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The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata

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Abstract

B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure. The absence of introns and presence of transposable elements with a reverse transcriptase domain flanking hnRNP Q-like sequences suggest that this gene was retroinserted into the B chromosome. RNA-Seq analysis did not show that the B variant retroinserted copies are transcriptionally active. However, RT-qPCR results showed variations in the canonical hnRNP Q-like copy expression levels among exons, tissues, sex, and B presence/absence. Although the patterns of transcription are not well understood, the exons of the B retrocopies were overexpressed, and a bias for female B+ expression was also observed. These results suggest that retroinsertion is an additional and important mechanism contributing to B chromosome formation. Furthermore, these findings indicate a bias towards female differential expression of B chromosome sequences, suggesting that B chromosomes and sex determination are somehow associated in cichlids.

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Abbreviations

CDS:

Coding DNA sequence

FPKM:

Fragments per kilobase of exon per million fragments mapped

FR:

Flanking regions

GDR:

Gene dose ratio

GLM:

Generalized linear model

hnRNP Q-like:

Heterogeneous nuclear ribonucleoprotein Q-like

ORFs:

Open reading frames

qPCR:

Quantitative PCR

RIN:

RNA integrity number

RT-qPCR:

Reverse transcription quantitative PCR

SNVs:

Single nucleotide variations

TEs:

Transposable elements

UBCE:

Ubiquitin-conjugating enzyme

UTRs:

Untranslated regions

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Acknowledgments

This work was financially supported through grants from the São Paulo Research Foundation (FAPESP) (2011/03807-7; 2013/04533-3; 2015/16661-1) and the National Counsel of Technological and Scientific Development (CNPq) (474684/2013-0; 305321/2015-3).

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Author notes

  1. These authors contributed equally to this work: BO Carmello and RLB Coan.

Authors and Affiliations

  1. Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil

    Bianca O. Carmello, Rafael L. B. Coan, Adauto L. Cardoso, Erica Ramos, Bruno E. A. Fantinatti, Diego F. Marques & Cesar Martins

  2. Institute of Biosciences, Department of Biostatistics, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil

    Rogério A. Oliveira

  3. Institute of Biosciences, Agronomic Science School, Department of Bioprocess and Biotechnology, Sao Paulo State University (UNESP), Botucatu, SP, 18610-307, Brazil

    Guilherme T. Valente

Authors
  1. Bianca O. Carmello
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  2. Rafael L. B. Coan
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  3. Adauto L. Cardoso
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  4. Erica Ramos
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  5. Bruno E. A. Fantinatti
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  7. Rogério A. Oliveira
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  8. Guilherme T. Valente
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  9. Cesar Martins
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Corresponding author

Correspondence to Cesar Martins.

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Ethics approval

The experimental procedure was conducted according to the international guidelines of Sao Paulo State University and approved through the Institutional Animal Care and Use Committee (IACUC) (protocol no. 486-2013-CEEA/IBB/UNESP). The animals were euthanized via immersion in a water bath containing benzocaine at 250 mg/l for 10 min.

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All raw data are available in SaciBase (http://sacibase.ibb.unesp.br/).

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The authors declare that they have no competing interests.

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Responsible Editor: Fengtang Yang.

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Carmello, B.O., Coan, R.L.B., Cardoso, A.L. et al. The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata . Chromosome Res 25, 277–290 (2017). https://doi.org/10.1007/s10577-017-9561-0

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