Contemporary plant cytogenetics • chromosome number changes (^ karyotypic variation) • structural chromosome changes (e.g. centromere repositioning) • collinearity and karyotype evolution (cross-species FISH and chromosome painting) Extraordinary Tertiary Constrictions of Tripsaciim dactyloides Chromosomes: Implications for Karyotype Evolution of Polyploids Driven by Segmental Chromosome Losses Dai-Hoe Koo and Jiming Jiang1 Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 Genetics 179 (2008) Extraordinary Tertiary Constrictions of Tripsacum dactyloides Chromosomes: Implications for Karyotype Evolution of Polyploids Driven by Segmental Chromosome Losses c 1 W {; . w * • ''*< í*" ^ Knob repeal * TF-B5-3 I Extraordinary Tertiary Constrictions of Tripsaciim daciyloides Chromosomes: Implications for Karyotype Evolution of Polyploids Driven by Segmental Chromosome Losses h An ideogram of the karyotype and a model of segmental chromosome loss in 7. dactyloides. Type II chromosome is the product of a terminal deletion of a type I chromosome. The small arrow points to the deletion breakpoint that is possibly linked to a tertiary constriction. The origin of a "Zebra" chromosome in wheat wheat CENs Elymus CEN z5A 2 zebra z5A + 40 wheat chromosomes Zhang et al. 2008, Genetics179 The origin of a "Zebra" chromosome in wheat via nonhomologous recombination £5fi, itf Chromosome z5A might have originated from nonhomologous recombination between 5A and 1 HtS chromosomes. 1) Initially, at least five breaks occurred in chromosome 5A, resulting in six chromatin blocks. 2) Four breaks in the 1HtS telosome split it into five chromatin blocks. 3) Rejoining of the prealigned 5AL and 1HtS blocks resulted in the formation of chromosome z5A. It was accompanied by the complete loss of 5AS, including the telomere and the loss of a very small distal centromeric end of 1 HtS. Special A * Speckes B n=l " n=2 Whole genome duplbcallon SftedeiQ n>3 Novel mechanism of step changes in chromosome number (chromosome number reduction) Centromere repositioning in curbit species Cross-species fosmid FISH in cucumber and melon (Cucurbitaceae) A Cucumber chromosome 7 B 7 í t 1^ i • .1 - 7-s • 1 -*-Cen * • c Melon chromosome II D * » .7-1 * * 7-3 *-Cůn • | - 7-6 t * » $ • • • __—7-3 74 ^^-70^ 7-6- .- 7-8 v^ — 7-7 - H ,.i- CLHíímber i-lirünHMmlL'7 '!.■■.■■■ tlmjuHsnnie II Hanetal. 2009, PNAS106 Fosmids (40 kb) are based on the bacterial F-plasmid. The cloning vector is limited, as a host (usually E coli) can only contain one fosmid molecule. Low copy number offers higher stability than comparable high copy number cosmids. Cm Cucumber chromwomro Melon (.JircilníMíiiii- ] Centromere repositioning in curbit species • centromere repositioning (CR) extensively documented in mammalian species (e.g. 5 CRs in the donkey after its divergence from zebra) scarce reports on CR in other eukaryots including plants • centromeres of cucumber and melon chromosomes are associated with distinct pericentromeric heterochromatin • centromere activation or inactivation were associated with a gain or loss of a large amount of pericentromeric heterochromatin c o o Cucumis melo 2n = 24 Cucumis sativus 2n = 14 Karyotype evolution \r\ Brassicaceae Chromosome painting (CISS) Chromosome painting generally refers to in situ identification of large-scale chromosome regions or whole chromosomes using chromosome-specific DNA probes (Pinkel et al. 1988, PNAS8S) Chromosomal In Situ Suppression (CISS) - unlabelled total genomic DNA or C0t-1 DNA (DNA fraction enriched for repetitive sequences) are used to suppress unspecific repetitive sequences from hybridization (Lichter et al. 1988, Hum Genet SO) Langer et al. (2004) Chromosome painting in human and animal cytogenetics Human metaphase chromosomes after the simultaneous hybridization of 24 differentially labelled chromosome painting probes SI X )) n u >%>- H mum nu ■ u ji n ii n IJ II II IS n n JI Comparative chromosome painting Human metaphase and interphase after hybridization with a chromosome-specific paint probe set derived from gibbon chromosomes fi n n E. Schröck, S. du Manoir, and T. Ried «:,: O o o I—I- cq' í At 1 Lysak et al. 2001, 2003; Fransz et al. 2002; Pecinka et al. 2004 Multicolour chromosome painting in Arabidopsis 2 3 4 5 q | Lysak et al. 2001, 2003; Pecinka et al. 2004 Comparative chromosome painting in Brassicaceae At1 Arabidopsis BAC contigs Brassicaceae is the only plant family in which large-scale comparative chromosome painting (CCP) is feasible Evolutionary and comparative cytogenetics in Brassicaceae W > Ar ' extent of chromosome homeology across the family chromosome number variation and karyotype evolution paleo- and mesopolyploid evolution evolutionary significance of karyotypic variation The way to an ancestral crucifer karyotype comparative genetic mapping showed that karyotypes of A lyrata (n=8) and Capsella rubella (n=8) are almost identical x=8 is the most frequent base number found in all Brassicaceae lineages, in consequence, x=8 is regarded as an ancestral chromosome number of the family Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species Martin A. Lysak*^ Alexandre Berr*, Ales Pecinka*, Renate Schmidt6, Kim McBreen11, and Ingo Schubert1 Proc. Natl. Acad. Sei. USA 103: 5224-5229 (2006) n = 8? ■ Hornuníäia ni pi na i . Unhedgea minutí flora I D«CUíalľlleae n=8? n = 8 revealing the extent of chromosome homeology and reconstructing evolutionary scenarios of chromosome number reduction... ■ calamine amara ■Nasturtium officinale Barbarea vulgaris ■Armnracia rusticana Rorippa aiphibia Smelowskia calycina | 5mebwikieae Lepidlům afMcanum ■Lepidlům virginicum ■Dtmorphocarpa «ilsUzenü . physaria fend led I Physane Erysimum capiratum ■ Arabidopsis thaliana H —U ■ Arabidopsis halieri ■Arabidopsis craatir Cardarnineae Lepidieae Camellneae , /—AraDiDopsns emails *-» *r—Arabidopsis 1 y rata fl —8 ^—Arabidopsis neglerm i Dlimarabidopsls pum i lay I Turritlí glabra n = 0|Camellr»ae nsiHa panlculata f\=t capseiia. bursa-pastori Capsplla rubell, Halimnlobos montana paswrivica a n=oi mein eat Pennellia lnngi folia Hg|irnokibeae Bailey et al. (2006) Pachycladon novae-zel andiae Trarisberingia bursifolia C ru ci h i mal aya hi mal ai ca Crud Himalaya iwallichii PolyCtertiUin fťemůntit Cuskkiella quad rl cos rata Nevada hoimorenrii fioechera laevigata Breche r a drumttondfi Boechera platysperma Camelineae The origin of the A. thaliana karyotype from a tentative Ancestral Karyotype (n=8) Ancestral Karyotype (n=8) AK1 AK2 AK3 AK4 AK5 AK6 AK7 AK8 DD A thaliana (n=5) AT1 AT2 AT3 AT4 AT5 Ipa/lpe Chromosome number reduction in Turritis glabra (n=6) and Homungia alpina (n=6) Turr itis glabra (n=6) AK3 AK3/5 HI AK2/8 1 II AK3/5 ^s—ü^> 1 AK5 Hornungia alpina (n=6) AK6 AK6/8 AK2/5 rpfhrj AK6/8 AK8 Chromosome number reduction followed different scenarios and involved different ancestral chromosomes NOR CEN A thaiiana Ml a = 1 n rr n=5 A /yrafa * n * U Ancestral Karyotype H alpina n ň AKÍ AK2 AK3 AK4 AK6 AK6 AK7 AK8 Q 1 n=7 n=8 N panh;tilata \ C. rubella II Ancestral Karyotype (n=8) Ancestral Karyotype pericentric inversion a reciprocal translocation mini-chromosome eliminated Ancestral Crucifer Karyotype (ACK): 8 ancestral chromosomes and 24 conserved genomic blocks TRENDS" | Plant Science Building blocks of crucifer genomes NO signal at the crossroads Bio-hydrogen production Photoperiodic control of flowering Novel traits through RNA interference Schranz, Lysak & Mitchell-Olds (2006) Trends Plant Sei. 11 AKÍ AK2 AK3 AK4 AK5 AK6 AK7 AK8 r\ B w D H K L M N r\ r\ O P ■ Q R S T U V w x w Crucifera ancestralis (n=8) Karyotype evolution in Brassicaceae ^ & f $ $ $ $ ŕ B i i ™ M » Ancestral Crucifer Karyotype (n=8) Aethionemeae Smelowskieae Lepidieae Descurainieae Physarieae Erysimeae Cardamineae Camelineae Halimolobeae Boechereae Camelineae Alysseae Cochlearieae Iberideae Noccaeeae Farsetieae Conringieae Calepineae Arabideae Thlaspideae Eutremeae Isatideae Brassiceae Schizopetaleae Sisymbrieae Aphragmeae Biscutelleae Heliophileae Chorisporeae Malcolmieae Hesperideae Anchonieae Euclid ieae Buniadeae Dontostemoneae Lineage I Lineage II Lineage III ACK: reconstructing karyotype and genome evolution across Brassicaceae ......*-* Lineage Brassiceae Isatideae, Sisymbrieae Eutremeae # ŕ # t> whole-genome triplication Calepineae Conringieae Noccaeeae AK2-AK5/6/8 reciprocal translocation secondary pericentric inversions Proto-Calepineae Karyotype (n=7) Ancestral Crucifer Karyotype (n=8) Lineage I ancestral karyotype (n=8) Mandakova and Lysak (2008) Plant Cell 20 i ■ •Mih"- -W r