Zipping the Three Nephews. Klaus Mayer MIPS, Helmholtz Center Munich
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1 Zipping the Three Nephews Klaus Mayer MIPS, Helmholtz Center Munich
2 Brachypodium Genome Synteny Rice Sorghum Maize r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 r11 r12 s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 m1 m2 m3 m4 m5 m6 m7 m8 m9 m10 bd1 bd2 bd3 bd4 bd5 Brachypodium b1 b2 b3 b4 b5 b6 b7 w1 w2 w3 w4 w5 w6 w7 Barley Wheat Triticeae orthologs indentified between Brachypodium/Triticeae/rice/maize/sorghum genomes and covering 99.4% of the brachypodium genome J. Salse
3 Syntenic integration aka Genome Zipper A B C
4 Syntenic integration aka Genome Zipper corresponding harvest35 marker cm brachy hit rice hit sorghum hit 454 shotgun reads - - Bradi2g Os05g ;47800; ; Os05g Sb09g ; ; ; - - Bradi2g Os05g Sb09g ;633922; ; - - Bradi2g Os05g ; ; ; Os05g ; ; 4437; - - Bradi2g Sb09g ;773802; ;7654; - - Bradi2g ; ; ; Os05g ; Os05g ; Bradi2g Os05g Sb09g ;815511; ;22527; 3_ Bradi2g Sb09g ; ; ;37116;16811; - - Bradi2g ; ; ; - - Bradi2g Os05g ;478745; Os05g ; 6499; - - Bradi2g ; ; 17363; 1_1223 0, _1354 0,77 Bradi2g Sb09g ;866014; ;37116;16811; 1_0895 0, _0842 0,95 Bradi2g Os05g Sb09g ; ; ; - - Bradi2g Os05g Sb09g ;553573; ;8447; - - Bradi2g ; 8447; - - Bradi2g ;248233; Bradi2g ; ; ;28045; - - Bradi2g Sb09g ; Bradi2g Sb09g ; ;911-1_1311 0,95 Bradi2g Os05g Sb09g ;715096; ; - - Bradi2g ;852057; ; 1_0460 0, ; ;39 197;204;207;332; Os05g ; ; Sb09g ; 17363; - - Bradi2g Os05g Sb09g ; ; 17363; - - Bradi2g Os05g Sb09g ; ; 6995; 2_1067 1,51 Bradi2g Os05g Sb09g ; ; ;16735; Bradi2g ; ; ; - - Bradi2g ; ; ; - - Bradi2g Os05g Sb09g ; ; ; 2_0502 1,51 Bradi2g Os05g Sb09g ; ; ; Associate - - syntenic - Os05g genes ; and 7504; accessory information 2_0836 1, ; 324;298; 3_0715 1, ; ; ; 3_1144 3, ;907983; ;16501; 2_1456 3, ; 5699; Sb09g ;680315; Sb09g ; ; Sb09g ; ; ; Os05g Sb09g ;787598; Os05g ; ; ; Sb09g ; ; ;4908; Sb09g ; Bradi2g Os05g Sb09g ; ; ;10110; - - Bradi2g ;36373; ;18906; Bradi2g ; ; ;5410;5409;52 1_0419 3,75 Bradi2g Sb09g ; ; ; Os05g Sb09g ; ; 11135; Sb09g ; Bradi2g Os05g ; ; Os05g ; - 2_0238 3,75 Bradi2g Sb09g ; Bradi2g Os05g Sb09g ; ; ;18045; Sb09g ; ; ; - - Bradi2g Os05g Sb09g ; Bradi2g Os05g Sb09g ;444103; ; 1_0410 3,75 Bradi2g Os05g Sb09g ;391681; ; 3_ ,52 Bradi2g Os05g Sb09g ;415098; ;13052; Os05g ;80764; Bradi2g ; ; Bradi2g Sb09g ;616154; ; - - Bradi2g ; 24793; - - Bradi2g Os05g ; ; ; - - Bradi2g Os05g Sb09g ; ; ;26065; - - Bradi2g ; - 2_ ,28 Bradi2g Sb09g ;589351; ;11683; Bradi2g ;910933; ; - - Bradi2g Os05g Sb09g ; Os05g Sb09g ;885298; Sb09g ; ; ;48323; - - Bradi2g ; ; 20331; - - Bradi2g ; ; Os05g Sb09g ; ; Bradi2g Os05g Sb09g ; ; Bradi2g Os05g Sb09g ;165929; 16155; Sb09g ; Os05g ; ; ; - - Bradi2g Sb09g ; ; ; - - Bradi2g Os05g Sb09g ; 17137; 1_ ,13 Bradi2g Os05g Sb09g ; ; ; Sb09g ; ; Bradi2g Os05g Sb09g ; ; ;11898; - - Bradi2g ; ; ; - - Bradi2g ;153885; Bradi2g ; ; Bradi2g Os05g Sb09g ;14758; ; Os05g Sb09g ; ; ;2487; - - Bradi2g ; ; ; - - Bradi2g Sb09g ; ; Bradi2g Os05g Sb09g ; Sb09g ;965193; ; - - Bradi2g Sb09g ; ; ;43594; Os05g ;147249; ;17184; - - Bradi2g Os05g Sb09g ; ; ; Sb09g ; ; 20203; Os05g Sb09g ; ; ;32860; Os05g Sb09g ; - 1_ ,47 Bradi2g Os05g Sb09g ; ; ;1640;15366; - - Bradi2g ; ; Bradi2g Os05g Sb09g ; ; Bradi2g ;372299; Bradi2g ; 21520; Sb09g ;807734; Bradi2g Os05g Sb09g ;732533; ; - - Bradi2g Sb09g ; ; Sb09g ; ; Bradi2g ; ; Bradi2g ; 19249; - - Bradi2g ; Os05g ; Sb09g ; 19249; - - Bradi2g Os05g Sb09g ; ;28-1_ ,47 Bradi2g Os05g Sb09g ; ; ; - - Bradi2g Os05g Sb09g ; ; ;794; - - Bradi2g ; 23921; - - Bradi2g Sb09g ; Bradi2g Os05g Sb09g ; ; Bradi2g Os05g ;865103; ; 3_ ,47 Bradi2g Os05g Sb09g ; 5390; 3_ _ Bradi2g Sb09g Sb09g Sb09g Os05g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Bradi2g Bradi2g Os05g Sb09g Bradi2g Bradi2g Os05g Sb09g Os05g Sb09g Bradi2g Os05g Sb09g Sb09g Bradi2g Bradi2g Os05g Bradi2g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Bradi2g Os05g Sb09g Bradi2g Bradi2g Sb09g Bradi2g Os05g Sb09g Bradi2g Sb09g Bradi2g Os05g Sb09g Sb09g Bradi2g Os05g Sb09g Bradi2g Bradi2g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Sb09g Os05g Bradi2g Sb09g Bradi2g Os05g Sb09g Os05g Bradi2g Sb09g Bradi2g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g _ Bradi2g Os05g Sb09g Sb09g Os05g Bradi2g Bradi2g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Bradi2g Sb09g Sb09g Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Bradi2g Sb09g Bradi2g Os05g Sb09g Sb09g Bradi2g Os05g Sb09g Os05g Bradi2g Bradi2g Os05g _ Bradi2g Os05g Sb09g Bradi2g Os05g Sb09g Os05g Os05g Sb09g Os05g
5 Wheat 4A is the most rearranges wheat chromosome Hernandez and Dolezel labs
6
7 Block Brachypodium Oryza sativa Sorghum A Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Os03g Os03g Os03g Os03g Os03g Os03g Sb01g Sb01g Sb01g Sb01g Sb01g Sb01g B Bradi4g Bradi4g Bradi4g Bradi1g Bradi1g Bradi1g Os11g Os11g Os11g Os03g Os03g Os03g Sb01g Sb01g Sb01g Sb01g Sb01g Sb01g C Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Os03g Os03g Os03g Os03g Os03g Os03g Sb01g Sb01g Sb01g Sb01g Sb01g Sb01g D Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Os03g Os03g Os03g Os03g Os03g Os03g Sb01g Sb01g Sb01g Sb01g Sb01g Sb01g E Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Bradi1g Os06g Os06g Os06g Os06g Os06g Os06g Sb10g Sb10g Sb10g Sb10g Sb10g Sb10g ! Intervalls and breakpoints can be precisly identified
8 19,720 GBS- SNP marker (obtained from Jesse Poland) Group A: 1A 7A Group B: 1B 7B Group D: 1D 7D hold 1 copy => 4366 removed from data set removed from data set same sequence different sequence same cm cm 7, ,101
9 # SNP marker per chromosome (unfiltered) = 19, Σ A B D # SNP marker per chromosome (filtered) = 15, Σ A B D
10 Group A Group B Group D 15,308 SNP marker 10,880,661 unmasked Ta conugs Vmatch, l = 63, e = 1 no match 6,399 c1 m1 1:1 7,747 1:n 1,162 c1 c2 m1 m1 same chr 1:1 7,635 same chr 1:n 520 n:1 8,192 m3 same cm ± 5 cm Σ 8,817 m2 m1 c1
11 # conug marker per chromosome arm (filtered) = 8,817 1S 1L 2S 2L 3S 3L 4S 4L 5S 5L 6S 6L 7S 7L Σ A B D centromere positions (cm) A B D
12 1A 2A 1B 2B 1D 2D
13 3A 4A 3B 4B 3D 4D
14 5A 6A 5B 6B 5D 6D
15 7A 7B 7D
16 Eduard Akhunov s GBS collecnon 241,180 marker = 25,153 SNP + 216,027 PA SNP = SNP polymorphism between the parent of SynOp populanons PA = presence/absence varianon # GBS tags (EA) per chromosome (unfiltered) = 241, Σ A 9,385 10,549 10,051 12,294 12,971 10,234 13,899 79,383 B 14,992 17,933 18,610 8,636 13,903 12,702 16, ,740 D 6,785 13,763 9,805 4,071 6,978 7,704 8,951 58,057
17 wheat chromosome arms: group A raw data repeat masked data chr/ chr arm size (Mbp) sequences (Mbp) coverage (x-fold) L50 % repeat content # contigs L50 1AS , ,792 4,769 1AL , ,745 6,369 2AS , ,721 6,678 2AL , ,892 6,677 3AS , ,942 3,846 3AL , ,822 3,789 4AS , ,078 7,499 4AL , ,363 6,601 5AS , ,718 8,713 5AL , ,571 5,355 6AS , ,040 7,091 6AL , ,029 6,589 7AS , ,174 4,397 7AL , ,585 5,849 5,727 3, ,236
18 chr/ chr arm size (Mbp) wheat chromosome arms: group B sequences (Mbp) raw data coverage (x-fold) L50 repeat masked data % repeat content # contigs L50 1BS , ,049 7,413 1BL , ,782 7,151 2BS , ,742 8,069 2BL , ,878 6,890 3B , ,021 6,855 4BS , ,514 8,755 4BL , ,575 5,883 5BS , ,000 7,365 5BL , ,886 7,537 6BS , ,565 4,972 6BL , ,726 4,824 7BS , ,118 6,435 7BL , ,553 4,144 6,202 3, ,409
19 chr/ chr arm wheat chromosome arms: group D Size (Mbp) sequences (Mbp) raw data coverage (xfold) L50 repeat masked data % repeat content # contigs L50 1DS , ,724 6,622 1DL , ,769 6,297 2DS , ,043 4,635 2DL ,445 3,247 3DS ,794 1,697 3DL ,258 2,941 4DS , , ,244 7,428 4DL , ,397 1,855 5DS , ,448 5,945 5DL , ,621 7,049 6DS , ,076 8,904 6DL , ,235 6,821 7DS , ,700 5,031 7DL , ,736 7,399 4,937 2, ,490
20 Sensitivity chr/ chr arm observed marker detection rate (sensitivity) chr/ chr arm Observed marker detection rate (sensitivity) chr/ chr arm Observed marker detection rate (sensitivity) 1AS 79,10 1AL 80,34 2AS 81,14 2AL 89,04 3AS 83,08 3AL 88,18 4AS 73,47 4AL 83,11 5AS - 5AL 85,16 6AS 80,86 6AL 85,99 7AS 88,70 7AL 83,12 1BS 73,31 1BL 81,40 2BS 74,52 2BL 71,39 3B 79,77 4BS 64,63 4BL 81,12 5BS 82,20 5BL 80,04 6BS 76,40 6BL 78,48 7BS 83,66 7BL 83,89 1DS 76,47 1DL 86,60 2DS 87,04 2DL 85,35 3DS 89,01 3DL 89,86 4DS 68,75 4DL 78,63 5DS 80,61 5DL 85,27 6DS 81,82 6DL 83,03 7DS 89,23 7DL 76,09
21 Gene counts Genes detected with: 1AS 1AL 2AS 2AL 3AS 3AL 4AS 4AL 5AS 5AL 6AS 6AL 7AS 7AL non redundant genes Brachypodium rice sorghum 3,372 3,489 3,543 2,031 2,087 2,081 4,096 4,268 4,349 2,934 3,054 3,098 3,309 3,437 3,489 2,229 2,357 2,362 4,308 4,494 4,591 2,414 2,520 2,487 3,963 4,093 4,122 1,558 1,620 1,584 2,783 2,965 2,938 2,425 2,490 2,504 2,929 3,052 3,062 3,032 3,117 3,195
22 Genes detected with: 1BS 1BL 2BS 2BL 3B_cov88x 4BS 4BL 5BS 5BL 6BS 6BL 7BS 7BL non redundant genes Brachypodium rice sorghum 3,303 3,494 3,557 2,092 2,218 2,211 4,503 4,693 4,796 3,185 3,359 3,430 6,127 6,323 6,456 3,182 3,278 3,434 2,914 3,094 3,096 5,837 6,074 6,222 1,677 1,745 1,755 2,681 2,764 2,813 2,297 2,359 2,350 3,256 3,324 3,389 2,105 2,175 2,240
23 Genes detected with: 1DS 1DL 2DS 2DL 3DS 3DL 4DS 4DL 5DS 5DL 6DS 7DL 7DS 7DL non redundant genes Brachypodium rice sorghum 3,290 3,364 3,451 1,695 1,782 1,772 5,098 5,214 5,349 2,847 2,992 3,042 3,676 3,749 3,870 2,022 2,104 2,054 4,882 5,464 5,569 2,164 2,362 2,302 4,353 4,508 4,604 1,608 1,659 1,632 2,862 2,980 3,023 1,832 1,962 1,923 2,989 3,189 3,173 3,072 3,243 3,290
24 Bd1 Bd3 7A 7B 7D
25
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