1-O2


INTERPHASEhistone H3 mono-

methylated lysine K9 (49-1006)

hetero-chromatin mark

DAPI H3K9me1


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


METAPHASEhistone H3 di-methylated

lysine K9 (49-1007)hetero-chromatin

mark

DAPI H3K9me2


Mainly stains centre of chromosomses where we assume the location of centromeric heterochromatin to be

B1-5-O12

Outputs–CROPS

– Fixed energy Inputs

–Light–Heat–Water–Gasses–NutrientsLand

Outputs–CROPS

– Fixed energy

25

Inputs

–Light–Heat–Water–Gasses–Nutrients

– Light– Heat

– Water– Gasses

– Nutrients

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

• 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

• 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)

Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential Trude Schwarzacher and Pat Heslop-Harrison [email protected] www.molcyt.org

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 2016Twitter, YouTube and Slideshare: pathh1

Pat Heslop-Harrison [email protected]

www.molcyt.org

Molecular Cytogenetics Groupwww.molcyt.com

Pat Heslop-HarrisonTrude Schwarzacher

and colleagues

Impacts outside academiaLegislation: 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 superdomesticationstrategies to exploit biodiversity

for sustainable agriculture

Work on hybrids and alien introgression with novel quality / disease resistance characters

Wheat with virus resistanceidentified 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 forbiotechnology

Food fraud and safety detection

Reviewing research programmesEditing Journals

http://www.molcyt.com/

banana, ensete and boesenbergia genomics - schwarzacher, heslop-harrison, harikrishna

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