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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. Cytogenetic, genetic and physical maps. Fluorescence in situ hybridization (FISH).

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

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  1. Update on the genomic mapping and sequencing initiative for banana and plantain Chris Town

  2. What can genomics tell us about bananas?

  3. Genome Projects provide us with lists of parts.

  4. Cytogenetic, genetic and physical maps Fluorescence in situ hybridization (FISH) In Medicago, all gene-rich BACs tested to date FISH to euchromatic arms. Repeats are centromeric or pericentromeric. Banana may well be similar.

  5. Counting Genes in Musa Borrowed from Chung-Jui Tsai, Michigan Tech University

  6. EST Sequencing in Musa 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 .

  7. 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.

  8. AAw Zebrina AAw Malaccencis AS Buya Mutika AAcv Banksii der AAw Banksii Orotava Ibota AAcv Malac. der AAcv Banksii der. Pome Mlali Cavendish Plantains Iholena Popoulou Maia Maoli Bluggoe Ney Mannan Monthan Awak Simili Radjah Figue pomme Neighbour joining tree design from 487 Musa accessions and 22 SSR markers The similarity is based on the number of shared alleles. AAw AAcv BB AB AS AAA AAB ABB Work of Isabelle Hyppolyte, CIRAD

  9. One of the genetic crosses used for mapping X Musa acuminata ‘Pisang lilin’ Cultivar ♂ Musa acuminata ‘Borneo’ Wild ♀ 280 Borli F1 individuals Work of Isabelle Hyppolyte, CIRAD

  10. Gr 1 Gr 2 GR 8 Gr 3 Gr 4 Gr 5 Gr6 CIR120-7* 0.0 Cir25-2* 0.8 295231 2.3 302740 299747 0 CIR151-2* 3.0 293785? 292849 2.3 CIR248-2* 291330 10.4 6.6 292918 292488 0.0 JARRET1_32 294947 7.2 11.1 Ma1-32 295606 4.0 CIR08 295482 291481 7.4 12.4 299129 13.1 Cir42-2* Gr7 8.9 292033 14.5 33.0 295995 291314 CIR241 14.2 CIR07-4* 15.9 33.9 290857 CIR03-1* 15.8 ECIR634-2* CIR156 291694-1* 18.0 35.4 21.1 293128 291199 293444-2* CIR110-3* 19.2 52.8 295550 292114 CIR109 21.8 294284-2* 20.5 56.8 301295 291390 292567 295000-2* 20.6 24.3 60.1 295703 291371 27.1 ECIR533-3* UCB92-6* 295681 CIR154 28.7 25.9 67.2 292147 302553 32.2 CIR172-6* 300550 78.2 27.7 293894 35.0 295688-2* CIR24-3* 78.7 300588 302807 36.9 298410 28.1 ECIR521-7* 298188 299313* 40.4 ECIR519-7* 79.8 29.3 303320-2* 300167-2* 47.5 ECIR599-7* 291639 82.5 292370-1* 48.0 CIR11-7* CIR252-4* CIR249-6* 27.7 84.7 282922 ECIR546-4* ECIR516-5* 48.6 85 293665-4* 295014-5* 48.8 CIR256-7* 28.8 293645-5* 301766-2* 299607-2* 293353-5* 48.9 90.1 299515-4* 29.3 299989-1* 301727-1* ECIR609-7* 294211-1* 49.4 CIR11-7* 293665-4* 91.6 285105-4* ECIR554-7* 50.2 301053-1* 302724-1* ECIR519-7* 31.1 ECIR562-7* 92.0 301919 50.4 CIR172-6* 94.6 300166 37.7 51.0 293227-1* 295688-2* 51.9 CIR163-7* 94.9 UCB92-6* CIR188-2* 39.8 52.6 302647 CIR180-3* 300335* 96.3 52.7 301793 43.7 CIR305-1* 291049-4* 285105-4* 96.8 54.0 CIR167-7* CIR167-7* 293318-4* 298351-7* 47.6 54.8 CIR180-3* 97.0 292922 ECIR554-7* 300831 64.8 99.6 295219-4* 48.9 300487 0.0 292364-1* 301202-4* 99.8 CIR289-7* 294264 3.2 50.0 CIR163-7* ECIR578-1* 301659-1* 291415 103.2 3.6 300528-7* ECIR599-7* 51.3 302676 4.8 106.6 293353-5* CIR189 7.3 295737-7* 52.7 109.7 295014-5* ECIR535 9.8 CIR138 295529-5* 111.7 301679 10.9 54.2 ECIR609-7* ECIR546-4* 12.5 ECIR551-2* 113.5 298985-1* ECIR0496-7* 54.8 13.5 298606 RGA8H_2 0.0 114.2 CIR215-7* 299380-1* 299355 15.0 ECIR571-2* 0.0 RGA8D_1 3.9 54.9 115.6 ECIR556-7* 291394 15.5 293412-3* 1.1 292976-6* ECIR542 6.0 58.5 301390-7* ECIR544 120.6 16.6 290800-4* 12.6 299809 7.9 302613-7* 291192-5* 293112-5* 295909 292409-3* 17.7 19.9 CIR20-7* 123.2 12.2 61.7 CIR152-5* 298946 Ma1-17-3* 30.2 20.2 13.4 302046-7* 292004-1* 124.5 ECIR564 302438 ECIR575-6* 301453-2* 32.5 298892 21.3 62.2 14.7 294420-7* 126.1 CIR39-1* 291993-2* 296102-2* 34.3 CIR17 293518-2* 23.7 16.8 CIR301-7* 63.2 ECIR583-2* 36.0 284904 291546-1* 299179-2* 25.5 131.6 20.4 ECIR623-7* 293783-2* 303077-2* 37.7 295671 302082-1* 27.4 21.3 294224 71.5 138.3 CIR174-1* 37.8 295674 28.0 296030-1* RGA41D_1-3* 23.5 141.1 ECIR619-2* 294576 29.4 79.6 41.2 293814 RGA22H_1-4* 25.3 300835-2* 147.9 302085 CIR137 30.9 ECIR618-2* 42.8 0.0 CIR115-1* 284666-2* CIR44 27.0 0.0 86.5 302090 34.4 291116-1* CIR280 42.9 154.8 0.5 285199 282961-1* 295291-2* RGA22H_2-2* 27.1 294530 295856 36.1 CIR285-2* 43.7 300203 8.6 4.1 292772 302225-2* 86.6 28.1 158.2 CIR103 298719 CIR274 45.1 CIR108 44.3 5.7 ECIR509 282897-2* ECIR620 28.4 86.6 291624 11.1 46.3 CIR28-3* 44.6 6.5 ECIR541-1* RGA22D_6-4* 292927 28.7 291379 RGA43D_4-7* 291849 301308 CIR235 49.1 53.3 300015 ECIR504-7* 9.1 29.1 290801 292992 93.8 27.1 ECIR561 298171 302295 292320 50.2 60.5 CIR162 9.2 30.0 ECIR610-7* 300238 303145 50.8 295639 61.3 94.4 CIR272 10.7 37.2 ECIR629-4* 282338 28.4 Gr 11 Gr10 300186 53.0 ECIR507 61.7 ECIR0500 11.6 37.5 291757 98.2 292935 298297 54.8 293338 RGA43D_1-7* 64.0 298965 44.0 291893-1* 0.0 12.1 RGA4H_2-7* 33.2 ECIR584 55.0 ECIR515 64.6 293479 44.1 291858-2* 12.5 101.0 291015 3.4 ECIR505-7* CIR184 292810 64.2 CIR247 65.2 33.7 302216 299708 14.8 CIR30-2* 292676-2* 44.3 104.5 8.5 CIR257-7* 282588 292336 65.3 284900 67.1 RGA43D_3 301402 299320-2* 14.9 45.0 45.7 ECIR602 66.2 CIR29 68.1 292136 10.7 303392 ECIR633-5* 291055-2* 47.7 291737-1* 107.2 CIR287 CIR169 296063 67.9 ECIR617 72.1 CIR102-1* 48.8 10.8 300608 46.4 CIR40 298954 70.1 CIR185 72.3 ECIR538 31.3 108.8 292234 298545-1* 302454 CIR170 52.5 293749 15.5 RGA4H_1-1* 71.3 303320-2* 82.8 CIR116 38.2 301356 298729 48.1 292436 302119 110.0 295730 83.1 40.0 300999 282985-1* 299796-1* 301708-7* 16.6 284980-7* 292340 293074 83.2 41.8 298592 49.2 298763-1* 303341 52.6 119.9 302606-7* 17.7 295426-7* 301035 302620 87.9 41.9 302764 296089 0.0 ECIR514 301610 298692 293193 ECIR570 294583-7* 300920-7* 51.9 141.4 18.9 88.3 302899 42.0 302756 9.0 294456 282859-1* 88.5 302621 42.9 302447 18.8 ECIR574 302416-7* CIR192 24.5 52.9 299555-2* 300679-2* 124.4 52.0 88.6 303066 299731 CIR157 25.7 CIR18-7* 294245 43.7 54.1 300914 291124-7* 24.8 300172 CIR168 89.4 CIR277 300878 28.5 282704 44.1 124.6 283019 54.4 52.7 ECIR565-7* 32.4 UCB125 95.0 294553 ECIR566 ECIR0494 45.6 32.5 0.0 ECIR536 300221 301168 54.5 298630 125.5 CIR129 96.5 293002 295038 294465-3* 45.7 36.4 8.1 302115 ECIR622-1* 57.4 32.8 55.2 301020 CIR150 CIR139 97.5 292972 282644 10.7 293987 45.8 38.5 CIR130-1* 55.5 ECIR560-7* 126.6 33.9 CIR229 CIR228 98.1 303101 298069 92.5 15.3 CIR210 46.1 41.4 295835-1* 56.0 CIR27 300582-7* 294469 ECIR518 37.9 100.3 295644 294362 300416 130.9 47.2 47.9 300961 CIR261-1* 21.7 56.2 292137 292173 94.4 294204 105.0 284658 295013-7* 50.4 291655-2* 23.5 290819 44.5 58.4 295155 131.4 CIR195 111.1 CIR297 291921 57.7 52.7 303203-2* 295850-2* 302982-2* 24.6 ECIR508-7* 95.0 54.2 302391-3* 59.1 299016 291835-2* CIR219 112.3 60.0 53.0 302000 132.9 30.8 290809-2* 295025-1* 299189-3* 114.4 302586 56.1 61.1 UCB152 53.8 299419 285318 32.1 59.2 CIR105-1* 295675-1* 96.6 134.9 117.3 301498-1* CIR124 ECIR513-6* 62.1 UCB103 54.8 ECIR511 299563 301145 32.7 61.2 Ma3-90 63.3 119.2 ECIR506-2* 54.9 291490 299716-2* 33.7 97.5 62.9 CIR21 CIR273 135.3 69.7 CIR112 55.0 ECIR525 43.8 63.0 CIR13 298571 98.0 72.2 57.0 300944 45.0 CIR122 64.1 ECIR579-1* 299332 296011 45.7 291803 64.6 302641 67.0 72.3 98.7 292923 53.1 300329 67.8 292151-3* 76.6 292385-4* 73.0 300886-1* 300507 68.1 58.8 ECIR573 284699-2* 76.8 99.1 293379 ECIR523 ECIR559 73.1 69.8 70.9 ECIR555-2* 295151 77.1 CIR254-3* 295699 80.3 299273 295017-1* 76.9 77.4 99.6 303229 74.7 293099 83.2 300671 CIR45-5* 77.0 ECIR549-2* 80.0 77.5 RGA13H 102.7 86.7 294988 CIR294 CIR111-4* 77.4 81.1 291518-4* 285134-7* 80.6 89.7 CIR117-2* 77.6 82.5 294293 CIR119-1* 103.0 284953 94.6 291674 77.9 105.1 292284-4* 85.4 CIR193-7* CIR113-1* 302644 105.2 290991 78.2 106.3 292027-3* 103.4 88.9 RGA12H_2-1* 106.3 299599 293659 290847 79.2 282876 106.7 290990 291606 96.0 86.4 CIR182 107.5 107.1 CIR260 87.9 ECIR601 98.4 CIR282 CIR25-4* ECIR502 115.3 89.7 292804-2* 108.5 113.4 ECIR612 CIR114 118.3 93.1 290922 ECIR547 108.8 290993-1* 119.7 99.5 CIR02-2* 115.0 301177 CIR151-4* 302235 119.8 102.5 302718-2* 110.6 ECIR631-1* ECIR510 135.9 CIR171-1* 107.0 CIR196-2* CIR248-2* 118.4 114.7 302439 139.3 293249 135.8 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

  11. Progress in Genome Sequencing * 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.

  12. A genome MA4_82I11.26 MA4_82I11.30 MA4_82I11.46 (CIR257) MA4_82I11.36 MA4_82I11.42 MA4_82I11.18 MA4_82I11.44 MA4_82I11.48 MA4_82I11.6 MA4_82I11.10 MA4_82I11.16 MA4_82I11.4 MA4_82I11.22 MA4_82I11 (103Kb) L1 L2 L3 L4 L5 L6 L7 L8 L9 L10 L11 L12 L13 L14 L15 L16 B genome MBP_81C12 (144Kb) MBP_81C12.36 MBP_81C12.40 MBP_81C12.16 MBP_81C12.10 MBP_81C12.26 MBP_81C12.22 MBP_81C12.14 MBP_81C12.18 MBP_81C12.42 MBP_81C12.46 MBP_81C12.12 (CIR257) MBP_81C12.44 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.

  13. 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.

  14. Participants at JGI Workshop/Strategy Meeting, January 18, 2008

  15. 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!

  16. 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.

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