Loss of centromere function drives karyotype evolution in closely related Malassezia species

  1. Sundar Ram Sankaranarayanan
  2. Giuseppe Ianiri
  3. Marco A Coelho
  4. Md Hashim Reza
  5. Bhagya C Thimmappa
  6. Promit Ganguly
  7. Rakesh Netha Vadnala
  8. Sheng Sun
  9. Rahul Siddharthan
  10. Christian Tellgren-Roth
  11. Thomas L Dawson
  12. Joseph Heitman  Is a corresponding author
  13. Kaustuv Sanyal  Is a corresponding author
  1. Jawaharlal Nehru Centre for Advanced Scientific Research, India
  2. Duke University Medical Center, United States
  3. The Institute of Mathematical Sciences (HBNI), India
  4. Uppsala University, Sweden
  5. Agency for Science, Technology and Research, Singapore

Abstract

Genomic rearrangements associated with speciation often result in chromosome number variation among closely related species. Malassezia species show variable karyotypes ranging between 6 and 9 chromosomes. Here, we experimentally identified all 8 centromeres in M. sympodialis as 3 to 5 kb long kinetochore-bound regions spanning an AT-rich core and depleted of the canonical histone H3. Centromeres of similar sequence features were identified as CENP-A-rich regions in Malassezia furfur with 7 chromosomes, and histone H3 depleted regions in Malassezia slooffiae and Malassezia globosa with 9 chromosomes each. Analysis of synteny conservation across centromeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of chromosome number reduction from an inferred 9-chromosome ancestral state: (a) chromosome breakage followed by loss of centromere DNA and (b) centromere inactivation accompanied by changes in DNA sequence following chromosome-chromosome fusion. We propose AT-rich centromeres drive karyotype diversity in the Malassezia species complex through breakage and inactivation.

Data availability

The Mtw1 ChIP sequencing reads reported in this paper have been deposited under NCBI BioProject (Accession number PRJNA509412). The genome sequence assemblies of M. globosa, M. slooffiae, and M. furfur have been deposited in GenBank with accession numbers SAMN10720087, SAMN10720088, and SAMN13341476 respectively.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Sundar Ram Sankaranarayanan

    Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  2. Giuseppe Ianiri

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3278-8678
  3. Marco A Coelho

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Md Hashim Reza

    Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  5. Bhagya C Thimmappa

    Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  6. Promit Ganguly

    Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  7. Rakesh Netha Vadnala

    The Institute of Mathematical Sciences (HBNI), Chennai, India
    Competing interests
    The authors declare that no competing interests exist.
  8. Sheng Sun

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Rahul Siddharthan

    The Institute of Mathematical Sciences (HBNI), Chennai, India
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2233-0954
  10. Christian Tellgren-Roth

    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  11. Thomas L Dawson

    Skin Research Institute Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  12. Joseph Heitman

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
    For correspondence
    heitm001@duke.edu
    Competing interests
    The authors declare that no competing interests exist.
  13. Kaustuv Sanyal

    Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
    For correspondence
    sanyal@jncasr.ac.in
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6611-4073

Funding

Tata Innovation Fellowship (BT/HRT/35/01/03/2017)

  • Kaustuv Sanyal

Department of Biotechnology , Ministry of Science and Technology (BT/INF/22/SP27679/2018)

  • Kaustuv Sanyal

National Institutes of Health (R37 award-AI39115-21; R01 award-AI50113-15)

  • Joseph Heitman

Agency for Science, Technology and Research (H18/01a0/016)

  • Thomas L Dawson

Jawaharlal Nehru Centre for Advanced Scientific Research (Graduate student fellowship)

  • Sundar Ram Sankaranarayanan

Science and Engineering Research Board (PDF/2016/002858)

  • Md Hashim Reza

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Wolf-Dietrich Heyer, University of California, Davis, United States

Publication history

  1. Received: November 26, 2019
  2. Accepted: January 20, 2020
  3. Accepted Manuscript published: January 20, 2020 (version 1)
  4. Version of Record published: February 17, 2020 (version 2)

Copyright

© 2020, Sankaranarayanan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,682
    Page views
  • 392
    Downloads
  • 17
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sundar Ram Sankaranarayanan
  2. Giuseppe Ianiri
  3. Marco A Coelho
  4. Md Hashim Reza
  5. Bhagya C Thimmappa
  6. Promit Ganguly
  7. Rakesh Netha Vadnala
  8. Sheng Sun
  9. Rahul Siddharthan
  10. Christian Tellgren-Roth
  11. Thomas L Dawson
  12. Joseph Heitman
  13. Kaustuv Sanyal
(2020)
Loss of centromere function drives karyotype evolution in closely related Malassezia species
eLife 9:e53944.
https://doi.org/10.7554/eLife.53944

Further reading

    1. Genetics and Genomics
    Oguz Kanca et al.
    Research Advance Updated

    Previously, we described a large collection of Drosophila strains that each carry an artificial exon containing a T2AGAL4 cassette inserted in an intron of a target gene based on CRISPR-mediated homologous recombination. These alleles permit numerous applications and have proven to be very useful. Initially, the homologous recombination-based donor constructs had long homology arms (>500 bps) to promote precise integration of large constructs (>5 kb). Recently, we showed that in vivo linearization of the donor constructs enables insertion of large artificial exons in introns using short homology arms (100–200 bps). Shorter homology arms make it feasible to commercially synthesize homology donors and minimize the cloning steps for donor construct generation. Unfortunately, about 58% of Drosophila genes lack a suitable coding intron for integration of artificial exons in all of the annotated isoforms. Here, we report the development of new set of constructs that allow the replacement of the coding region of genes that lack suitable introns with a KozakGAL4 cassette, generating a knock-out/knock-in allele that expresses GAL4 similarly as the targeted gene. We also developed custom vector backbones to further facilitate and improve transgenesis. Synthesis of homology donor constructs in custom plasmid backbones that contain the target gene sgRNA obviates the need to inject a separate sgRNA plasmid and significantly increases the transgenesis efficiency. These upgrades will enable the targeting of nearly every fly gene, regardless of exon–intron structure, with a 70–80% success rate.

    1. Computational and Systems Biology
    2. Genetics and Genomics
    Jayashree Kumar et al.
    Research Article Updated

    Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.