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The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes

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Abstract

Dipteryx alata Vog. (Fabaceae) is a species of tree native to the Brazilian Cerrado that has economic potential due to its use for food, forage, medicinal, recovery of degraded areas, landscaping and wood extraction. The objective of the present study was to sequence, assemble and annotate the chloroplast genome sequence (cp genome) of D. alata and perform comparative analysis with the cp genome of other species of Fabaceae. The chloroplast is 158,647 bp in length and exhibits a quadripartite structure, with a pair of inverted repeats (IRs: 24,948 bp) separated by the large single copy (LSC: 88,769 bp) and small single copy (SSC: 19,982 bp) regions. It contains 125 genes, of which 109 are unique, including 76 protein-coding genes (CDS), 29 transporter RNA genes (tRNA) and four ribosomal RNA genes (rRNA). Comparative analysis of the cp genome of D. alata with the genome of other Fabaceae indicated similarity to the gene content, but gene losses and rearrangements have been identified. Comparative analysis indicated that the genes located in the IR regions were the most conserved, with average values of nucleotide diversity (Pi) of 0.03 followed by SSC (Pi-0.08) and LSC (Pi-0.09). Some non-coding regions exhibited relatively high divergence of sequences. The chloroplast genome contains also 131 simple sequence repeats (SSRs) of which 121 are located in intergenic regions and ten in protein-coding regions. The most frequent SSR repetition was A/T and AT/TA. The complete cp genome sequence of D. alata reported in this paper represents a valuable addition to the scarce available genomic resources for this Brazilian Cerrado species. This work shows the first complete plastoma of a species belonging to the ADA clade, within the Papilionoideae subfamily, and contributes to improve studies of phylogeny and plastoma evolution of the Fabaceae family. In addition, it provides new genetic information on plastid sequences useful for designing conservation and breeding strategies. Chloroplast sequences will be useful in phylogenetic studies, population genetics, phylogeography and molecular systematics.

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Acknowledgements

Our research was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Fundação de Amparo à Pesquisa do Estado de Goiás (FAPEG). Project “Núcleo de Excelência em Recursos Genéticos Vegetais do Cerrado (CERGEN)”-GECER (PRONEX/FAPEG/CNPq#CP07-2012). Research network GENPAC (“Geographical Genetics and Regional Planning for Natural Resources in Brazilian Cerrado”) from CNPq/Fapeg/PRO-CENTRO-OESTE nº 31/2010, GENPAC 02-Proc. 563839/2010-4 and 201110267000125. M.P.C.T. and T.N.S has been continuously supported by productivity fellowships from “Conselho Nacional de Desenvolvimento Científico e Tecnológico” (CNPq), and A.M.A has been supported by doctorate and postdoctoral fellowships from “Coordenação de Aperfeiçoamento de Pessoal de Nível Superior” (Capes), which we gratefully acknowledge. Current research is developed in the context of National Institutes for Science and Technology (INCT) in Ecology, Evolution and Biodiversity Conservation, supported by MCTIC/CNPq (Proc. 465610/2014-5) and FAPEG.

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Telles and Antunes elaborated the research project. Telles collected the samples. Antunes extracted the genomic DNA. Telles and Antunes constructed the DNA Libraries and genome sequencing. Antunes, Novaes and Coelho conducted the bioinformatics analyses and generated assembly and annotations of the genome. Antunes andTargueta conducted the phylogenetic analysis. Antunes uploaded the raw read data, genome assembly and annotation in the NCBI databases. Antunes wrote the paper. Telles, Soares, Targueta, Novaes and Coelho reviewed the paper. All authors read and approved the final manuscript.

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Correspondence to Adriana Maria Antunes.

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Antunes, A.M., Soares, T.N., Targueta, C.P. et al. The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes. Braz. J. Bot 43, 271–282 (2020). https://doi.org/10.1007/s40415-020-00599-3

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