Genome and chromosome synteny and collinean'ty High level of genome col linearity between Helianthus species (Asteraceae) Helianthus annuus (ANN), H. petiolaris (PET): parental species H. anomalus (ANO), H. deserticola (DES), and H. paradoxus (PAR): diploid hybrid derivatives ANN ANO DES PAR PET ANN ANO DES PAR PET ANN ANO DES PAR PET ANN ANO DES PAR PET DES PAP. PET 1 ^7 •J ■■; ■J % i 3 § s -z g ■í o '-JJ ■í ANN ANO DES PAR PET ANN ANO DES PAR PET 3 S i 3 r" M O ■.:■ 1 1 * 1 i ... i § 3 * o dl i C* 1 ANN ANO DES PET ANN ANO DES PAR PET r:-. O IL i 3 ■c o -1 * o J o ĽJ o ■■-? o o ANN ANO DES PAR PET ANN ANO DES PAR PET § § in c; 1 I S —1 i i 1 1 i 1 1 s CD 3 5 5 § ANN ANO DES PUR PET ANN ANO DES PAR PET ANN ANO DES PAR PET ANN AHO DES PAR PET ANN ANO DES PAR PET ANN ANO DES PAR PET / / 1 i ■2 s T» I 1 ANN ANO DES PAP PET < -J 3 S ■1 J ■i '■-. 3 4 'i 3 -r. -] iL : ■o •3 ANN ANO DES PAR PET ANN ANO OES PAR PET ANN ANO DES PAF PET ■--1 < < r--5 I ■í 5 Segments containing inversions are indicated by hatched lines. Limited synteny between Arabidopsis and Asferaceae species • what is the level of synteny between the model species Arabidopsis thaliana and Asteraceae species (Compositae)! • macrosyntenic patterns covering large segments of the chromosomes were not evident • significant levels of local synteny (microsynteny) were detected at a fine scale; the syntenic patches are often not colinear i r r i i i i i i i r r i i i i i i i i » D :'. 32 48 £4 SD 96 1L2 12B 144 160 cM j___J_ ' " ŕ ■■■h' i j''i *Af ■ iŕ* ■■—■■' ťi Avs,bi<3opBÍB Chr™ioBC>B9 5 (17.B - 23.1 Mh) Physical positions of conserved orthologous sequences in a 5.5-Mb region of Arabidopsis chromosome 5 and their corresponding mapped positions on the nine linkage groups of Lactuca sativa (LG 1-9) Timmis etal. 2006 Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes m Sook Jung*1, Dorne Main2, Margaret Staton1, Ilhyung Cho3, Tatvana Zhebentvaveva1, Pere Arús4 and Albert Abbott1 j^^.i ^Můfliií — Xl-r. EE PWflHHWrV ^ In I F-* ' »«■ urn -5*OT| I .-. . S as.! í: i «E ..r .r. ^-. , . j ■Vy»»* I1' 'j ±-31U ■ 111 ::üi.l;i=£'-Laiüi, I:' ĚE] _♦<* H Ľ-----f. ■ 'Mf--■■*-, ^rr L:«'.ŕi---- ■ %JEEr A\ Nw j.-,* urny/ _ Zg/S^ I fí"! [wr w • syntenic regions were short and contained only a couple of conserved gene pairs • all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes • conserved syntenic regions in the pseudoancestral Arabidopsis genome: in many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region Genome synteny between pepper (n=12; Capsicum) and tomato (n=12; Solanum lycopersicum) Qp2^ T6 fp6^ T7 fplj T10 fPllJ T3 comparative genome structure of pepper (P) and tomato (T) (ps) T9 Q9) T12 Q^ Til (pu\ TS (p^ T4 (^) • 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome • 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper Livingstone eta/. 1999 Genome synteny between Solanaceae species in the molecular phylogenetic context Solanum tuberosum Solanum sitiens Chromosome 10 inversion Solanum tycopersiewn * .J • comparative mapping studies showed that tomato (Solanum tycopersicum) and potato (Solanum tuberosum) are differentiated by a series of whole-arm paracentric inversions of chromosomes 5, 9, 10, 11, and 12 • the chromosome 10 inversion arose within the tomato lineage after the split from the common ancestor with potato Rieseberg & Livingstone 2003 Crop Circle: collinearity between grass genomes Crop Circle diagram showing the currently known relationships between the genomes of eight species belonging to three different subfamilies Right-hand side: microcolinearity of Adh-orthologous regions of rice, sorghum and the two maize homoeologs (genes are indicated by red and blue arrows). • the most comprehensive comparative dataset obtained to date • What is the extent of colinearity at the DNA-sequence level? - Many small rearrangements that disturb collinearity in orthologous chromosome regions. Devos 2005 Maize-rice colinearity Wei et al. 2007, PloS Genet 3 2n=20 in coUinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to 2 regions in maize as a result of its recent polyploid origin. ancient whole-genome duplication in the maize/rice progenitor 2n=24 /ľ*^€^l2 inversions account for the majority of chromosome structural variations during subsequent maize diploidization. There was also clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. recent allotetraploidy in maize Change of chromosome numbers during speciation of cereals 3 | ■■§ & n 'R ml as ■i 7 3 ■n 2 J 5 U T* 5:1 ■L B w lít J Li i J :r. ft Iru ňň lir B 'L 'Ü Aň I «O ď - E"--Z* ďTTH i DÉDĎDDD»riD í A. Iľ:, Current Maize Genome Chromosome Reconstruction ] 6 i. n s 7 i r, . 10 Maize Progenitor Genome Oryzeae IIDID Sorghum ■ IV, , llQO IIDID Cereal ancestor (2ns±24.x=t2} Panicoideae Mi ^ n iĚn-řQ xpíDí Wei et al. 2007, PloS Genet 3 llü \ 2n=40 Maize progenitors Zca mays 2n=20 01 Shared duplications between rice (2n=24) and wheat (2n=42) and evolution of grass genomes • comparing 42,654 rice gene sequences with 6,426 mapped wheat ESTs (sequence alignment and statistical analysis) • identified 29 inter-chromosomal duplications covering 72 % of the rice genome and 10 duplication blocks covering 67.5 % of the wheat genome • orthologous relationships between the two genomes assessed: 13 blocks of colinearity representing 83.1 and 90.4% of the rice and wheat genomes, respectively • integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions -» common orgin (also maize and sorghum) Seven duplicated regions shared between wheat and rice wheat (Triticum aestivum) í v/2 w3 w4 w5 Vtf6 w7 r1 r2 r3 r4 r5 rfi r7 r8 rS MO M1 M2 rice (Oryza sativa) • —» a model of grass genome evolution from a common ancestor with n=5 through a series of whole genome and segmental duplications, chromosome fusions, and translocations Salse et al. 2008, Plant Cell Synteny between cereal genomes (wheat, rice, and maize) five colours represent the orthologous relationships referring to the five ancestral chromosomes Bolot et al. 2009, Curr. Opin. PI. Biol. Model of karyotype evolution in rice, wheat, sorghum, and maize genomes from a common ancestor with n=5 chromosomes Salse et al. 2008, Plant Cell AS AT A11 AS A4 n=5 Ancestral genome n=10 #1 WGD i] Da i d y a k w- aa DD DD II DD 90 MYň A1 AS A7A10 A11A12 A3 AS A4 AS At AS A7A10, A11A12 AS A9 #2 Breakage/fusion n=12 x m aa dJ A3 Daa ,D A4 AB dJ A2 DDD At AS AT AW A3 A11A12 AB A9 A4 AS A2 u u i_y ■46MYA 1 -^ ■ 50-70 MYA Rice aa a0 g aa iiGnr: Al Ai AIM? *1 Affair Í8 4S AA Ab Al MrS r7r10r3r11rl2 r8r9 r4 r6r2 U uw n=72 =5+5+2 vWieat i HI ■lnDC ■" U At - / - 23 aj yd aaa°G!i: iePtí A) AS fl^flíO jlJ ATTjqjí ^BflS ÍHA6 Ai #3 i_y____.__i 5 Fusions Sorghum aa is- aa ib"ddg AT fl5 ÍHÍÍ5 ÄS Ai AB A2 sAsG sC sHsE sJ sB sD sl sF LJ LJ i_y n=10 =5+5+2-2 Malz» aa &:?» aa i b«odg Al AS AUflt? A8 MJP j!? aa ss» aa i b^q Al A5 AtlAll A9 tá AS Al aa s™ aa i bí?ddd 4T7ÄÍ? 4ö €;;,^E >m ^B^ir*§i>Brp*: m9 m6 nn8 m3 mi m5 ml (BIO ItriZ____tn7 n=70 =(,5+5+2-2Jjc2-10 OGüGGQa IIddG A1 A5 A7A10 A3 A11A12 A8 A9 A4 A6 A2 n=12 U u L_y - 46 MYA í _^ - 50-70 MYA J Rice wheat maanm iin°üra[ioDDaa n^oi ;*ÍSÍ a™'i Jh Lysak <& Lexer Genome col linearity in crucifers: Arabidopsis - Brassica Eight linkage groups (Gl-8) of B. rapa compared to five A. thaliana chromosomes A. thaliana