Tertiary trisomics in the garden pea as a model of B chromosome evolution in plants

B chromosomes are extra chromosomes to the standard complement that occur in many organisms. They can originate in a number of ways including derivation from autosomes and sex chromosomes in intraand interspecies crosses. Their subsequent molecular evolution resembles that of univalent sex chromosomes, which involves gene silencing, heterochromatinization and the accumulation of repetitive DNA and transposons. B-chromosome frequencies in populations result from a balance between their transmission rates and their effects on host fitness. Their long-term evolution is considered to be the outcome of selection on the host genome to eliminate B chromosomes or suppress their effects and on the B chromosome's ability to escape through the generation of new variants. Because B chromosomes interact with the standard chromosomes, they can play an important role in genome evolution and may be useful for studying molecular evolutionary processes.

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B Chromosome Variants of the Grasshopper Xyleus discoideus angulatus Are Potentially Derived from Pericentromeric DNA

Cytogenetic and Genome Research ◽

10.1159/000480036 ◽

2017 ◽

Vol 152 (4) ◽

pp. 213-221 ◽

Cited By ~ 5

Author(s):

Andrezza C.S. Bernardino ◽

Diogo C. Cabral-de-Mello ◽

Carolina B. Machado ◽

Octavio M. Palacios-Gimenez ◽

Neide Santos ◽

...

Keyword(s):

Repetitive Dna ◽

Evolutionary Dynamics ◽

Chromosome Evolution ◽

Pericentromeric Region ◽

B Chromosome ◽

B Chromosomes ◽

Different Populations ◽

B Chromosome Evolution ◽

Shed Light

B chromosomes, extra elements present in the karyotypes of some eukaryote species, have been described in the grasshopper Xyleus discoideus angulatus. Although some studies have proposed an autosomal origin of the B chromosome in X. d. angulatus, little is known about its repetitive DNA composition and evolutionary dynamics. The aim of the present work was to shed light on the B chromosome evolution in X. d. angulatus by cytogenetic analysis of 27 populations from Pernambuco and Ceará states (Brazil). The frequency of B chromosomes in the different populations was determined, and chromosome measurements and fluorescence in situ hybridization (FISH) with C0t-DNA and telomeric and B chromosome sequences were performed in cells from B-carrying individuals. The results revealed variations in B chromosome prevalence among the populations and showed that some B chromosomes were smaller in certain populations. FISH produced similar patterns for the C0t-DNA probe in all hybridized individuals, whereas telomeric and B chromosome probes, obtained by microdissection, exhibited variations in their distribution. These results indicate the presence of 3 morphotypes of B chromosomes in X. d. angulatus, with variation in repetitive DNA composition during their evolution. In this species, B chromosomes have an intraspecific origin and probably arose from the pericentromeric region of A chromosomes.

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Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

BMC Genomics ◽

10.1186/1471-2164-13-109 ◽

2012 ◽

Vol 13 (1) ◽

pp. 109 ◽

Cited By ~ 50

Author(s):

Qi Zhou ◽

Hong-mei Zhu ◽

Quan-fei Huang ◽

Zhao-lin Xuan ◽

Guo-jie Zhang ◽

...

Keyword(s):

Chromosome Evolution ◽

Draft Genome ◽

B Chromosome ◽

Drosophila Albomicans ◽

B Chromosome Evolution

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Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

10.20944/preprints201811.0110.v1 ◽

2018 ◽

Author(s):

Frances Clark ◽

Matthew Conte ◽

Thomas Kocher

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Cichlid Fish ◽

B Chromosome ◽

Lake Malawi ◽

B Chromosomes ◽

Sequence Coverage ◽

Specific Sequence ◽

Genomic Characterization ◽

B Chromosome Evolution

B chromosomes (Bs) were discovered a century ago, and since then most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function and evolution of B chromosomes remain unanswered. Here we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with and without B chromosomes. We examine the efficiency of this method, and compare results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets are identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified candidate genes located on the B chromosome which may regulate the segregation and maintenance of the B chromosome.

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Evolution of a sex megachromosome

10.1101/2020.07.02.182808 ◽

2020 ◽

Author(s):

Matthew A. Conte ◽

Frances E. Clark ◽

Reade B. Roberts ◽

Luohao Xu ◽

Wenjing Tao ◽

...

Keyword(s):

Sex Determination ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Focal Point ◽

Alternative Hypothesis ◽

Cichlid Fish ◽

B Chromosome ◽

Sex Chromosome Evolution ◽

Evolutionary Genomic ◽

Size And Morphology

AbstractChromosome size and morphology vary within and among species, but little is known about either the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual megachromosome that is ~3 times longer than any of the other chromosomes. This megachromosome functions as a sex chromosome in some of these species. We explore two hypotheses of how this sex megachromosome may have evolved. The first hypothesis proposes that it developed by the accumulation of repetitive elements as recombination was reduced around a dominant sex-determination locus, as suggested by traditional models of sex chromosome evolution. An alternative hypothesis is that the megachromosome originated via the fusion of an autosome with a highly-repetitive B chromosome, one of which had carried a sex-determination locus. Here we test these hypotheses using comparative analysis of several chromosome-scale cichlid and teleost genomes. We find the megachromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. A WZ sex-determination locus encompasses the last ~105Mbp of the 134Mbp megachromosome and the last 47Mbp of the megachromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal the megachromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Although the origin of this megachromosome remains ambiguous, it has clearly been a focal point of extensive evolutionary genomic conflicts. This megachromosome represents an interesting system for studying sex chromosome evolution and genomic conflicts.

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Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Genes ◽

10.3390/genes9120610 ◽

2018 ◽

Vol 9 (12) ◽

pp. 610 ◽

Cited By ~ 9

Author(s):

Frances E. Clark ◽

Matthew A. Conte ◽

Thomas D. Kocher

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Cichlid Fish ◽

B Chromosome ◽

Lake Malawi ◽

B Chromosomes ◽

Sequence Coverage ◽

Specific Sequence ◽

Genomic Characterization ◽

B Chromosome Evolution

B chromosomes (Bs) were discovered a century ago, and since then, most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function, and evolution of B chromosomes remain unanswered. Here, we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with or without B chromosomes. We examined the efficiency of this method, and compared results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets were identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified genes and gene fragments located on the B chromosome, some of which may regulate the segregation and maintenance of the B chromosome.

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Supernumerary chromosome evolution in the Simulium vernum group (Diptera: Simuliidae)

Genome ◽

10.1139/g89-477 ◽

1989 ◽

Vol 32 (4) ◽

pp. 516-521 ◽

Cited By ~ 18

Author(s):

Charles Brockhouse ◽

J. A. B. Bass ◽

R. M. Feraday ◽

N. A. Straus

Keyword(s):

Sibling Species ◽

Related Species ◽

Chromosome Evolution ◽

Polytene Chromosomes ◽

Nucleolar Organizer ◽

Chromosome Analysis ◽

B Chromosome ◽

Supernumerary Chromosome ◽

Closely Related Species ◽

Black Fly

B chromosomes are present in a cluster of closely related species of black fly in the Simulium vernum group including six sibling species within the S. vernum complex, Simulium costatum, and Simulium juxtacrenobium. The S. vernum siblings all possess the same small metacentric supernumerary, while S. juxtacrenobium carries three different supernumeraries (two telocentrics and one metacentric) and S. costatum has both a metacentric and a telocentric B chromosome. Analysis of the polytene chromosomes in the larval salivary glands has revealed relationships between the supernumeraries of the different species. The metacentric B chromosome of the S. vernum siblings apparently results from a fusion of the two telocentric supernumeraries of S. juxtacrenobium. Acquisition of a nucleolar organizer then gave rise to the metacentric B chromosome in S. juxtacrenobium. The acquisition of a nucleolus by a S. juxtacrenobium telocentric gave rise to one of the S. costatum supernumeraries. Two alternate models for the origin of black fly supernumeraries are presented.Key words: supernumerary chromosome, black fly, polytene chromosome, chromosome evolution.

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Euchromatic Supernumerary Chromosomal Segments—Remnants of Ongoing Karyotype Restructuring in the Prospero autumnale Complex?

Genes ◽

10.3390/genes9100468 ◽

2018 ◽

Vol 9 (10) ◽

pp. 468 ◽

Cited By ~ 3

Author(s):

Tae-Soo Jang ◽

John Parker ◽

Hanna Weiss-Schneeweiss

Keyword(s):

In Situ Hybridisation ◽

Chromosome Complement ◽

B Chromosome ◽

Chromosome 1 ◽

Fluorescence In Situ Hybridisation ◽

Genomic In Situ Hybridisation ◽

B Chromosome Evolution ◽

Diploid Level ◽

Prospero Autumnale

Supernumerary chromosomal segments (SCSs) represent additional chromosomal material that, unlike B chromosomes, is attached to the standard chromosome complement. The Prospero autumnale complex (Hyacinthaceae) is polymorphic for euchromatic large terminal SCSs located on the short arm of chromosome 1 in diploid cytotypes AA and B7B7, and tetraploid AAB7B7 and B6B6B7B7, in addition to on the short arm of chromosome 4 in polyploid B7B7B7B7 and B7B7B7B7B7B7 cytotypes. The genomic composition and evolutionary relationships among these SCSs have been assessed using fluorescence in situ hybridisation (FISH) with 5S and 35S ribosomal DNAs (rDNAs), satellite DNA PaB6, and a vertebrate-type telomeric repeat TTAGGG. Neither of the rDNA repeats were detected in SCSs, but most contained PaB6 and telomeric repeats, although these never spanned whole SCSs. Genomic in situ hybridisation (GISH) using A, B6, and B7 diploid genomic parental DNAs as probes revealed the consistently higher genomic affinity of SCSs in diploid hybrid B6B7 and allopolyploids AAB7B7 and B6B6B7B7 to genomic DNA of the B7 diploid cytotype. GISH results suggest a possible early origin of SCSs, especially that on chromosome 1, as by-products of the extensive genome restructuring within a putative ancestral P. autumnale B7 genome, predating the complex diversification at the diploid level and perhaps linked to B-chromosome evolution.

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