scholarly journals Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 610 ◽  
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.

scholarly journals Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

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.

scholarly journals Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Frances E. Clark ◽  
Thomas D. Kocher
Keyword(s):  
Linkage Group ◽  
Transmission Rate ◽  
Cichlid Fish ◽  
Meiotic Drive ◽  
B Chromosome ◽  
Lake Malawi ◽  
B Chromosomes ◽  
Normal Complement ◽  
Biased Sex Ratio ◽  
Average Transmission

AbstractB chromosomes are extra, non-essential chromosomes present in addition to the normal complement of A chromosomes. Many species of cichlid fish in Lake Malawi carry a haploid, female-restricted B chromosome. Here we show that this B chromosome exhibits drive, with an average transmission rate of 70%. The offspring of B-transmitting females exhibit a strongly female-biased sex ratio. Genotyping of these offspring reveals the B chromosome carries a female sex determiner that is epistatically dominant to an XY system on linkage group 7. We suggest that this sex determiner evolved to enhance the meiotic drive of the B chromosome. This is some of the first evidence that female meiotic drive can lead to the invasion of new sex chromosomes solely to benefit the driver, and not to compensate for skewed sex ratios.

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

scholarly journals B-chromosome evolution

2000 ◽  
Vol 355 (1394) ◽  
pp. 163-178 ◽  
Author(s):  
Juan Pedro M. Camacho ◽  
Timothy F. Sharbel ◽  
Leo W. Beukeboom
Keyword(s):  
Molecular Evolution ◽  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
B Chromosome ◽  
B Chromosomes ◽  
Transmission Rates ◽  
Term Evolution ◽  
B Chromosome Evolution

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.

scholarly journals Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jordana Inácio Nascimento-Oliveira ◽  
Bruno Evaristo Almeida Fantinatti ◽  
Ivan Rodrigo Wolf ◽  
Adauto Lima Cardoso ◽  
Erica Ramos ◽  
...  
Keyword(s):  
Cichlid Fish ◽  
B Chromosome ◽  
B Chromosomes ◽  
Differentially Expressed ◽  
Protein Coding ◽  
Mirna Targets ◽  
High Interaction ◽  
Big Data Technologies ◽  
Interactive Networks ◽  
Mirnas Expression

Abstract Background B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood. Results We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B−) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples. Conclusions This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.

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

2017 ◽  
Vol 152 (4) ◽  
pp. 213-221 ◽  
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.

scholarly journals Structural and Functional Analysis of Transposable Elements Focusing on B Chromosomes of the Cichlid Fish Astatotilapia latifasciata

2018 ◽  
Author(s):  
Rafael Coan ◽  
Cesar Martins
Keyword(s):  
Transposable Elements ◽  
Repetitive Sequences ◽  
Chromosome Complement ◽  
Cichlid Fish ◽  
B Chromosome ◽  
B Chromosomes ◽  
Sequencing Data ◽  
Taxonomic Groups ◽  
African Cichlids

B chromosomes (B) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). Bs origin is generally linked to the A chromosome complement (A). The first report of a B chromosome in African cichlids was on Astatotilapia latifasciata, which can harbor 0, 1 or 2 B chromosomes. Classical cytogenetics studies found high TE content on the species B chromosome. In this study, we aim to understand TE composition and expression on A. latifasciata genome and its relation to the B chromosome. We use bioinformatics analysis to explore TEs genome organization and also their composition on the B chromosome. Bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq) we showed that all major TE classes are transcribed in brain, muscle and male/female gonads. The evaluation of TE expression between B- and B+ individuals showed that few elements have differential expression among groups and expanded B elements were not highly transcribed. Putative silencing mechanisms may the acting on the B chromosome of A. latifasciata to prevent adverse consequences of repeat transcription and mobilization in the genome.

scholarly journals Dynamic Sequence Evolution of a Sex-Associated B Chromosome in Lake Malawi Cichlid Fish

2016 ◽  
Vol 108 (1) ◽  
pp. 53-62 ◽  
Author(s):  
Frances E. Clark ◽  
Matthew A. Conte ◽  
Irani A. Ferreira-Bravo ◽  
Andreia B. Poletto ◽  
Cesar Martins ◽  
...  
Keyword(s):  
Cichlid Fish ◽  
B Chromosome ◽  
Lake Malawi ◽  
Sequence Evolution

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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