scholarly journals The effects of chromosome fusions on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size

2021 ◽  
Author(s):  
Francesco Cicconardi ◽  
James J Lewis ◽  
Simon Henry Martin ◽  
Robert D. Reed ◽  
Charles G Danko ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Gc Content ◽  
Population Level ◽  
Chromosome Length ◽  
Adaptive Divergence ◽  
Chromosome Size ◽  
Turnover Rates ◽  
Chromosome Fusion ◽  
Chromosome Fusions ◽  
Chromosome Level

Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with the chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 21 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. Following fusion, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.

scholarly journals Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 312
Author(s):  
Veronika Borůvková ◽  
W. Mike Howell ◽  
Dominik Matoulek ◽  
Radka Symonová
Keyword(s):  
Large Scale ◽  
Open Space ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Chromosome Size ◽  
Vertebrate Genome ◽  
Fish Cytogenetics ◽  
Large Variability ◽  
The Relationship ◽  
Chromosome Level

Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.

scholarly journals Epigenetic dynamics of centromeres and neocentromeres in Cryptococcus deuterogattii

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009743
Author(s):  
Klaas Schotanus ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Dna Methylation ◽  
Transposable Element ◽  
Fungal Pathogen ◽  
Fusion Partner ◽  
Epigenetic Memory ◽  
Chromosome Fusion ◽  
Human Fungal Pathogen ◽  
Chromosome Fusions ◽  
The Impact ◽  
Active Centromere

Deletion of native centromeres in the human fungal pathogen Cryptococcus deuterogattii leads to neocentromere formation. Native centromeres span truncated transposable elements, while neocentromeres do not and instead span actively expressed genes. To explore the epigenetic organization of neocentromeres, we analyzed the distribution of the heterochromatic histone modification H3K9me2, 5mC DNA methylation and the euchromatin mark H3K4me2. Native centromeres are enriched for both H3K9me2 and 5mC DNA methylation marks and are devoid of H3K4me2, while neocentromeres do not exhibit any of these features. Neocentromeres in cen10Δ mutants are unstable and chromosome-chromosome fusions occur. After chromosome fusion, the neocentromere is inactivated and the native centromere of the chromosome fusion partner remains as the sole, active centromere. In the present study, the active centromere of a fused chromosome was deleted to investigate if epigenetic memory promoted the re-activation of the inactive neocentromere. Our results show that the inactive neocentromere is not re-activated and instead a novel neocentromere forms directly adjacent to the deleted centromere of the fused chromosome. To study the impact of transcription on centromere stability, the actively expressed URA5 gene was introduced into the CENP-A bound regions of a native centromere. The introduction of the URA5 gene led to a loss of CENP-A from the native centromere, and a neocentromere formed adjacent to the native centromere location. Remarkably, the inactive, native centromere remained enriched for heterochromatin, yet the integrated gene was expressed and devoid of H3K9me2. A cumulative analysis of multiple CENP-A distribution profiles revealed centromere drift in C. deuterogattii, a previously unreported phenomenon in fungi. The CENP-A-binding shifted within the ORF-free regions and showed a possible association with a truncated transposable element. Taken together, our findings reveal that neocentromeres in C. deuterogattii are highly unstable and are not marked with an epigenetic memory, distinguishing them from native centromeres.

scholarly journals Heterozygosity and Chain Multivalents during Meiosis Illustrate Ongoing Evolution as a Result of Multiple Holokinetic Chromosome Fusions in the Genus Melinaea (Lepidoptera, Nymphalidae)

2017 ◽  
Vol 153 (4) ◽  
pp. 213-222 ◽  
Author(s):  
Melanie McClure ◽  
Bernard Dutrillaux ◽  
Anne-Marie Dutrillaux ◽  
Vladimir Lukhtanov ◽  
Marianne Elias
Keyword(s):  
Chromosome Evolution ◽  
Taxonomic Revision ◽  
Variable Number ◽  
Chromosome Fusion ◽  
Meiotic Chromosomes ◽  
In Captivity ◽  
Chromosome Fusions ◽  
The Common ◽  
Multiple Spindle ◽  
Complex Chromosome

Mitotic and meiotic chromosomes from 2 taxa of the genus Melinaea, M. satevis cydon and M. “satevis” tarapotensis (Lepidoptera: Nymphalidae), and from hybrids produced in captivity were obtained using an improved spreading technique and were subsequently analyzed. In one of the taxa, the presence of trivalents and tetravalents at diakinesis/metaphase I is indicative of heterozygosity for multiple chromosome fusions or fissions, which might explain the highly variable number of chromosomes previously reported in this genus. Two large and complex multivalents were observed in the meiotic cells of the hybrid males (32 chromosomes) obtained from a cross between M. “s.” tarapotensis (28 chromosomes) and M. s. cydon (40-43 chromosomes). The contribution of the 2 different haploid karyotypes to these complex figures during meiosis is discussed, and a taxonomic revision is proposed. We conclude that chromosome evolution is active and ongoing, that the karyotype of the common ancestor consisted of at least 48 chromosomes, and that evolution by chromosome fusion rather than fission is responsible for this pattern. Complex chromosome evolution in this genus may drive reproductive isolation and speciation, and highlights the difficulties inherent to the systematics of this group. We also show that Melinaea chromosomes, classically considered as holocentric, are attached to unique, rather than multiple, spindle fibers.

scholarly journals An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)

2020 ◽  
Vol 12 (4) ◽  
pp. 456-462 ◽  
Author(s):  
Warren Brian Simison ◽  
James F Parham ◽  
Theodore J Papenfuss ◽  
Athena W Lam ◽  
James B Henderson
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Trachemys Scripta ◽  
Future Research ◽  
Chromosome Counts ◽  
Trachemys Scripta Elegans ◽  
Chromosome Fusion ◽  
Slider Turtle ◽  
Tetrapod Evolution ◽  
Chromosome Level

Abstract Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68 Mb and N90 = 19 Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.

Karyological study in fifteen Leucocoryne taxa (Alliaceae)

Biologia ◽  
2012 ◽  
Vol 67 (2) ◽  
Author(s):  
Paola Jara-Arancio ◽  
Pedro Jara-Seguel ◽  
Claudio Palma-Rojas ◽  
Gina Arancio ◽  
Raul Moreno
Keyword(s):  
Chromosome Number ◽  
Secondary Constriction ◽  
Chromosome Morphology ◽  
Chromosome Size ◽  
Chromosome Fusion ◽  
Karyological Study ◽  
Karyotype Asymmetry ◽  
Additional Chromosome ◽  
Karyotype Formula ◽  
Haploid Karyotype

AbstractThe karyotype of fifteen Leucocoryne taxa was studied, assessing characteristics such as chromosome morphology and size, secondary constriction location, and asymmetry level. Two groups of Leucocoryne taxa were described based on chromosome number (2n = 10 and 2n = 18) and karyotype asymmetry. The haploid karyotype formula for the group 2n = 10 was 3m + 2st (or 2t), whereas for the group 2n = 18 was 7m + 2st (or 2t). Such results corroborate the karyotype descriptions previously carried out for some taxa of the genus. Leucocoryne taxa showed a high resemblance in chromosome morphology, but inter-specific differences were found in mean chromosome size. These data and previous studies based on gross chromosome morphology support Crosa’s hypothesis, which suggests that the cytotype 2n = 10 is diploid and perhaps ancestral, whereas that the cytotype 2n = 18 is tetraploid but with an additional chromosome fusion being probably a derived status.

scholarly journals Nucleic acid content and Chromosome morphology in Chrysanthemum

1969 ◽  
Vol 13 (3) ◽  
pp. 241-250 ◽  
Author(s):  
G. J. Dowrick ◽  
A. S. El Bayoumi
Keyword(s):  
Nucleic Acid ◽  
Chromosome Number ◽  
Dna Content ◽  
Chromosome Numbers ◽  
Chromosome Length ◽  
Chromosome Morphology ◽  
Nucleic Acid Content ◽  
Chromosome Size ◽  
Dna Contents ◽  
The Relationship

1. The DNA contents of twenty-eight different species and forms of Chrysanthemum have been measured by photometry. It is shown that there are large differences in DNA content between some species with identical chromosome numbers.2. The DNA contents of natural polyploids are frequently not those expected when comparison is made with diploid forms of the same species. The DNA contents of induced polyploids are those expected.3. Chromosome length and volume are positively correlated with DNA content.4. The relationship between chromosome number, chromosome size, DNA content and gene number is considered, and it is suggested that the differences in DNA content may result from the presence of differing amounts of genetically inactive DNA in the chromosomes.

scholarly journals Indicators of zinc status at the population level: a review of the evidence

2008 ◽  
Vol 99 (S3) ◽  
pp. S14-S23 ◽  
Author(s):  
Rosalind S. Gibson ◽  
Sonja Y. Hess ◽  
Christine Hotz ◽  
Kenneth H. Brown
Keyword(s):  
Serum Zinc ◽  
Population Level ◽  
Molecular Techniques ◽  
Collaborative Group ◽  
Zinc Status ◽  
Turnover Rates ◽  
Functional Responses ◽  
Zinc Metalloenzymes ◽  
Zinc Concentrations ◽  
New Biomarkers

The role of zinc deficiency as an important cause of morbidity and impaired linear growth has prompted the need to identify indicators of population zinc status. Three indicators have been recommended – prevalence of zinc intakes below the estimated average requirement (EAR), percentage with low serum zinc concentrations, and percentage of children aged < 5 years who are stunted. This review outlines steps to estimate the prevalence of inadequate intakes, and confirm their validity based on the EARs set by International Zinc Nutrition Collaborative Group. Next, the appropriateness of serum zinc as a biochemical marker for population zinc status is confirmed by a summary of: (a) the response of serum zinc concentrations to zinc intakes; (b) usefulness of serum zinc concentrations to predict functional responses to zinc interventions; (c) relationship between initial serum zinc and change in serum zinc in response to interventions. Height- or length-for-age was chosen as the best functional outcome after considering the responses of growth, infectious diseases (diarrhoea, pneumonia), and developmental outcomes in zinc supplementation trials and correlation studies. The potential of other zinc biomarkers such as zinc concentrations in hair, cells, zinc-metalloenzymes, and zinc-binding proteins, such as metallothionein, is also discussed. Molecular techniques employing reverse transcriptase (RT)-polymerase chain reaction to measure mRNA in metallothionein and ZIP1 transporter hold promise, as do kinetic markers such as exchangeable zinc pools (EZP) and plasma zinc turnover rates. More research is needed to establish the validity, specificity, sensitivity, and feasibility of these new biomarkers, especially in community-settings.

scholarly journals Comparative cytogenetics in Cyclopogon (Orchidaceae)

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Mauro Grabiele ◽  
Juan Cerutti ◽  
Diego Hojsgaard ◽  
Rubén Almada ◽  
Julio Daviña ◽  
...  
Keyword(s):  
Genome Size ◽  
Karyotype Analysis ◽  
Chromosome Length ◽  
The Novel ◽  
Comparative Cytogenetics ◽  
Molecular Approaches ◽  
Chromosome Fusions ◽  
Karyotype Morphology

AbstractA cytotaxonomical description of Cyclopogon (Spiranthinae, Orchidaceae) is carried out through a deep karyotype analysis of four species from NE Argentina. Distinctive karyotype parameters concerning the chromosomes number, morphology, size and symmetry and the genome size associate to each taxon. Cyclopogon calophyllus (2n = 2x =28; 18m + 10sm), C. congestus (2n = 2x = 32; 26m + 6sm), C. elatus (2n = 2x = 28; 18m + 10sm) and C. oliganthus (2n = 4x = 64; 40m + 24sm) possess symmetrical karyotypes (i-mean = 40.01–42.84; A 1 = 0.24–032; r>2 = 0.06–0.29) and excluding C. congestus (A 2 = 0.26; R = 2.62) unimodality is the rule (A 2 = 0.12–0.20; R = 1.73–1.92). Diploid taxa show a terminal macrosatellite in the m pair no. 2 (large arm) and share a comparable mean chromosome length (ca. 2.75 μm) and genome size (ca. 40 μm), superior to the tetraploid C. oliganthus (ca. 2 and 32 μm, respectively). The novel data added to preceding cytological, morphological and molecular approaches involving Cyclopogon and those related taxa of Spiranthinae largely based on x = 23 support the hypothesis that the unusual 2n and the karyotype morphology of Cyclopogon is an evolutionary advance within Spiranthinae with a basic reduction to x = 14 or 16 by chromosome fusions. A polyploid-dysploid series added to dibasic hybridization explain the extant 2n diversity though a paleopolyploid series on x = 7–8 is also possible.

scholarly journals The intranuclear relationship between centromere volume and chromosome size in Festuca scariosa X drymeja

1981 ◽  
Vol 47 (1) ◽  
pp. 117-125
Author(s):  
G. Jenkins ◽  
M.D. Bennett
Keyword(s):  
Serial Section ◽  
Chromosome Length ◽  
Individual Chromosome ◽  
Chromosome Size ◽  
Preferential Pairing ◽  
Frequency Distributions ◽  
Positive Correlation ◽  
Serial Section Reconstruction

In the hybrid Festuca scarisoa X drymeja where pairing is incomplete at pachytene, there is preferential pairing between the longer chromosomes of the complement. EM serial-section reconstruction of nuclei at zygotene and pachytene reveals that there is equally pronounced preferential pairing between larger centromeres. This evidence suggests that the longer chromosomes have large centromeres and that centromere volume is correlated with chromosome length. Confirmation of this comes from the comparison of the frequency distributions of observed centromere volumes and those predicted on the basis of chromosome length. Although there is a positive correlation between centromere volume and chromosome length, it is not possible to identify the centromeres of each individual chromosome within the complement because (a) the differences between the lengths of each chromosome are small and (b) the estimates of relative centromere volumes vary significantly between cells.

scholarly journals Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

2020 ◽  
Author(s):  
Anna Tigano ◽  
Arne Jacobs ◽  
Aryn P. Wilder ◽  
Ankita Nand ◽  
Ye Zhan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Structural Variation ◽  
Demographic History ◽  
Genome Structure ◽  
Genomic Variation ◽  
Adaptive Divergence ◽  
Effective Population ◽  
Atlantic Silverside ◽  
A Genome ◽  
Chromosome Level

AbstractThe levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

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