Genome and chromosome synteny and col linearity 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 ANN DES PAP. PET 1 ^7 •J ■■; ■J % i 3 § s -z g ■í ■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 l3 1 3 -1 1 3 * o J o U 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 «NN ANO DES PAR PET ANN ANO DES PAR PET / / í i ■2 S s T» I 1 ANN ANO DES PAR PET ANN ANO MS PAR PET < -J 3 S ■1 J ■i '■-. 3 4 'i 3 -r. -] iL : ■r, •3 ANN ANO DES PAR PET Segments containing inversions are indicated by hatched lines. ANN ANO DES PAH PET ANN ANO DES PAR PET ANN ANO DES PAF PET ■--5 -í ■■■ r--5 I ■í 5 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 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 • 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). opinion in Plant Biology • 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 Level of genome conservation between legume species (Fabaceae) Macrosyntenic relationship of Medicago truncatula and Lotus japonicus Line color indicates the number of conserved genes between two clones: black, two; blue, three to four; red, five or more. M- tmncstuh Medicago truncatula (n=6) M. sativa (n=16) Pisum sativum (n=7) Glycine max (n=20) Vigna radiata (n=11) Phaseolus vulgaris (n=11) Lotus japonicus (n=6) ■" ■■ ■" Id eU • broad conservation of genome macrostructure • chromosomal rearrangements that may underlie the variation in chromosome number between the species Lotus japonicus Consensus comparative map data for 6 legume species • comparison between M. truncatula, L. japonicus and G. max -^ high conservation between the genomes of M. truncatula and L japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max Choi efal. 2004 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 rxror "TÍUMCÍI*1 MIK ĚE r^i dTTÜHll--------- j~| Tí« __«rnEH E» lEpC+iJO v.j ■<-» I rj "- " I 11 ľ "V "ii I »<"■ I «i» n,r!l.Lh>-_L ■ JJ.l^M ji 'VJ-JUT1BA I Ifc 3 \\\ UK r*ľi r^~ k-I MM It----K-_|jf-0«Wfll I-" '■ rp*r«-n •(-»"■ X ÍÍ^ffJi^itmbY i—-i UK í! . »j-.i!—Fyj wi-M — mm I ?i HU I H ,ir^-ťV lLiIuii ■'-- ■ "" bo i lunuľi CED ♦• »jbhhfjcj -'iwi.jiíH.iflsi I • 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 collinearity in crucifers (ßrass/caceae) • eight linkage groups of Arabidopsis lyrata and Capsella rubella (n=8) show a high level of collinearity to the five chromosomes of A. thaliana (n=5) • A. lyrata and C. rubella genomes exhibit almost identical structure AL3 sctol Fusion/breakage 1 nversion 3 \&J lnnHiS«n7 Ts) Inversion 5 -^T1 * LI At I f A J Lysak <& Lexer 2006 Genome col linearity in crucifers: Arabidopsis - Brassica Eight linkage groups (Gl-8) of B. rapa compared to five A. thaliana chromosomes A. thaliana ch 1 2 3 urn romosomes 4 5 n • B. rapa and all modern diploid Brassica species have triplicated genomes and probably descended from a hexaploid ancestor • the duplications were accompanied by an exceptionally high rate of chromosomal rearrangements • the B. nigra linkage groups show a typical pattern of relatively large blocks of markers from particular A. thaliana chromosomes interrupted by a few markers from one or more other from A. thaliana chromosomes Lagercrantz 1998 Painting the A. thaliana genome 38.0 30.2 Mb 262 o, o 27.8 26.8 X x X Q Chromosome painting in Arabidopsis 8 8 u Lysak et al. 2001 Pecinka et a/. 2004 Studying genome and chromosome collinearity across the Brassicaceae by comparative chromosome painting (CCP) Fluorescently labelled Arabidopsis BAC contigs are hybridized in situ to pachytene chromosomes of other cruciferous species CC? in Brassicaceae* Arabidopsis BAC contigs designed according to the Arabidopsis-^ rubella comparative map modified from Boivin et al. 2004 G Chromosome collinearity between A. thaliana and closely related ßrass/caceae species Chromosome homeology and chromosome number reduction in Nesliapaniculata {r\-7) Ancestral Karyotype AK1 AK2 AK3 AK4 AK5 AKS AK7 AK8 ill Neslia \z J I f AK4/5 4 AK2<3» ť **f ^\ v AK4/5 ^ * I E ^=> AK4 Q AK4/5 r ^ AK5 Ancestral Karyotype AK1 AK2 AK3 AK4 AK5 AK6 AK7 AK8 M fl Chromosome homeology between the Ancestral Karyotype and two n=6 species Turr itis glabra (n=6) AK3 AK3/5 HI AK2/8 n e ^> AK3/5 P AK2'5 AK5 Hornungia alpina (n=6) AK6 AK6/8 ^yT|-| AK6/8 AK8 There is high level of chromosome homeology and collinearity shared by A. thalianaand its close relatives Ancestral Karyotype (n=8) AK1 AK2 AK3 AK4 AK5 AK6 AK7 AK8 * ■ * * * A. thaliana J If J tr n=5 H. alpina III1. n=ó Chromosome number reduction in the Arabidopsoid dade followed different scenarios and involved different ancestral chromosomes A. t y rat a 1 I I I * ' ' "Hi Ancestral n=8 Karyotype n=7 N. panicuiata ■ ■ i* = 1 n=B C. rubella Ancestral Karyotype Lysak et a/. 2006 23 The ABC's of comparative genomics in the Brassicaceae* Ancestral Karyotype Ancestral karyotype (AK) Arabidopsis lyrata and Capsella rubella AK1 AK2 AK3 AK4 AK5 AK6 AK7 AK8 D I K ol R v A ■ L P o E F I ■ ŕ t" w J M Q x | b G, U u H N R C Lysak et a/. 2006 • the building blocks can be rearranged to model the genome structures of A. thaliana, A. lyrata, Capsella rubella, Brassica rapa and other crucifers rends:;---------- Plant Science • unified comparative genomic framework across Brassicaceae • system of 24 conserved chromosomal blocks (A-X) • order, orientation and color-coding of the blocks are based on their positions in the Ancestral Karyotype (n = 8) Building blocks of crucifer genomes NO signal at the crossroads Bio-hydrogen production Photoperiodic control of flowering Novel traits through RNA interference Acc.snicl Schranz, Lysak & Mitchell-Olds 2006 24 ancestral building blocks were identified to model karyotypes of A. thaliana, B. rapa and other crucifer species .<■ i ■— AUgOOOH r _. A13^55K> T tAi3g25W4 AOg29772 u s — At3^tar40 _ At3^iH!tJ"Q AUgOftfSö _- At4tji2nrQ ~ AHglHr&Q - At4ť|lB14S "■ At4g16250 AM g3S770 : A. thaliana (n=5) . At5g22Ů» - AL5g3?5ůů Aljg2&í Í7 Acgraai AEg+iSQO - ALSgiHTO _. Al5g603» - At5gSD550 IOL" N1 N2 N3 N4 N5 N 1 1 + Ml M V K Q I N 6 h I 'I B X D 1 _ "Íl V Ľ N7 N8 N9 N10 Oil QI a|i p| a w l Brassica rapa (n-10) TRENDS in Plant Science Genomic building blocks based on the ancestral karyotype will facilitate genome comparisons across Brassicaceae Schranz, Lysak <& Mitchell-Olds 2006