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

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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.

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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

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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).

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  1. Tiago Ribeiro

    Present address: Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Av. Fernando Correa da Costa, 2.367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil

  2. Brena Van-Lume and Yennifer Mata-Sucre have contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil

    Brena Van-Lume, Yennifer Mata-Sucre, Mariana Báez, Tiago Ribeiro, Andrea Pedrosa-Harand & Gustavo Souza

  2. Max Planck-Genome-center Cologne, Cologne, Germany

    Bruno Huettel

  3. Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK

    Edeline Gagnon

  4. Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK

    Ilia J. Leitch & Gwilym P. Lewis

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Van-Lume, B., Mata-Sucre, Y., Báez, M. et al. Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition. Planta 250, 2173–2186 (2019). https://doi.org/10.1007/s00425-019-03287-z

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