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

Jehangir, Maryam; Ahmad, Syed Farhan; Cardoso, Adauto Lima; Valente, Guilherme Targino; Martins, Cesar

doi:10.1007/s00412-019-00707-7

Cited by 14 publications

(23 citation statements)

References 85 publications

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“…Among the B enriched functions, we found that most of them are involved in developmental processes, particularly morphogenesis. The gene indian hedgehog b ( ihhb ), involved in morphogenesis, was previously identified as highly duplicated on the B chromosome of the cichlid fishes [ 61 , 62 ]. These commonly enriched functions shared among the Bs of different species suggest that B chromosomes exhibit a conserved behavior to acquire a certain role, although their genetic makeup in may vary across different taxa.…”

Section: Discussionmentioning

confidence: 99%

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

et al. 2020

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Background One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis. Results We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success. Conclusions This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.

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Section: Discussionmentioning

confidence: 99%

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

et al. 2020

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“…The research using Bs as a model can help elevate our understanding about the mechanisms that can shape the formation of new chromosomes during the evolutionary course of a genome. Although the latest studies [24,25,43,103] involving large scale genome analysis of polymorphisms and variations of B sequences have enabled us to predict the process of formation and to trace the evolutionary history of Bs, our knowledge of how genomic variations cause their evolution is still limited. Chromosome rearrangements are triggers of evolutionary changes and are also of huge importance in disease origins.…”

Section: Bs: An Exciting Model System To Study Genome Evolutionmentioning

confidence: 99%

The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses

Ahmad

Martins

2019

Cells

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Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call “B-omics”. We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.

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“…The third approach was predicting miRNAs using the miRBase reference and the sRNAseq, as the previous strategies, but set the genomic “B-blocks” filtered by Jehangir et al [ 37 ] as the reference background. With this strategy we would like to confirm if no duplicated miRNAs were missed in our manual coverage ratio strategy (first strategy).…”

Section: Resultsmentioning

confidence: 99%

“…B chromosomes were detected in several cichlid species [ 30 , 33 , 34 ]. Among them, the African cichlid Astatotilapia latifasciata , which carries one or two B chromosomes in both sexes, has been extensively investigated through classical cytogenetics [ 33 , 35 ], molecular biology [ 9 , 36 ] and, more recently, genomic approaches [ 11 , 15 , 19 , 37 ]. Repetitive elements [ 9 ], coding genes [ 11 ] and a long noncoding RNA [ 19 ] have already been identified in the B chromosome of A. latifasciata.…”

Section: Introductionmentioning

confidence: 99%

“…In this work, the microdissected B chromosome sequences were compared to Metriaclima zebra reference genome, and the first B-genes of A. latifasciata were reported. Later, the A. latifasciata draft genome was constructed using Illumina high scale data and identified several duplicated contigs in the B chromosome [ 37 ]. The coverage ratio compares coverage of sequenced among B − and B + samples aligned against a reference assembled genome, which allows to identify higher coverage regions on the B + sequencing dataset, that represent duplicated regions in the B chromosome [ 11 , 39 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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

Cited by 14 publications

References 85 publications

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses

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

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