The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149,000 Mb, divided into n=2 to n= approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.

/pdf/organisation-of-the-plant-genome-in-chromosomes-m714q914k5.pdf

Organisation of the plant genome in chromosomes

https://www.cell.com/trends/plant-science/pdf/S1360-1385(10)00096-8.pdf

A triptych of the evolution of plant transposable elements.

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh

/pdf/compact-genome-of-the-antarctic-midge-is-likely-an-1403a0exht.pdf

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

The fish, Erythrinus erythrinus, shows an interpopulation diversity, with four karyomorphs differing by chromosomal number, chromosomal morphology and heteromorphic sex chromosomes. Karyomorph A has a diploid number of 2n = 54 and does not have differentiated sex chromosomes. Karyomorph D has 2n = 52 chromosomes in females and 2n = 51 in males, and it is most likely derived from karyomorph A by the differentiation of a multiple X1X2Y sex chromosome system. In this study, we analyzed karyomorphs A and D by means of cytogenetic approaches to evaluate their evolutionary relationship. Conspicuous differences in the distribution of the 5S rDNA and Rex3 non-LTR retrotransposon were found between the two karyomorphs, while no changes in the heterochromatin and 18S rDNA patterns were found between them. Rex3 was interstitially dispersed in most chromosomes. It had a compartmentalized distribution in the centromeric regions of only two acrocentric chromosomes in karyomorph A. In comparison, in karyomorph D, Rex3 was found in 22 acrocentric chromosomes in females and 21 in males. All 5S rDNA sites co-localized with Rex3, suggesting that these are associated in the genome. In addition, the origin of the large metacentric Y chromosome in karyomorph D by centric fusion was highlighted by the presence of internal telomeric sites and 5S rDNA/Rex3 sites on this chromosome. We demonstrated that some repetitive DNAs (5S rDNA, Rex3 retroelement and (TTAGGG)n telomeric repeats) were crucial for the evolutionary divergence inside E. erythrinus. These elements were strongly associated with the karyomorphic evolution of this species. Our results indicate that chromosomal rearrangements and genomic modifications were significant events during the course of evolution of this fish. We detected centric fusions that were associated with the differentiation of the multiple sex chromosomes in karyomorph D, as well as a surprising increase of associated 5S rDNA/Rex3 loci, in contrast to karyomorph A. In this sense, E. erythrinus emerges as an excellent model system for better understanding the evolutionary mechanisms underlying the huge genome diversity in fish. This organism can also contribute to understanding vertebrate genome evolution as a whole.

/pdf/chromosome-spreading-of-associated-transposable-elements-and-52fcctnrsc.pdf

Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish

It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12247

Genome size variation in wild and cultivated maize along altitudinal gradients.

F rom the thousands of species that have already been analyzed, it is now clear that genome size varies considerably between species. This variation is mainly because of the differing amounts of various repeated sequences, including satellite DNA, transposable elements (TEs) and ribosomal genes in different genomes. The idea of within-species variation, that is, variation between populations and between individuals, has won less general acceptance, despite various studies revealing its existence. This is sometimes because of mistrust and suspicion (Gregory and Johnston, 2008), sometimes to the concept underlying the definition of species (Murray, 2005) and sometimes to artefacts in the technique used (Greilhuber, 2005; Gregory and Johnston, 2008). For example, some of the variation observed in genome size between populations subjected to different environmental conditions over the geographical range of the species can be accounted for by the chromatin state, which can affect the accessibility of the DNA to fluorochromes (see Nardon et al., 2003 and references therein). However, we do not have to throw the baby out with the bath water as all these confounding factors can be taken into account by using appropriate protocols and statistical methods, which take different levels of sampling and replicates into account, for determining withinand between-species variation. A recent study of genome size in various Drosophila species (Bosco et al., 2007) concludes that there is a significant statistical difference in genome size between species, and some significant differences between strains in some species. Vieira et al. (1999, 2002) have also identified genome-size differences between populations of both Drosophila melanogaster and D. simulans, but no differences between replicates of batches of flies reared in the same vial. In the Bosco et al. (2007) paper, the variation in genome size was related to variation in heterochromatin composition, mostly of satellite DNA, whereas TEs were mostly involved in the Vieira et al. (1999, 2002) study. Such data give credibility to between-individual variations in the amount of heterochromatic TEs that have been estimated using dot blots and in situ hybridization in Drosophila (Charlesworth et al., 1994). These results show that both TEs and satellite DNA can influence genome size, and lead to within-species variation. Satellite DNA is indeed a major constituent of the genomes of many organisms (see Palomeque and Lorite, 2008 for a review), and it explains why the genome of the species D. orena (0.28 pg) is so much larger than that of D. melanogaster (0.18 pg) (Boulesteix et al., 2006). Marked differences in genome size between closely related lines of flax (Linum usitatissimum) have been shown to occur over a very short period, and to involve a change in rDNA amount (Cullis, 2005; Davison et al., 2007), as well as specific LIS-1 insertion events, although possible changes in the amount of other repetitive sequences were not determined. Mobilization and integration of novel copies of TEs are not always observed in genome changes, which can simply result from segmental duplication of centromeric regions, as reported in rice (Ma and Jackson, 2006). Centromeres and the Y chromosome seem to have a major function in the change in genome size reported both withinand between-species. In most species, the heterochromatic Y chromosome consists mainly of numerous repeated sequences, mostly satellites and TEs (Palomeque and Lorite, 2008), within which only a few genes, mostly fertility genes, are embedded. For instance, it has been reported that in Anopheles gambiae the fully heterochromatic Y chromosome varies in length and banding pattern in natural populations, a finding consistent with the rapid satellite expansion mechanism in this species (Bonaccorsi et al., 1980). Hence, in addition to changes in centromere composition and whole genome structure, the Y chromosome, because of its highly degenerated heterochromatic state (Charlesworth, 2002) and the fact that it differs in size in different populations, seems to make a particular contribution to the variation in genome size, as reported in some plants (Meagher et al., 2005). This implies that the suggestion that changes in the composition of the Y chromosome could be responsible for geographical adaptive genetic differences between temperate and tropical populations of Drosophila melanogaster (Rohmer et al., 2004) warrants further investigation. The reasons for differences in the amounts of repeated sequences present in different populations are not clearly understood. In addition to the impact of the effective population size (Lynch and Conery, 2003), at least two explanations are conceivable. A global change could have occurred as a result of the stressful environmental conditions encountered by the species when they invaded new geographical areas, or of confrontations between populations that had not encountered each other earlier (Biémont and Vieira, 2005 and references therein). TE transposition and amplification have been reported in inter-species hybrids in Drosophila and in the Australian wallaby (see references in Biémont and Vieira, 2005), but few data are available about intra-species hybridization. Only certain specific TEs, as in dysgenic crosses in Drosophila (Kidwell, 2002), or other kinds of repeated sequence, may be involved. A survey of various TEs during mating between Magnaporthe grisea isolates from Triticum and Setaria revealed new insertions of the LTR (Long Terminal Repeat) retrotransposon MAGGY in the progeny, but very rarely any movements of other TEs (Eto et al., 2001). Transposition of the LINE (Long Interspersed Nuclear Element: non-LTR retrotransposon) MGL (M. grisea LINE) was also observed in another experiment in which two M. grisea isolates from rice were crossed (Nishimura et al., 2000), and the Ds-like element, Ascot-1, has been shown to excise during mating in Ascobolus immersus b2 (Colot et al., 1998). No evidence of TE amplification was, however, found in crosses between A. nidulans strains (Li Destri Nicosia et al., 2001). These findings strongly suggest that the transposition of TEs may be enhanced during mating in fungi, but only some TE families are involved. Although amplification, deletion and rearrangements of various repeated DNA sequences do indeed account for differences in DNA composition, the frequency of such events and their Heredity (2008) 101, 297–298 & 2008 Macmillan Publishers Limited All rights reserved 0018-067X/08 $32.00

Genome size evolution: Within-species variation in genome size

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Genome size evolution: Within-species variation in genome size