Genome and chromosome
evolution
Martin A. Lysák
CEITEC, Masaryk University
www.plantcytogenomics.org
Genome and chromosome evolution
 genome size variation
 chromosome number variation
 variation in coding DNA amount
 variation in non-coding DNA
Genome size variation
Polychaos dubium
…perhaps the largest known genome –
670 billion base pairs (670 Gb)
(~200-times larger than the human
genome, 3.2 Gb; some authors suggest
treating the value with caution)
Eukaryotes: minimal chromosome numbers
Myrmecia pilosula „Jack jumper ant“,
Australia; males (haploid) n = 1, females
(diploid) 2n = 2
five angiosperm species
e.g., Haplopappus gracilis, Asteraceae,
n = 2
Eukaryotes: highest chromosome numbers
Polyommatus atlanticus
n = c. 220
fern Ophioglossum reticulatum
n = c. 530
Genome size   Chromosome number
decrease
increase
Variation in genome size and chromosome number is driven by 
two principal processes
DNA/genome duplication DNA recombination
recombination
Genome size increase
• amplification of retrotransposons
(and tandem repeats)
• gene and segmental duplications
• polyploidy
Genome size variation in angiosperms is driven by 
amplification (and elimination) of repetitive DNA
LTR (Long Terminal Repeat) retrotransposons (LTR‐RTs)
Gag – gene for the Gag protein
INT – integrase
PBS – primer binding site
PR – protease
RT – reverse transcriptase
VLP – virus-like particle
(a) rt is inserted into itself
(c) DNA structure after 2 rounds
of retrotransposition
(b) the event is repeated
Genome size increase by retrotransposition
(nested retrotransposon insertion)
Genome size increase by gene duplication
• replication slippage (errors in replication  gene
duplication)
• ectopic recombination (between two direct repeats,
typically TEs)
• unequal crossing-over in meiosis (due to missaligned
chromosomes)
• via retrotransposition = retrogenes (cellular mRNA is
transcribed into cDNA by reverse transcriptase of a
retrotransposon or retrovirus; retrogene does not
contain introns = lacking regulatory elements =
pseudogene, but can evolve into a functional gene)
Retrogenes
• mRNA is reverse-transcribed into cDNA and inserted in a new genomic position
inactive gene copy retrogene chimeric retrogene
(functional by capturing
elements of another gene)
Science 325, 995 (2009)
(overexpression)
Segmental duplications
• duplicated segment of chromosomal DNA 
(usually defined as  1 kb in length)
• either tandem or interspersed organization, 
either intra‐chromosomal or inter‐
chromosomal
• also known as low copy repeats
• human genome: 159 Mb gene‐rich duplicated 
(5.5% of the genome) = c. Arabidopsis genome
Variation in the segmentally
duplicated amylase locus in
humans
Polyploidy (whole‐genome duplication)
HegartyandHiscock2008,
CurrentBiol
AUTOPOLYPLOIDY
ALLOPOLYPLOIDY
Hegarty and Hiscock 2008,
Current Biol
Examples of allopolyploid speciation
T. aestivum (2n = 6x = 42)
T. turgidum
2n = 28
Ae. tauschii
2n = 14



Phylogenomic history of bread wheat (Triticum aestivum; AABBDD). 
Three rounds of hybridization/polyploidy.
Marcussen et al. (2014), Science
• the unicellular eukaryote Paramecium tetraurelia
• most of 40,000 genes arose through at least 3
successive whole-genome duplications
• most recent duplication most likely caused an
explosion of speciation events that gave rise to the P.
aurelia complex (15 sibling species)
• some genes have been lost, some retained
• many retained (duplicated) genes do not generate
functional innovations but are important because of
the gene dosage effect
Whole‐genome duplications in protozoa
Whole‐genome duplications in yeast
• genome comparison between two yeast
species, Saccharomyces cerevisiae (n = 16) and
Kluyveromyces waltii (n = 8)
• each region of K. waltii corresponding to two
regions of S. cerevisiae
• the S. cerevisiae genome underwent a WGD after
the two yeast species diverged
• in nearly every case (95%), accelerated
evolution was confined to only one of the two
paralogues (= one of the paralogues retained an
ancestral function, the other was free to evolve
more rapidly and acquired a derived function)
Kellis et al. 2004, Nature
First evidence of a WGD in plants
What does the duplication in the
Arabidopsis genome tell us about the
ancestry of the species? As the majority
of the Arabidopsis genome is represented
in duplicated (but not triplicated)
segments, it appears most likely that
Arabidopsis, like maize, had a
tetraploid ancestor …The diploid
genetics of Arabidopsis and the extensive
divergence of the duplicated segments
have masked its evolutionary history.
AGI (2000)
Nature 449, 2007
The formation of the palaeo-hexaploid
ancestral genome occurred after
divergence from monocots and before
the radiation of the Eurosids. Star = a
WGD (tetraploidization) event.
β
γ
αp The γ triplication may have been an ancient
auto-hexaploidy formed from fusions of three
identical genomes, or allo-hexaploidy formed
from fusions of three somewhat diverged
genomes.
Tang et al. 2008, Genome Res
WGD events in seed plants and angiosperms
Jiao et al. (2011) Nature; Clark and Donoghue (2017) Proc R Soc
399 – 381 319 – 297 Myr ago
Theres is evidence of ancient polyploidy throughout the
major angiosperm lineages. It means that a genome-scale
duplication event probably occurred PRIOR to the rapid
diversification of flowering plants
Charles Darwin’s abominable mystery solved (?)
"The rapid development as far as we can judge of all the higher
plants within recent geological times is an abominable mystery."
(Charles Darwin in a letter to Sir Joseph Hooker, 1879)
assumed ancient
whole-genome
duplication events
(e.g.  - gamma WGD)
De Bodt et al. 2005
Archaefructus liaoningensis
(140 million year old fossil)
 (319 – 297)
Afropollis
(245 million year old angiosperm pollen)
lag 27 – 65 million years
diversification (267 – 247)
Van de Peer (2017) Nat Rev
Genet (modified)
Dicots
Monocots
Angiosperms
Gymnosperms
Gamma (6x)
Epsilon (4x)
Tau (4x)
Multiple whole‐genome duplications
in evolution of land plants
PNAS 106 (2009)
Could WGD event(s) help plants to survive
the mass extinction (one or more
catastrophic events such as a massive
asteroid impact) at the Cretaceous–
Tertiary boundary ?
Possible establishment of polyploid plants following the K/Pg 
mass extinction (66 million y. ago)
Lohaus and Van de Peer (2016) Curr Opin Pl Biol
 WGDs clustered around the
Cretaceous–Tertiary (KT)
boundary
 the KT extinction event the
most recent mass
extinction (one or more
catastrophic events such as a
massive asteroid impact and/or
increased volcanic activity)
 the KT extinction event extinction
of 60% of plant
species, as well as a majority
of animals, including dinosaurs
28
Polyploidization – Diploidization cycle
„diploids“ polyploids
genome reshuffling
descending dysploidy (chromosome no. reduction)
genome downsizing and/or upsizing
diversification / species radiation
WGD – 4x / WGT – 6x
Wendel et al. (2016) Genome Biol
Whole‐genome duplication and diploidization
Genome diploidization: biased fractionation and (sub)genome dominance
Liang and Schnable (2018) Mol Plant
Subgenome 1
Subgenome 2
Biased (sub)genome fractionation and dominance can 
be explained by the mode of polyploidization
Class IIClass I
Garsmeur et al. (2013) Mol Biol Evol
The fate of duplicated genes
Adams and Wendel (2005)
Genome evolution through cyclic
WGD and diploidization
Genome size decrease
(downsizing)
• recombination
• chromosome rearrangements
Recombinational deletions after double-strand breaks (DSBs) – DSB repair
Chromosome rearrangements (…in principle again DSBs and recombination)
lost
Robertsonian translocationLarge‐scale deletion
• unequal homologous recombination including unequal crossing‐over
• illegitimate recombination (non‐homologous end joining, NHEJ)
Genome size decrease (downsizing)
Genome size decrease by unequal homologous 
recombination between two LTRs or between two LTR‐
retrotransposons
~70% of retrotransposon sequences in the A. thaliana genome are no longer autonomous:
solo LTRs = probably the consequence of unequal homologous recombination = inactive,
truncated elements cannot contribute to genome expansion
Deletion through unequal crossing‐over
complementary nucleotides
Two main pathways of non-homologous end joining (NHEJ)
DNA lost
(but some DNA can be inserted - filler DNA)
microhomology-mediated end joining (MMEJ)
NHEJ in plant somatic cells
• NHEJ seems to be the main mode of DSB repair in higher eukaryotes
• NHEJ might lead, in some cases, to genomic changes (deletions, insertions or various kinds of
genomic rearrangements)
• genomic alterations in meristematic cells can be transferred to the offspring
• alternative NHEJ can mediate genome size loss
Arabidopsis vs. tobacco (genome size larger in tobacco)
- tobacco: almost every second deletion event is accompanied by the insertion of filler sequence
- Arabidopsis: no insertions
- overall length of the deletions is about one-third shorter in tobacco than in Arabidopsis
>>> inverse correlation between genome size and the medium length of deletions
>>> ??? species-specific differences in DSB repair pathways can contribute to the
evolution of eukaryotic genome size ???
1C = 4.5 Gb
1C = 157 Mb
- A. thaliana (157 Mb) has lost 6 more introns than Arabidopsis lyrata (210 Mb) since the
divergence of the two species but gained very few introns
Chromosome number variation:
chromosome rearrangements
39
n = 8
n = 8
n = 7
n = 8
n = 5
n = 6
DSB
miss‐repair
Chromosome rearrangements results from double‐strand breaks 
and their miss‐repair
chromosome rearrangement
Chromosome rearrangements – the role of repeats
In organisms with repetitive DNA, homologous repetitive segments within one
chromosome or on different chromosomes can act as sites of DSBs and their missrepair,
i.e. non-allelic homologous recombination.
Deletion formation by breakage and rejoining
Deletion formation by intra‐chromosomal (unequal) recombination
Sometimes during meiosis two chromatids from homologous
chromosomes (A) are misaligned during a cross-over event
(B) as a result, one chromatid gained a duplicated region
and the another lost a deleted region (C). The duplication
as well as the deletion are inherited by resulting gametes.
Deletion (and duplication) formation by unequal cross‐over
misaligned homologous
chromosomes
Inversions
Inversions as balanced rearrangements are generally viable and show no particular
abnormalities at the phenotypic level. Many inversions can be made homozygous.
Inversion heterozygote - cells that contain one normal haploid chromosome set plus
one set carrying the inversion. Microscopic observation of meioses in inversion
heterozygotes reveals an inversion loop.
meiotic inversion loop
Inversion formation by intra‐chromosomal recombination
inverted repeats
inversion
Two types of inversions
mechanism of inversion formation: breakage and rejoining
Can be “adaptive” when it stabilizes/disrupt a superior combination
of alleles on a chromosome (examples seen in Drosophila)
Inversions and recombination: evolutionary significance
Inversions may suppress recombination
Chromosome rearrangements (typically inversions) may reduce
gene flow by suppressing recombination. Inversions allow genes
located in these regions to differentiate, in contrast to genes in
freely recombining collinear regions.
Reciprocal translocations
attachment of chromosome fragment to a
non-homologous chromosome (leading to
deletions and duplications in the progeny)
exchange of chromosome fragments
between non-homologous chromosomes
Unequal reciprocal translocation
Robertsonian translocations are the most
common recurrent structural anomaly in
humans, with about 1 in 1000 individuals
carrying this rearrangement. The carriers
of ROBs have 45 chromosomes instead
of the normal 46.
Robertsonian translocations ‐ ROBs (centric „fusions“)
• type of a reciprocal translocation between two acrocentric/telocentric chromosomes
• also called whole-arm translocations or centric-fusion translocations
• named after the American insect geneticist W. R. B. Robertson, who first described a
Robertsonian translocation in grasshoppers in 1916
• evolutionary significance >>> chromosome number reduction (from 2 acrocentric
chromosomes one metacentric chromosome)
lost lost
Dicentric ROB
(more frequent)
Monocentric ROB
Speciation by Robertsonia translocations („centric fusions“)
End‐to‐end chromosome translocations („chromosome fusions“)
centromere inactivation/elimination
In principle unequal reciprocal translocation with breakpoints in (sub)telomeric regions.
The second translocation product is minute and eliminated.
Chromosome „fusion“ – the origin of the human (dicentric) chromosome 2
2n = 48
2n = 46
2n = 48
2n = 46
Chromosome „fusion“ – the origin of the human (dicentric) chromosome 2
inactive centromere
active centromere
Chiatante et al. (2017), MBE
Did the origin of „fusion“ chromosome 2 contributed to reproductive isolation 
of hominid species from great apes?
2n = 482n = 48
2n = 462n = 46
• different no. of chromosomes  reproductive isolation
• loss of gene(s)  adaptive advantage
• gene linkage? changed regulation of gene expression?
57
Evolution of chromosome number and karyotype
Allopolyploid origin and diploidization in the tribe Microlepidieae (Brassicaceae)
• Australia: 15 genera, 47 species
• New Zealand: Pachycladon, 11 species
• chromosome number variation (from n = 4 to n = 24)
♂♀
Crucihimalayeae
n = 8
Descurainieae/
Smelowskieae
n = 7
allotetraploid ancestor
n = 15
INTER‐TRIBAL
HYBRIDIZATION
Pachycladon 
n = 10
crown group
n = 4 ‐ 7 n = 12
LONG DISTANCE DISPERSAL
(15 genera / 42 spp.)
Mandáková et al.
(2010) Plant Cell
(2010) BMC Evol Biol
(2017) Mol Ecol
Arabidella
n = 24
2n = 4x = 30
2n = 8, 10, 12,
14, 20
(1 / 11)
(1 / 3)
AUTOPOLYPLOIDY
Evolution of chromosome number and karyotype
Post‐polyploid karyotype evolution in the tribe Microlepidieae
one diploma & one doctoral
student
martin.lysak@ceitec.muni.cz
www.plantcytogenomics.org