Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

Download Full-text

Identification of a family of repeated sequences on the rye B chromosome

Genome ◽

10.1139/g90-137 ◽

1990 ◽

Vol 33 (6) ◽

pp. 908-913 ◽

Cited By ~ 62

Author(s):

Michael J. Sandery ◽

John W. Forster ◽

Richard Blunden ◽

R. Neil Jones

Keyword(s):

Secale Cereale ◽

Direct Evidence ◽

B Chromosome ◽

Repeat Sequence ◽

B Chromosomes ◽

Repeated Sequences ◽

Significant Heterogeneity ◽

Origin And Evolution ◽

The Family

A novel family of highly repeated sequences on the B chromosome of rye (Secale cereale) has been identified. The D1100 family has not been detected on the rye A chromosomes and shows little or no homology to any previously described repeat sequence in rye. In addition, different rye species, and different B chromosomes within the same species, show significant heterogeneity in the arrangement of the D1100 sequences. An EcoRI clone of a member of the family has been obtained. These results provide direct evidence for the organisation and nature of the B-chromosome DNA in rye, and they are discussed in relation to the origin and evolution of rye B chromosomes.Key words: B chromosome, Secale cereale, repeated sequences.

Download Full-text

De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes

Chromosoma ◽

10.1007/s00412-019-00707-7 ◽

2019 ◽

Vol 128 (2) ◽

pp. 81-96 ◽

Cited By ~ 3

Author(s):

Maryam Jehangir ◽

Syed F. Ahmad ◽

Adauto L. Cardoso ◽

Erica Ramos ◽

Guilherme T. Valente ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Cichlid Fish ◽

B Chromosomes ◽

De Novo Genome Assembly ◽

Genomic Polymorphism

Download Full-text

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.

Download Full-text

Magnetotactic bacteria in Tengchong hot springs, China

10.5194/egusphere-egu2020-12310 ◽

2020 ◽

Author(s):

Jia Liu ◽

Wensi Zhang ◽

Fang Yuan ◽

Yongxin Pan ◽

Wei Lin

Keyword(s):

Hot Springs ◽

Hot Spring ◽

Extreme Environments ◽

Magnetotactic Bacteria ◽

Origin And Evolution ◽

Water Columns ◽

Genomic Analyses ◽

Ph Range ◽

Identification And Characterization

<p>Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and can use the geomagnetic field to navigate towards specific microenvironments in water columns and sediments. MTB are a model system to study the mechanisms of microbial magnetoreception and biomineralization. The majority of MTB identified so far are from environments with pH values near neutral and at the normal range of temperature. MTB from extreme environments, such as hot springs, has not been observed and described until recently. However, our knowledge on extremophilic MTB is still very limited. Here we report the identification and characterization of various MTB in Tengchong hot springs, China, with a temperature range of 41.3-69.5 &#176;C and a pH range of 7.1-8.6. Although MTB are diverse in cell morphology, they all form bullet-shaped magnetite magnetosomes organized into either one chain or multiple bundles of chains. Through genome-resolved metagenomics, we have reconstructed five genome bins of hot spring MTB that are all affiliated within the <em>Nitrspirae</em> phylum. Genomic analyses and metabolic reconstructions are now in progress. These results will help to better understand the extremophilic MTB and may shed new lights on the origin and evolution of microbial magnetoreception and biomineralization.</p>

Download Full-text

Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species

Genes ◽

10.3390/genes9110523 ◽

2018 ◽

Vol 9 (11) ◽

pp. 523 ◽

Cited By ~ 9

Author(s):

Diogo Milani ◽

Vanessa Bardella ◽

Ana Ferretti ◽

Octavio Palacios-Gimenez ◽

Adriana Melo ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescent In Situ Hybridization ◽

B Chromosome ◽

B Chromosomes ◽

Satellite Dnas ◽

Grasshopper Species ◽

Repetitive Dnas ◽

Origin And Evolution ◽

Chromosomal Position

Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species.

Download Full-text

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

Scientific Reports ◽

10.1038/s41598-019-55774-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

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.

Download Full-text

The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies

BMC Genetics ◽

10.1186/1471-2156-11-1 ◽

2010 ◽

Vol 11 (1) ◽

pp. 1 ◽

Cited By ~ 56

Author(s):

Andréia B Poletto ◽

Irani A Ferreira ◽

Cesar Martins

Keyword(s):

18S Rrna ◽

Cichlid Fish ◽

18S Rrna Gene ◽

B Chromosomes ◽

Rrna Gene ◽

African Cichlid ◽

Gene Copies

Download Full-text

The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

Genome Biology and Evolution ◽

10.1093/gbe/evz260 ◽

2019 ◽

Vol 12 (1) ◽

pp. 3534-3549

Author(s):

Mosè Manni ◽

Felipe A Simao ◽

Hugh M Robertson ◽

Marco A Gabaglio ◽

Robert M Waterhouse ◽

...

Keyword(s):

Draft Genome ◽

Gene Families ◽

Sister Group ◽

Sensu Stricto ◽

Comparative Genomic ◽

Gene Repertoire ◽

Animal Group ◽

Origin And Evolution ◽

Genomic Analyses ◽

Metabolism Gene

Abstract The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-021-07651-w ◽

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.

Download Full-text