Abstract
Main conclusion
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses.
Abstract
Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
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Abbreviations
- AAF:
-
Assembly and alignment free
- cpSSR:
-
Chloroplast simple sequence repeat
- IR:
-
Inverted repeat
- LSC:
-
Large single copy
- Pi:
-
Nucleotide diversity
- SSC:
-
Small single copy
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Acknowledgements
We thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, PELD process 403770/2012-2, Universal process 426738/2018-7), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES code 0001), and the Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE, processes BIC-0846-2.02/17, BIC-0624- 2.02/18) for financial support. We also thank Tatiane Menezes for assistance during field work, Davi Jamelli for drawing the map, Brena Van-Lume and Yennifer Mata-Sucre for DNA extraction and Benoit Loeuille and Cícero Almeida for critical reading of the manuscript. We also would like to thank the Sequencing Platform of CB-UFPE and Heidi Lacerda from LABBE for their help with genotyping. APH, GS, and IRL also thank CNPq for productivity grants (processes 310804/2017-5, 310693/2018-7, and 308300/2018-1, respectively).
Funding
Funding for this study was provided by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, PELD process 403770/2012-2, Universal process 426738/2018-7), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES code 001), and the Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE, processes BIC-0846-2.02/17, BIC-0624-2.02/18).
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425_2021_3655_MOESM1_ESM.tif
Supplementary file1 Fig. S1 Phylogenetic tree of twenty-six species from the Caesalpinia group obtained by different partitions of the plastome withdrawing the gaps in the alignment. Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were performed for each partition. Bootstraps and Posterior probabilities are indicated. Conflict positions are marked in red. Leucaena trichandra and Senna tora are outgroups. a, Small Single Copy region (SSC, 13,959 bp). b, Long Single Copy region (LSC, 70,992 bp). c, Alignment of 113 genes (83,728 bp). d, Total alignment without the IRa (110,495 bp) (TIF 26546 KB)
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Supplementary file2 Fig. S2 Phylogenetic tree of twenty-six species from the Caesalpinia group obtained by different partitions of the plastome and including the gaps. Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were performed for each partition. The Assembly and Alignment-Free (AAF) analysis was performed with total plastome data. Bootstraps and Posterior probabilities are indicated. Conflict positions are marked in red. Leucaena trichandra and Senna tora are outgroups. a, Small Single Copy region (SSC). b, Long Single Copy region (LSC). c, Alignment of 113 genes. d, Total alignment without IRa, including the Assembly and Alignment Free (AAF) phylogenetic tree (TIF 37023 KB)
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Aecyo, P., Marques, A., Huettel, B. et al. Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics. Planta 254, 27 (2021). https://doi.org/10.1007/s00425-021-03655-8
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DOI: https://doi.org/10.1007/s00425-021-03655-8