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Planta

, Volume 250, Issue 6, pp 2173–2186 | Cite as

Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition

  • Brena Van-Lume
  • Yennifer Mata-Sucre
  • Mariana Báez
  • Tiago Ribeiro
  • Bruno Huettel
  • Edeline Gagnon
  • Ilia J. Leitch
  • Andrea Pedrosa-Harand
  • Gwilym P. Lewis
  • Gustavo SouzaEmail author
Original Article

Abstract

Main conclusion

We demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA.

Abstract

The Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.

Keywords

Chromosome evolution CMA+ bands Genome skimming Next-generation sequencing (NGS) RepeatExplorer Repetitive DNA SatDNA Tekay RT 

Abbreviations

CMA

Chromomicin A3

DAPI

4′,6-diamidino-2-phenylindole

FISH

Fluorescent in situ hybridization

LTR

Long-terminal repeat

RT

Retrotransposons

satDNA

Satellite DNA

TEs

Transposable elements

Notes

Acknowledgements

The authors wish to thank the Brazilian agencies Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE-APQ-0970-2.03/15) for financial support. G.S. thanks to Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) by a post-doctoral grant (Estágio Pós-Doutoral 88881.119479/2016-01). This study was financed in part by the CAPES (Brazil)—Finance Code 001. G.S. and A.P.-H. receive fellowship from CNPq (process numbers PQ-310693/2018-7 and PQ-310804/2017-5, respectively).

Supplementary material

425_2019_3287_MOESM1_ESM.docx (813 kb)
Supplementary material 1 (DOCX 813 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Brena Van-Lume
    • 1
  • Yennifer Mata-Sucre
    • 1
  • Mariana Báez
    • 1
  • Tiago Ribeiro
    • 1
    • 5
  • Bruno Huettel
    • 2
  • Edeline Gagnon
    • 3
  • Ilia J. Leitch
    • 4
  • Andrea Pedrosa-Harand
    • 1
  • Gwilym P. Lewis
    • 4
  • Gustavo Souza
    • 1
    Email author
  1. 1.Laboratory of Plant Cytogenetics and Evolution, Department of BotanyFederal University of PernambucoRecifeBrazil
  2. 2.Max Planck-Genome-center CologneCologneGermany
  3. 3.Royal Botanic Garden EdinburghEdinburghUK
  4. 4.Department of Comparative Plant and Fungal BiologyRichmondUK
  5. 5.Department of Botany and Ecology, Institute of BiosciencesFederal University of Mato GrossoCuiabáBrazil

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