last  page PLNT3140 Introductory Cytogenetics
Lecture 23, part 1 of 3
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  December 5, 2017
GENOME EVOLUTION


REFERENCES:
1. Cytogenetics - the chromosome in division, inheritance and evolution. Carl P. Swanson, Timothy Merz and William J.Young. 2nd Edition. Prentice-Hall. Chapter 9. Evolution of the karyotype.
2. Walbot, V.W. and Cullis, C.A. 1985 .Rapid genome change in higher plants. Ann. Rev. Physiol. 36: 367-96.
3. Genome analysis Chapter 7. in Singh, R. 1993. Plant Cytogenetics. CRC Press.
4. Parkin, E.A.P., A.G. Sharpe, D.J. Keith, and D.J. Lydiate.1995. Identification of the A and C genome of amphidiploid Brassica napus (oilseed rape). Genome 38:1122-1131.
5. Schröck, E. et al. (1996) Multicolor spectral karyotyping of human chromosomes. Science 273: 494-497.



Learning checklist:


1. Understand how life history can constrain genome size.
2. Understand why changes in ploidy level can lead to chromosomal rearrangements
3. Be able to define synteny, microsynteny.
4. Understand how comparative genomics can reveal microsynteny and ancient polyploidization events.
5. Understand the experimental data which demonstrates that interspersed repetitive sequences can be gained, lost and amplified and selectively deleted during genome evolution:


In introductory genetics, we are presented with linkage maps that make the eukaryotic genome look like it is cast in concrete. Indeed, perhaps the most difficult thing for many geneticists to swallow about transposition was the Pandora's box of genomic chaos that it implied. Transposition relegated the gene from its status as a house built upon a rock, to more of a molecular mobile home. Perhaps it is not entirely a coincidence that not long after McClintock's publications of transposition, that the model of plate tectonics shook the science of geology like an earth quake.

The eukaryotic genome has never been the same since. In retrospect, we can see that evolution requires a fluid, dynamic genome. Without change, there is no evolution. We can now make several generalizations regarding genome evolution:

1) Genome sizes and karyotypes can differ drastically even among closely-related species. This necessarily demands that fundamental changes in genome structure can occur over relatively short evolutionary times.
2) Most of the changes occur in the middle repetitive fraction of the genome.
3) Most of these changes are in non-coding DNA.


I. EVOLUTION OF GENOME SIZE

A. Chromosome size and number.


The sizes of chromosomes in Crepis species are drawn to scale, accompanied by drawings of florets and achenes, also to scale.

This example illustrates how drastically genome size and chromosome number can change in short evolutionary times.

It also illustrates something often observed, which is that the sizes of plant organs such as leaves, stems or fruit are often larger in species with larger chromosomes.
Fig. 9-19. Species of the genus Crepis showing the size relations of chromosomes, florets (lacking ovaries), and achenes, all drawn to the same magnification so that the sizes are relative to each other. A. C. sibirica; B, C. kashmirica ; C, C. conyzaefolia; D, C. mungierii; E, C. leontodontoides ; F, C. capillaris; G, C. suffreniana; H, C. fuliginosa (rearranged from Babcock, 1947). from Cytogenetics - the chromosome in division, inheritance and evolution. Carl P. Swanson, Timothy Merz and William J.Young. 2nd Edition. Prentice-Hall. Chapter 9. Evolution of the karyotype.

achene (əkēn') , dry, simple, one-seeded fruit with the seed attached to the inner wall at only one point. Achenes are indehiscent, i.e., they do not split open at maturity. The so-called seed of a sunflower is an achene; the shell is the wall of the fruit, and the true seed lies within. A strawberry consists of many achenes embedded in a fleshy receptacle.
 

B. Genome Size is Related to Life History

The time required for mitosis and meiosis increases with genome size.

Table 9.6. Duration of mitosis and meiosis in a number of plant species, together with their DNA values in picograms and their annual or perennial habit; where the DNA values are different, both are given.
Species Picograms per
Haploid Genome
Mitosis in Hours Meiosis in Hours Plant Habit
Crepis capillaris 1.20 10.8 -- Annual
Haplopappus gracillis 1.85 10.5 36.0 Annual
Pisum sativum 3.9, 4.8 10.8 -- Annual
Ornithogalum virens 6.43 -- 96.0 Perennial
Secale cereale 8.8, 9.6 12.8 51.2 Annual
Vicia faba 13.0, 14.8 13.0 72.0 Annual
Allium cepa 14.8, 16.25 17.4 72.0 Perennial
Tradescantia paludosa 18.0 18.0 126.0 Perennial
Endymion nonscriptus 21.8 -- 48.0 Perennial
Tulipa kaufmanniana 31.2 23.0 -- Perennial
Lillium longiflorum 35.3 24.0 192.0 Perennial
Trillium erectum 40.0 29.0 274.0 Perennial
Source: Van't Hof, 1965, and Bennett, 1972.

You might think that genome size shouldn't affect mitotic cycle time. If the number of replication origins per Mb stays the same, all genomes should replicate at the same rate. Therefore, there must be other limiting factors eg. nuclear or cytoplasmic volume probably doesn't double when genome size doubles. Therefore, the concentration of dNTPs could be a major limiting factor.

Annuals tend to have smaller genomes and shorter mitotic cycles. Perennial plants tend to have larger genomes and longer cell cycles.

Annuals have to grow very rapidly in spring. Therefore, ecological competition forces annuals to have smaller genomes.

Question: Is the perennial habit more tolerant of a longer mitotic cycle? What is the advantage of a larger genome or longer mitotic cycle?

Bigger organs means more biomass utilized, which means more biomass needed. Big genomes are probably better tolerated  when habitat is not limiting eg. food, water, light, space. The prediction would be that small genomes are favored under limiting conditions. This may be why our crops have big genomes. We pamper them with a good environment. Domesticated crops are poor competitors outside of cultivation.


DISCUSSION QUESTION
What is cause and which is effect: genome size  or habit?

Take home lesson: Genome evolution can be constrained by life history.

We will next examine in more detail some of the mechanisms by which genome size and chromosome organization evolve.

C. Allopolyploids and Speciation

evolution - The change in allele frequencies within a population. This definition could encompass any genetic change, from single point mutations, to major chromosomal rearrangements.

speciation - The evolutionary process by which two populations diverge, resulting in decreased ability to hybridize. As populations diverge genetically, reproductive barriers arise, preventing mating, interfering with meiosis, or resulting in hybrids that are less fit than progeny from within-population matings. When fertile progeny can no longer result from matings between two populations, speciation can be said to be complete.

Speciation is not necessarily a sudden event.  Although every speciation event is probably a special case, in general speciation is brought about through reproductive isolation and genetic divergence. Reproductive isolation can be the result of geographical or physical separation of populations, or due to divergence of chromosome structure or number. In turn, genomic changes can serve as barriers to interbreeding between two populations. Eventually, enough divergence has occurred that interbreeding is impossible. It is at this point that, strictly speaking, two distinct species exist.

However,  taxonomists often define phenotypically distinct populations as species, even when reproductive barriers are not complete.  On the one hand, the greater the genetic divergence between two species, the lower the fertility rate will be in interspecific hybrids.  On the other hand, when interspecific hybridization does occur, it can often result in the creation of a new species, distinct from the parental species.

The creation of allopolyploid species is through interspecific hybridization between morphologically distinct diploid species, with retention of both chromosome complements. This effectively doubles the genome size C and the chromosome number  n. (amphidiploidy= allopolyploidization)

Determination of ancestral species can be made based on geographical distribution, morphological features, chromosome counts, karyotype analysis, isozyme banding patterns and molecular studies.

Putative ancestors can be verified through interspecific hybridization, synthesis of allopolyploids, comparison of morphological traits, meiotic pairing and fertility in the allopolyploids and their hybrids.
 

1. Relationships between the allopolyploid species of Brassica napus 2n=4x=38, B.juncea 2n=4x=36, and B.carinata 2n=4x=34.

The genus Brassica consists of three elementary or basic genomes Brassica campestris A n=10, B.oleracea C n=9, and B.nigra B n=8. These diploids are secondary polyploids from an extinct species with a basic chromosome number of x=6, based on pachytene chromosome analysis in the haploid genomes. If 1-6 represent the ancestral basic six chromosomes, the following represents individual diploid genomes' complement of these basic six chromosomes.

Species
Genome
n
haploid complement

B.nigra 

n=8 
1 2 3 44 5 66 
double tetrasomic

B.oleracea 

C
n=9
1 22 33 4 55 6
triple tetrasomic
B. rapa
A
n=10
11 2 3 44 5 666 
double tetrasomic and hexasomic
B. rapa x B. nigra
AB
n=18
111 22 33 4444 55 66666



U (1935) demonstrated the genome relationships by studying the meiotic chromosome pairing in triploid hybrids


Resynthesis of B.carinata - 2n= 34 BB CC by hybridizing B. nigra BB and B. oleracea CC followed by doubling produced an amphidiploid BB CC with 0 to 4 IV (tetravalents) and 9 to 17 II (divalents) at metaphase I followed by a nearly normal second meiosis and some production of fertile pollen. Another synthesis of
B.carinata showed a normal meiosis with 17 II and high seed fertility.

Resynthesis of B.
napus and B. juncea - normal meiosis, resemble the 'natural' allo-tetraploid species and are fertile. The 'natural' allotetraploids have a more stable meiotic behavior than the newly synthesized amphidiploids, presumably due to selection pressure.

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