Genome Size Variation: Consequences and Evolution Ilia Leiten and Martin Lysak Genome size variation: consequences and evolution (i) How genome size varies across plants (ii) What are the consequence of this variation (iii) How did such variation evolve C-value paradox • A. Boivin, R. & C. Vendrely (Boivin et al. 1948, Venderely & Vendrely 1948) - systematic comparisons of DNA contents in different cattle tissues (thymus, liver), liver from pig and guinea pig: - remarkable constancy DNA amount in different tissues - approx. double of DNA content in sperm - 'constancy in DNA amount is PROBABLY proportional to the number of genes' • Mirsky & Ris (1951) discovered totally unexpected finding: 'an aquatic salamander has 70x as much DNA as is found in a cell of the domestic fowl' • more studies confirmed the phenomenon >> C-value paradox (C.A. Thomas, 1971) - simple organisms have more DNA than complex ones - organisms have more DNA than would be predicted from gene number - some morphologically similar groups have divergent DNA contents Non-coding DNA was not known in that time. Today C-value paradox is replaced by C-value enigma (T.R. Gregory, 2001) The Origin, Evolution and Proposed Stabilization of the Terms * Genom e Size' and 'C-Valuc' to Describe Nuclear DNA Contents JOHANN GRE1LHUBER1*. JAROSLAV DOLEŽEL1, MARTIN A. LYSÁK3 and MICHAEL D. BENNETT* Holoploid genome - the whole chromosome set with chromosome number n (irrespective of polyploidy, aneuploidy etc.) Monoploid genome - one chromosome set of an organism and its DNA having the chromosome base number x Genome size - covering term for the amount of DNA in both holoploid and monoploid genomes Sometimes terminology matters... • C-value - DNA content of a holoploid genome with chromosome number n • 1 C-value - DNA content of one non-replicated holoploid genome with chromosome number n (= the half of a holoploid non-reduced genome with the chromosome number 2n); cf. 2C-value, 4C-value,... • Cx-value - DNA content of a monoploid genome with chromosome base number x • Diploids: 1 C-value = 1Cx-value Polyploids: example 2C-value of allohexaploid wheat (Triticum aestivum; 2n=6x=42) is 34.6 ^^ 1 C-value: 17.3 pg; 1Cx-value: 5.8 pg (34.6 : 6) Remember ! 1 pg = 980 Mbp C means Constant (Swift H. 1950. Proc. Natl. Acad. Sei. USA 36: 643-654.) Plant ONA C-values database VALUE www.kew.org/genomesize/homepage.html 5150 species Land plants 4427 angiosperms 207 gymnosperms 87 pteridophytes 176 bryophytes Algae 91 Chlorophyta 44 Phaeophyta 118 Rhodophyta KeV' PLANTS PEOPLE POSSIBILITIES C-values m angiosperms range nearly 2000-fold Genlisea margaretae Utrioirtmifin rfäiJňfái folium Fritillaria assyriaca 1C = 0.065 pg ICTC&OWhpBpg 1C = 127.4 pg Greilhuber eř al. 2006. Greilhuötff eí af, 3Q8& Plant Biology PlantTQItÓOjg/íya 8: 770-777 8:37:0í3^-1338 Bennett. 1972. Proc. Roy. Soc. Lond. B 181: 109-135. +j TO a ■ö a) a) co V i^; Angiosperms (1.4%) Gymnosperms (25%) Monilophytes (0.6%) Lycophytes (0.4%) Bryophytes (1%) 0.065-127.4 2.3-36.0 0.8 - 72.7 0.16-12.0 -r 25 50 75 100 0.09 6.4 -I 0 I25 I50 1C DNA amount (pg) Range of DNA Angiosperms Gymnosperms Monilophytes Lycophytes Bryophytes Phaeophyta (2.9%) Rhodophyta (1.8%) Chlorophyta (1.3%) ÄU amounts in algae 0.065-127.4 2.3-36.0 0.8-72.7 0.16-12.0 0.09-6.4 0.1 -0.9 0.017-1.4 0.013-23.4 0 25 50 75 100 125 ISO K DNA amount (pq) Smallest, free living plant Ostreococcus tauri (Prasinophyta) 1C = 0.013 pg (12.5 Mb) (smallest chromosome of A. thaliana has 17 Mb) Chrétiennot-Ďinet eta/. (1995) PhycologiaZA: 285-292. Unicellular green alga Osfreococcus fauri(Prasinophyceae): the world's smallest free-living eukaryote Derelle et al. (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. PN AS 103 The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Genome size variation / Fritillaria assynaca 1C = 127.4 pg Genlisea margaretae] 1C = 0.065 pg Sg ■** *- i-: -\ 0.1 ^m Osŕreococcas ŕaari 1C = 0.01 pg C-value enigma Gregory TR. 2001. Coincidence, co-evolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews 76: 65-101. Mechanisms of DNA amount increase in plants • (Paleo)polyploidy • Amplification of transposable elements, TEs (especially retrotransposons) Bennetzen & Kellogg (1997) Ďo Plants Have a One-Way Ticket to Genomic Obesity? We do agree, however, that a mechanism that leads to rapid increases in genome size does exist. Thus, unless evidence for a comprehensive mechanism for removing interspersed repetitive DNAs is found, and/or strong selective pressures for reducing genome size can be determined, we must conclude that plants may indeed have a one way ticket to larger genome sizes. Approx. linear relationship between genome size and the amount of TEs Atgllcps >pp. 8.3, 11.0. 13.0 Tri t team arartu 11.4 icum monccoccum 7.0, 11.3, 11,0 Tetni&ttlerum captlt-madusat 8,fl Seca't Cŕľ**í* 18.S Hordcum vulgar* 1 0.0 Brentu* *pp. 11 ,* Feacuca spp. 5.6 ivtivm spp- 5,3 Br Izs maxima 10.6 Dt 3 champs I a spp. 5.4, 10.0 Csrynephtrua canasctns 2.3 Aiapr curtly recombination between two 5 LTRs, two 3 LTRs, or the 33Pm&<: ■ '" '-■*^=ciB=t=> internal regions of two elements. mi__________ppf IHDJI I TB ~l PBS _L-__- F°H | .Tit M Mri" f-TB "I- ruš -Ti—i i I*" I -l- FFT\_LJS_tn$, I ■*am=tz> (E) "Solo" LTR resulting from recombination between 3 and 5 LTRs of two elements. Double-strand break repair and genome size Background Puchta (2005) Double-strand breaks (DSBs) have to be eliminated before genomes can be replicated. Therefore, the repair of DSBs is critical for the survival of all organisms. Generally, DSBs can be repaired via two different pathways: • homologous recombination (HR) • non-homologous end-joining (NHEJ; also known as illegitimate recombination) Literature Kirik et al. (2000) EMBO Journal 19: 5562-5566. Orel et al. (2003) Plant Journal 35: 604-612. Orel and Puchta (2003) Plant Mol Biology 51: 523-531. Puchta (2005) / Exp Bot 56:1-14. Double-strand break repair and genome size Kirik et al. (2000) A comparison of deletion formation in somatic cells of tobacco and Arabidopsis, two plant species with an over 20-fold difference in genome size. Surprisingly large differences in DSB repair were found: - the overall length of the deletions was about one-third shorter in tobacco than in Arabidopsis. Thus, there is an inverse correlation between genome size and the medium length of deletions could be detected. Reasons? Orel and Puchta (2003) During DSB repair the size of a deletion depends on the processing of DNA ends. If broken ends are not religated directly the processing of such ends might result in the loss of DNA at the break site. Depending on the efficiency of DNA degradation more or less information will be lost. Indications were found that plasmid DNA is degraded to a lesser extent in tobacco than Arabidopsis. Chromosome number reduction via pericentric inversion-reciprocal translocation events pericentric inversion reciprocal translocation mini-chromosome eliminated DNA loss Is there genome size equilibrium ? Genome size INCREASE Genome size DECREASE Variation of genome size: Consequences at nuclear level Anderson etal. 1985. Exp. Cell Res. 156: 367-378. Baetckeeŕa/. 1967. Proc. Natl. Acad. Sei. USA 58: 533-540. Variation of Consequenc ~ 30 Mitosis T---------r 30 60 90 100 DNA amount per cell (pg) Van't Hof & Sparrow AH. 1963. Proc. Natl. Acad. Sei. USA 49: 897-902. genome size: es of timing Meiosis £, oUU o | 200h ° 1 ■2 100H 3 Q y* íl i 15 30 45 1C DNA amount (pg) Bennett MD. 1977. Phil. Trans. Roy. Soc. B 277: 201-277. Variation of Consequences at c Relationship between pollen volume and DNA amount in 16 grass species. Bennett etal. 1972 genome size: ell and tissue level Relationship between seed weight and DNA amount in 12 Allium species. Bennett era/. 1972 Consequences of variation \r\ DNA amount Whole plant level a) Life cycle options b) Life strategy options c) Ecology options d) Coping with environmental change Consequences of variation \r\ DNA amount Whole plant level a) Life cycle options Bennett MD. 1972. Nuclear DNA content and minimum generation time in herbaceous plants. Proceedings of the Royal Society of London Series B-Biological Sciences 181: 109-135. Consequences: life cycle options 400 » 30° "to o "Ö5 £ 200 o c o 2 100 Q Fhtillaha meleagris 1C = 70.7pg 0 50 100 150 200 3C DNA amount (pg) 250 Bennett MD. 1977. Phil. Trans. Roy. Soc. B 277: 201-277. No species in this triangle Obligate | perennials I A 1^ 1 3 _l A Ó < H Annuals and ^^^^^H O Max. limiting DNA amount—► • for ephemerals á B^m ťí(|Í Ephemerals BBfflfflffl|||||||||||||||fl^ffl f ^Bi & i r^K X B Í weeks weeks MINIMUM GENERATION TIME Bennett MD. 1972. Proc. Roy. Soc. Lond. B181: 109-135 Consequences of variation \r\ DNA amount cycle options Conclusions DNA amount can impose limits on the type of life cycle a species can display Species with small genomes may be ephemerals, annuals or perennials Species with large genomes are restricted to being obligate perennials Consequences of variation \n DNA amount Whole plant level a) Life cycle options b) Life strategy options c) Ecology options d) Coping with environmental change Consequences of variation \r\ DNA amount Whole plant level b) Life strategy options: Potential to become a weed Bennett, Leitch & Hanson. 1998. DNA amounts in two samples of angiosperm weeds Annals of Botany 82: 121-134. Consequences: option to be a weed Method DNA amounts for 156 angiosperms recognised as weeds compared with 2685 non-weed species 250 u, 200 a) o 150 d) » 100 o d 50 0 Non-weed species (c. 0.1 - 127.4 pg) Mean 1C 7.0 pg 0 Max = 127.4 pg 25 50 75 100 125 1C DNA amount (pg) 25 20 ü 15 S" io ° 5 O z o i 0 Weeds (0.16-25.1 pg) Mean 1C 2.9 pg Max = 25.1 pg ■ ■f ^~j i i i i i i i r 25 50 75 100 125 1C DNA amount (pg) Bennett, Leitch & Hanson. 1998. DNA amounts in two samples of angiosperm weeds. Annals of Botany 82: 121-134. Success of an invasive weed Rapid establishment or completion of reproductive development Short generation time Rapid production of many small seeds Consequences of variation \r\ DNA amount Whole plant level a) Life cycle options b) Life style options c) Ecology options d) Coping with environmental change Pop. Several Picea sitchensis Sp. Tropical vs. temperate grasses Sp. 329 tropical vs. 527 temperate plants Sp. 17 Poaceae and 15 Fabaceae crops Pop. 24 Berber is in Patagonia latitude Miksche 1967, 1971 Avdulov 1931 Levin and Funderburg 1979 Bennett 1976 B ottini et al. 2000 + correlation Consequences: ecology options 401 species . in the state of California frUnd Knight & Ackerly. 2002. Variation in nuclear DNA content across environmental gradients: a quantile regression analysis. Ecology Letters 5: 66-76. c O E Species with large genomes excluded from extreme environments Species with small genomes can occupy all environments Ecological parameter e.g. temperature Knight & Ackerly. 2002. Ecology Letters 5: 66-76. Consequences: ecology options Summary The relationship between genome size and environmental factors is not uniform but appears to be stronger for species with large genomes Species with large genomes are excluded from extreme environments Consequences of variation \r\ DNA amount Whole plant level a) Life cycle options b) Life style options c) Ecology options d) Coping with environmental change (i) Pollution (ii) Threat of extinction Consequences: Coping with environmental change Pollution: The question What effect does genome size have on the survival of plants in lead polluted soils? B. Vilhar, T. Vidic and J. Greilhuber Consequences: Genome size and pollution «Ali 1 ***" ™ ■ y}*3 *&£& %É^ 'írV liff'^.J*.. ; I Lead smelter Smelter chimney Study plots Dolina smrti in Slovenia Consequences: Genome size and pollution Reference plot Cone, lead in soil = 0.1% ■ m I ■! ^ '■ ■ da / % ' ':% 670 m O 520 m 420 33ftjm Cone, of lead in soil 0.7% 1.5% 2.0% Smelter chimney Lead smelter ^* i -«fc. a Conseque Genome size at '&* -iiJs^v-^ 670 m O 520 m 420 m <ř> *a^- .* i- SSfi +1- JE Consequences: Genome size and pollution Percentage of species with large genomes in individual plots in oU " .Reference plot O U) • Í 20- • • pecies' genom o ■ • w **- o Site closest 0 to smelter """"■».^ 0 10 20 30 1 Concentration of Pb (g kg ) Consequences: Genome size and pollution Conclusions Species with large genomes are at selective disadvantage in extreme environmental conditions induced by pollution. Consequences of variation \r\ DNA amount Whole plant level a) Life cycle options b) Life style options c) Ecology options d) Coping with environmental change (i) Pollution (ii) Threat of extinction Consequences: Genome size and threat of extinction wmmm ;v%i-:.b§f.- ■^ Is genome size important? Vinogradov AE. 2003. Selfish DNA is maladaptive: evidence from the plant Red List. Trends in Genetics 19: 609-614. Consequences: Genome size and threat of extinction Data and analysis iPlant DNAl C-values database VALUE 3036 species Global concern = 305 Local concern = 1329 No concern = 1402 Vinogradov AE. 2003. Selfish DNA is maladaptive: evidence from the plant Red List. Trends in Genetics 19: 609-614. Consequences: Genome size and threat of extinction U) 1 7 N 1-0 "35 (0 c o o a> N "35 a> E o c a) O 0.0Ö 0.06 0.03 0 -0.03 -0.06 * * No concern Local concern \ Global concern Conservation status Vinogradov AE. 2003. Trends in Genetics 19: 609-614. Consequences: Genome size and threat of extinction Conclusions Species with large genomes are at greater risk of extinction than those with small genomes. - Independent of life cycle type (at least partially) - Independent of polyploidy Consequences: Genome size and threat of extinction DNA amount variation and consequences Summary O Huge variation in DNA amount in plants O Consequences of this variation visible at: Cellular level Tissue level Whole organism level O Possession of large genomes appear to impose constraints which operate at: Functional level Ecological level Evolutionary level Variation of genome size 1. Consequences of genome size variation in plants 2. Evolution of genome size variation Modified from: Leitch, Chase, Bennett MD. 1998. Annals of Botany 82: 85-94. i------ Asterids(SlS) i— Soxif rag ales (45) "L Rasids (1097) ------ Santalales ------ CaryophyUtiles (133)+ i— Berberidopsidaceae [1) I— Aextoxkaceae (0) ------- Gunnerales (1) ------- Trochodendro«ae{l) ------- Buxnteae (2J ------- Proteales(3) ------- Sablaceae ------- Ranunculal«s (192) ------- (hlo rant hate ae (3) ------- Ceratophyllaceae [1) ------- magnolilds (65) ------- Monocots ____ Austro bailey a les (7) ____ Nymphaeateae (2) ____ Amborellateoe (1) T-------1-------1-------1-------1- 25 50 75 100 125 K DNA amount (pg) Q) O o .y O T3 D d) D) C Ô) tfí d) > o u I1 o o ■B 3 LU V) E i_ a) Q. tn g Bi c CC tn (O CD Angiosperms with Very large' genomes (> 35 pg) MONOCOTS Liliales A - Lihaceae - Melanthiaceae As pa rag a I es - Alliaceae - Alstroemeriaceae - Orchidaceae - Xanthorrhoeaceae Commelinids - Commelinaceae CORE EUDICOTS Santalales - Santalaceae Viscum Large scale analysis of genome size evolution in angiosperms Data: Method: Genome sizes for 4,119 species The 'All most parsimonious states' resolving option of MacClade C-value range <1.4pg ^ 3.5 pg 3.51 - 13.99 pg >14pg >35pg Description Very small Small Intermediate Large Very large Soltis, Soltis, Bennett, Leitch. 2003. Am J Bot 90: 1596-1603. Large scale analysis of genome size evolution in angiosperms Out-group BASAL' ANGIOSPERMS EUDICOTS monocots magnoliids early diverging eudicots core eudicots #"5? 5 iilW «MfltLkH! lillilllli . fhi ífiíiilifF I iiiyiiiiiiifiiiiiiiiiJlllJJlJlillil! as „ & i u ill. IUI?!* ■3 -B * -8 DDDDSSaDDBQDQIDDDDEIDDnDDBGDCIDDaDlnnnDDnDDnDnaHDDDnilSDnnDDGBSaDDEinnSaiDQDBDIEinnnDDIDDDIS Hf5ä£53f^ď^^2äl#j Prótea I es Ranunculales Caryophyllales magnoliids eudicots monocots All angiosperms 1C value (pg) (unordered) I I Very small (£1.40) Small (1.41-3.50) 3 Intermediate (3.51-13.99) I I L.irgť (14-34.99) ^H Very large (>35) 1- • -1 Equivocal 80 Reconstruction of C-value diversification across angiosperms Out-group BASAL ANGIOSPERMS EUDICOTS en OJ oj n; a; BS OJ £ O) u ES -fí ^SU-S « S o q h Ö P ^ "tí rÜ S R U DDQDBDDDD core eudicots HU I í |g * š š 3 Si ^ a U j u uuo S < DDQDOFs a«aa d s »III m E 1 öBBonDonsiDnnH 111 03<<<íxí5k IC value (pg) (unordered) I I Very small (<1.40) Small (1.41-3.50) 3 Intermediate (3.51-13.99) I Large (14-34.99) | Very large (>35) y • -i Equivocal 8368 Reconstruction of C-value diversification across angiosperms BASAL ANGIOSPERMS EUDICOTS monocots core eudicots y • 1 Equivocal 80 Acknowledgements Jodrell Laboratory,Royal Botanic Gardens, Kew, UK Mike Bennett Mike Fay Lynda Hanson Masaryk University, Brno,Czech Republic Martin Lysak California Polytechnic State University, USA Charley Knight Arjun Pendharkar Biological Sciences, Yale University, USA Jeremy Beaulieu The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae Ma r t in Lvsak, * Ma re us Koch;\. Jerem v Beau lie u,í Armin M ei s ter,§ and ilia Le it ch\\ * Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Masaryk University. Brno, Czech Republic; tHeidelberg Institute of Plant Sciences, Biodiversity and Plant Systematics, University of Heidelberg, Heidelberg, Germany; 2 Department of Ecology and Evolutionary Biology, Yale University; § Leibniz-Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany; and ||Jodrell Laboratory, Royal Botanic Gardens, Richmond, Surrey, Kew, United Kingdom Crucifers (Brassicaceae, Cruci ferae) are a large family comprising some 338 genera and c, 3,700 species. The family includes important crops as well as several model species in various fields of plant research. This paper reports new genome size (GS) data for more than LOO cruciferous species in addition to previously published C values (the DNA amount in the unreplicated gametic nuclei) to give a data set comprising 185 Brassicaceae taxa, including all but I of the 25 tribes currently recognized. Evolution of GS was analyzed within a phylogenetic framework based on gene trees built from five data sets (matK, ciis, adh, rr/iLF, and ITS), Despite the l ň,2-fold variation across the family, most Brassicaceae species are characterized by very small genomes with a mean IC value of 0.63 pg. The ancestral genome size (ancGS) for Brassicaceae was reconstructed as jnMC = 0,50 pg. Approximately 50% of c rue if er taxa analyzed showed a decrease in GS compared with the ancGS, The remaining species showed an increase in GS although this was generally moderate, with significant increases in C value found only in the tribes Anchonieae and Physarieae, Using statistical approaches to analyze GS, evolutionary gains or losses in GS were seen to have accumulated disproportionately faster within longer branches. However, we also found that GS has not changed substantially through time and most likely evolves passively (i.e., a tempo that cannot be distinguished between neutral evolution and weak forms of selection). The data reveal an apparent paradox between the narrow range of small GS s over long evolutionary time periods despite evidence of dynamic genomic processes that have the potential to lead to genome obesity (e.g., transposable element amplification and polyploidy). To resolve this, it is suggested that mechanisms to suppress amplification and to eliminate amplified DNA must be active in Brassicaceae although their control and mode of operation are still poorly understood. Genome size (pg) HUE aiiFiiii lulaúT UüUtkV 3rlü_-| UHiltfT.i TAnUiu-i ■." "i ľ . luiiFUMrifruJia íúKTMhlŕali irr i:.--;: '»Uhr*- um& :*:;■ iciim: ;....,., , [tXJ Milní ........:: IithJd a'i[3 :-rffa ú ;vYjiH KWum'i ÚJ.■ K:■ i < D U* H-Ui IT I -n D 3 Q- H CO OJ Basic facts on GS evolution in Brassicaceae 1C DNA amount (pg) the 16.2-fold GS variation across the family mean 1C = 0.63 pg crucifers have very small (< 1.4 pg) or small (< 3.5 pg) genomes (Leitch et al. 1998) ancGS 1C = 0.54 pg GS has not changed substantially through time GS evolves most likely passively (i.e., a tempo that cannot be distinguished between neutral evolution and weak forms of selection) an apparent paradox of GS evolution: the narrow range of small GSs vs. genomic processes leading to genome obesity (e.g., transposable element amplification and polyploidy) poorly understood mechanisms suppressing amplification and/or eliminating amplified DNA must be active Paradox of GS evolution in Brassicaceae'. large genomes in (some) species with a low chromosome number Í4 chromosome no. increase, GS increase chromosome no. decrease (diploidization) GS stasis or decrease Y^afterTang eta/. (2008) ^ ^ ^ CL n QJ ■co CL n QJ ^ Ě? ft) 8L CTQ CD O 3 CD n QJ neopolyploid duplications paleopolyploid duplications