# Presentation: 858108

## Update on the genomic mapping and sequencing initiative for banana and plantain 

**Update on the genomic mapping and sequencing initiative for banana and plantain **

- Chris Town

## What can genomics tell us about bananas?

## Genome Projects provide us with lists of parts.

| Species | Common name | Genome size | Completed
 | Number of Genes |
| --- | --- | --- | --- | --- |
| Arabidopsis thaliana | Mouse-ear cress | 120 Mb | 2000 | 30,000 |
| Oryza sativa | rice | 400 Mb | 2002-2005 | 50,000 |
| Populus trichocarpa | poplar | 500 Mb | 2004-2006 | 45,000 |
| Sorghum bicolor | sorghum | 770 Mb | 2007 | 50,000 |
| Vitis vinifera | grape | 500 Mb | 2007 | 30,000 |
| Glycine max | soybean | 1115 Mb | 2007-2008 | 59,000 |
| Zea mays | corn | 2600 Mb | 2008-? | 60,000 |

## Cytogenetic, genetic and physical maps

- In Medicago, all gene-rich BACs tested to date FISH to euchromatic arms. Repeats are centromeric or pericentromeric. Banana may well be similar.

- Fluorescence *in situ* hybridization (FISH)

## Counting Genes in Musa

- Borrowed from Chung-Jui Tsai, Michigan Tech University

## EST Sequencing in Musa

| Species/subgroup | Genotype | Description | ESTs |
| --- | --- | --- | --- |
| M. acuminata

  | Grande Naine | Development leaf/ fruit | 41,352 |
|  |  | Mycosphaerella infected leaves | 5,643 |
|  |  | Embryogenesis cells | 369 |
|  |  | Development | 252 |
|  | Calcutta 4 | Mycosphaerella infected leaves | 12,067 |
|  |  | Hot and Cold stresses | 2,269 |
|  |  | Development Root/Flower/ Peel/Root | 5,145 |
| M. balbisiana | Pisang Klutuk Wulung | Development Leaf/root | 4,636 |
| ABB | Cachaco | shoot tip meristem cultures submitted to osmotic stress | 15,630 |
|  | Pisang Awak | drought non-stressed leaf/shoot | 5,767 |
| AB | Sukari Ndizi |  |  |
| AAA | Matooke |  |  |
| AAB | Penkelon Noir | BSV activated and non-activated vitro plantlets | 250 |

*These 100,103 sequences collapse into 12,385 assemblies and 14,533 singletons for a total of 26,918 unigenes. *

- By contrast, there are  8 million from human, 1.5 million each from Arabidopsis and maize, 570,000 from Brassica and 394,000 from soybean .

## Most wild bananas are diploid (2n = 22) and contain either a AA genome or BB genomes

- “Cavendish” the most common dessert banana is triploid parthenocarpic and sterile (AAA genome). Other cooking bananas and plantains may be AAB or ABB.

## AAw

- The similarity is based on the number of shared alleles.

- AAcv
- BB
- AB
- AS
- AAA
- AAB
- ABB

- Work of Isabelle Hyppolyte, CIRAD

## X

*Musa acuminata*** ‘Borneo’**
- Wild **♀**

*Musa acuminata*** ‘Pisang lilin’**
- Cultivar** ♂**

**X**

**280 Borli F1 individuals**

- Work of Isabelle Hyppolyte, CIRAD

## A “Standard” Musa genetic map

**Gr 9**

**1218 cm 551 Markers (177 SSR, 354 DArTs, 19 RFLP)**
**1mkr/2.2 cm**

- Mkrs name 1* distortion P< 0.05, 2* P<0.01, 3* P<0.005, 4* P<0.001; 5* P<0.0005, 6* P<0.0001,7* P<0.00005

- Work of Isabelle Hyppolyte, CIRAD

## Progress in Genome Sequencing

| Type of Sequence | Performed by | Amount | Total Sequence |
| --- | --- | --- | --- |
| BAC End Sequencing | TIGR/JCVI | 6,252 reads | 4.4 Mb |
| BAC sequencing* | KUL Leuven | 2 BACs | 0.22 Mb |
| BAC sequencing* | TIGR/EMBRAPA/UCB Brasilia | 13 BACs | 1.8 Mb |
| BAC sequencing* | NIAB/GCP | 57 BACs | 6 Mb |
| BAC End Sequencing | JGI/Stanford/PRI | 100,000 reads | In progress |
| 454 Sequencing■ | IEB, Czech republic | 1 run | 90 Mb |

- * BAC sequencing of the entire genome would require 3,000 to 5,000 BACs.
- ■ 454 sequencing of the entire genome would require 60 454 runs PLUS lots of paired end reads using conventional Sanger technology.

## What have we learned so far?

- Much of the genome is gene-rich, with a similar gene density to Arabidopsis where about one half of the genome is devoted to protein-coding genes. In Musa we expect that one half of the genome will be gene-rich and protein coding, while the other half will contain various classes of repetitive DNA.

- The A and the B genomes are very similar (95% in coding regions; 85% overall) having diverged from one another ~ 4 million years ago.

***Hence the A genome sequence will inform us about the B genome also.***

## Plans for sequencing the whole Musa genome

- Technology has moved on; almost all projects of this scale are whole genome shotgun, rather than BAC by BAC.
- Improved assembly algorithms can cope with large and quite repetitive genomes (e.g. the recently sequenced soybean genome).
- Next Generation sequencing technologies, already orders of magnitude ahead in quantity (10-100x more sequence per $$) are also improving in quality.
- We (the Global Musa Genomics Consortium) have proposed a Musa whole genome shotgun project to the DoE Joint Genomes Institute.

## Participants at JGI Workshop/Strategy Meeting, January 18, 2008

| Name | Institution | Country |
| --- | --- | --- |
| Francis Quetier | Genoscope | France |
| Jean Christophe Glaszmann | CIRAD/GCP | France |
| Felix Franca | Director EMBRAPA-LABEX USA | USA |
| Tom Farewell | Dole Corporation | USA |
| Nicolas Roux  | Bioversity International | France |
| Richard Markham | Bioversity International | France |
| Chris Town  | J. Craig Venter Institute | USA |
| Gert Kema  | WUR-Plant Research International | Netherlands |
| Manoel Souza  | Embrapa Labex-Europe | Netherlands |
| Rony Swennen  | Katholiek Universiteit Leuven | Belgium |
| Pat Heslop Harrison | University of Leicester | UK |
| Marty Dickmann  | Texas Agricultural and Mining University | USA |
| Romano Orlich  | President, Corbana - Costa Rica | Costa Rica |
| George Jaksch | Chiquita,  Senior Director  Corporate Responsibility and Public Affairs | EU |
| Andrzej Kilian | DArT - novel genetic mapping technology | Australia |
| Dan Koppel | Banana Book | USA |
| Jorge Sandoval | Research Director, Corbana - Costa Rica | Costa Rica |
| Frank Shotkoski | Agricultural Biotechnology Support Project, Cornell University | USA |
| Evert Jacobsen | Wageningen Agricultural University | Netherlands |
| Jim Bristow | Deputy Director, DoE Joint Genomes Institute | USA |
| Dan Rokhsar | DoE Joint Genomes Institute | USA |
| Igor Grigoriev | DoE Joint Genomes Institute | USA |
| Terry Berry | DoE Joint Genomes Institute | USA |
| Erika Lindquist | DoE Joint Genomes Institute | USA |

## Musa Genome Project: Plan of Action

- _Overall Strategy:_
- Sequence entire A genome of DH Pahang to ~ 8x coverage using a combination of small, medium, large and BAC insert libaries.
- Assemble and annotate sequence.

- _Implementation:_
- 1. Request sequencing from JGI through its community sequencing program. Total request 1 Gigabase of sequence = 2x genome coverage; proposal submitted.
- 2. Commitment of 4x sequence coverage from Agence Nationale de la Recherche (French National Research Agency, ANR);
- 3. Solicitation of financial support for 2x additional coverage from national bodies and research corporations (encouragement given at JGI meeting).

_***Conclusion***_***: Prospects are very good for a complete whole genome sequence within the next two years!***

## Acknowledgements

_**Proposal Management Group**_
**Nicolas S. Roux: **Global *Musa *Genomics Consortium (GMGC)
**Angelique D’Hont**, Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), Montpellier, France
**Jaroslav Dolezel**, Institute for Experimental Botany, Olomouc, Czech Republic
**Pat Heslop-Harrison**, University of Leicester, UK
**Gerrit H.J. Kema**, Plant Research International (PRI), Wageningen, The Netherlands
**Manoel Souza**, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA: Brazilian Agricultural Research Corporation), Brazil
- And hundreds of other researchers worldwide.
- Financial support from various international funding agencies.