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Current Genomics

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ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

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Research Article

Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses

Author(s): Juliana Borges Pereira Brito*, Adriana Maria Antunes, Ramilla dos Santos Braga Ferreira, Mariana Pires de Campos Telles, Cíntia Pelegrineti Targueta and Thannya Nascimento Soares

Volume 24, Issue 4, 2023

Published on: 25 October, 2023

Page: [236 - 249] Pages: 14

DOI: 10.2174/0113892029244147231016050434

Price: $65

Abstract

Background: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.

Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.

Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.

Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.

Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.

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[1]
Khan, A.; Asaf, S.; Khan, A.L.; Al-Harrasi, A.; Al-Sudairy, O. AbdulKareem, N.M.; Khan, A.; Shehzad, T.; Alsaady, N.; Al-Lawati, A.; Al-Rawahi, A.; Shinwari, Z.K. First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees. PLoS One, 2019, 14(1), e0208511.
[http://dx.doi.org/10.1371/journal.pone.0208511] [PMID: 30629590]
[2]
Li, W.; Chen, C.; Bai, G.; Li, B.; Chen, H.; Zhou, Y.; Li, S. The complete chloroplast genome sequence of Abies chensiensis (Pinaceae: Abietoideae), an endangered species endemic to China. Mitochondrial DNA B Resour., 2018, 3(2), 984-985.
[http://dx.doi.org/10.1080/23802359.2018.1507636] [PMID: 33474387]
[3]
Daniell, H.; Lin, C.S.; Yu, M.; Chang, W.J. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol., 2016, 17(1), 134.
[http://dx.doi.org/10.1186/s13059-016-1004-2] [PMID: 27339192]
[4]
Kersten, B.; Faivre Rampant, P.; Mader, M.; Le Paslier, M.C.; Bounon, R.; Berard, A.; Vettori, C.; Schroeder, H.; Leplé, J.C.; Fladung, M. Genome sequences of populus tremula chloroplast and mitochondrion: implications for holistic poplar breeding. PLoS One, 2016, 11(1), e0147209.
[http://dx.doi.org/10.1371/journal.pone.0147209] [PMID: 26800039]
[5]
Xiao-Ming, Z.; Junrui, W.; Li, F.; Sha, L.; Hongbo, P.; Lan, Q.; Jing, L.; Yan, S.; Weihua, Q.; Lifang, Z.; Yunlian, C.; Qingwen, Y. Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Sci. Rep., 2017, 7(1), 1555.
[http://dx.doi.org/10.1038/s41598-017-01518-5] [PMID: 28484234]
[6]
Brouard, J.S.; Otis, C.; Lemieux, C.; Turmel, M. The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae. Genome Biol. Evol., 2010, 2(0), 240-256.
[http://dx.doi.org/10.1093/gbe/evq014] [PMID: 20624729]
[7]
Mohanta, T.K.; Mishra, A.K.; Khan, A.; Hashem, A.; Abd Allah, E.F.; Al-Harrasi, A. Gene loss and evolution of the plastome. Genes, 2020, 11(10), 1133.
[http://dx.doi.org/10.3390/genes11101133] [PMID: 32992972]
[8]
Souza, U.J.B.; Nunes, R.; Targueta, C.P.; Diniz-Filho, J.A.F.; Telles, M.P.C. The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): Comparative analysis with related Mimosoid species. Sci. Rep., 2019, 9(1), 14206.
[http://dx.doi.org/10.1038/s41598-019-50620-3] [PMID: 31578450]
[9]
Xue, S.; Shi, T.; Luo, W.; Ni, X.; Iqbal, S.; Ni, Z.; Huang, X.; Yao, D.; Shen, Z.; Gao, Z. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Hortic. Res., 2019, 6(1), 89.
[http://dx.doi.org/10.1038/s41438-019-0171-1] [PMID: 31666958]
[10]
Antunes, A.M.; Soares, T.N.; Targueta, C.P.; Novaes, E.; Coelho, A.S.G.; Telles, M.P.C. The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): Genomic features and comparative analysis with other legume genomes. Rev. Bras. Bot., 2020, 43(2), 271-282.
[http://dx.doi.org/10.1007/s40415-020-00599-3]
[11]
Dong, F.; Lin, Z.; Lin, J.; Ming, R.; Zhang, W. Chloroplast genome of rambutan and comparative analyses in sapindaceae. Plants, 2021, 10(2), 283.
[http://dx.doi.org/10.3390/plants10020283] [PMID: 33540810]
[12]
Wang, W.; Yang, T.; Wang, H.L.; Li, Z.J.; Ni, J.W.; Su, S.; Xu, X.Q. Comparative and phylogenetic analyses of the complete chloroplast genomes of six almond species (Prunus spp. L.). Sci. Rep., 2020, 10(1), 10137.
[http://dx.doi.org/10.1038/s41598-020-67264-3] [PMID: 32576920]
[13]
Zhang, X.F.; Landis, J.B.; Wang, H.X.; Zhu, Z.X.; Wang, H.F. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC Plant Biol., 2021, 21(1), 219.
[http://dx.doi.org/10.1186/s12870-021-02985-9] [PMID: 33992095]
[14]
De Almeida, S.P.; Proença, C.E.B.; Sano, S.M.; Ribeiro, J.F. Cerrado: Espécies vegetais úteis; Embrapa Publisher, 1998.
[15]
Barroso, Gm.; Morim, Mp. Frutos e sementes. Morfologia aplicada à sistemática de dicotiledôneas, , Editora UFV: Viçosa.1999
[16]
Cardoso, D.; Pennington, R.T.; de Queiroz, L.P.; Boatwright, J.S.; Van Wyk, B-E.; Wojciechowski, M.F.; Lavin, M. Reconstructing the deep-branching relationships of the papilionoid legumes. S. Afr. J. Bot., 2013, 89, 58-75.
[http://dx.doi.org/10.1016/j.sajb.2013.05.001]
[17]
LIMA. S. Filogeografia de Pterodon emarginatus E Pterodon pubescens (LEGUMINOSAE); PhD Universidade Federal de Goiás, 2019.
[18]
Bavaresco, O.S.A.; Pereira, I.C.P.; Melo, C.D.; Lobato, F.; Falcai, A. Bomfim, MRQ Utilização popular da Pterodon spp no tratamento de doenças reumáticas. Biomed. Res. J., 2016, 8(1), 81.
[http://dx.doi.org/10.24863/rib.v8i1.32]
[19]
Araújo, L.A.; Assunção, L.A.; Silva-Júnior, N.J.; Lemes, S.R.; Melo-Reis, P.R. Angiogenic activity of sucupira (Pterodon emarginatus) oil. Sci. Med, 2015, 1-7.
[http://dx.doi.org/10.15448/1980-6108.2015.2.20351]
[20]
Hansen, D.; Haraguchi, M.; Alonso, A. Pharmaceutical properties of ‘sucupira’ (Pterodon spp.). Braz. J. Pharm. Sci., 2010, 46(4), 607-616.
[http://dx.doi.org/10.1590/S1984-82502010000400002]
[21]
Negri, G.; Mattei, R.; Mendes, F.R. Antinociceptive activity of the HPLC- and MS-standardized hydroethanolic extract of Pterodon emarginatus Vogel leaves. Phytomedicine, 2014, 21(8-9), 1062-1069.
[http://dx.doi.org/10.1016/j.phymed.2014.04.009] [PMID: 24854569]
[22]
Oliveira, A.E.M.F.M.; Duarte, J.L.; Amado, J.R.R.; Cruz, R.A.S.; Rocha, C.F.; Souto, R.N.P.; Ferreira, R.M.A.; Santos, K.; da Conceição, E.C.; de Oliveira, L.A.R.; Kelecom, A.; Fernandes, C.P.; Carvalho, J.C.T. Development of a larvicidal nanoemulsion with pterodon emarginatus vogel oil. PLoS One, 2016, 11(1), e0145835.
[http://dx.doi.org/10.1371/journal.pone.0145835] [PMID: 26742099]
[23]
Pascoa, H.; Diniz, D.G.A.; Florentino, I.F.; Costa, E.A.; Bara, M.T.F. Microemulsion based on Pterodon emarginatus oil and its anti-inflammatory potential. Braz. J. Pharm. Sci., 2015, 51(1), 117-125.
[http://dx.doi.org/10.1590/S1984-82502015000100013]
[24]
Doyle, J.J.; Doyle, J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue., 1987. Available from: https://worldveg.tind.io/record/33886
[25]
Andrews, S. A quality control tool for high throughput sequence data., Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
[26]
Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30(15), 2114-2120.
[http://dx.doi.org/10.1093/bioinformatics/btu170] [PMID: 24695404]
[27]
Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 2009, 10(3), R25.
[http://dx.doi.org/10.1186/gb-2009-10-3-r25] [PMID: 19261174]
[28]
Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; Pyshkin, A.V.; Sirotkin, A.V.; Vyahhi, N.; Tesler, G.; Alekseyev, M.A.; Pevzner, P.A. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 2012, 19(5), 455-477.
[http://dx.doi.org/10.1089/cmb.2012.0021] [PMID: 22506599]
[29]
Wyman, S.K.; Jansen, R.K.; Boore, J.L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 2004, 20(17), 3252-3255.
[http://dx.doi.org/10.1093/bioinformatics/bth352] [PMID: 15180927]
[30]
Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E.S.; Fischer, A.; Bock, R.; Greiner, S. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res., 2017, 45(W1), W6-W11.
[http://dx.doi.org/10.1093/nar/gkx391] [PMID: 28486635]
[31]
Lagesen, K.; Hallin, P.; Rødland, E.A.; Stærfeldt, H.H.; Rognes, T.; Ussery, D.W. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res., 2007, 35(9), 3100-3108.
[http://dx.doi.org/10.1093/nar/gkm160] [PMID: 17452365]
[32]
Lowe, T.M.; Eddy, S.R. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 1997, 25(5), 955-964.
[http://dx.doi.org/10.1093/nar/25.5.955] [PMID: 9023104]
[33]
Lohse, M.; Nagel, A.; Herter, T.; May, P.; Schroda, M.; Zrenner, R.; Tohge, T.; Fernie, A.R.; Stitt, M.; Usadel, B. Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ., 2014, 37(5), 1250-1258.
[http://dx.doi.org/10.1111/pce.12231] [PMID: 24237261]
[34]
Beier, S.; Thiel, T.; Münch, T.; Scholz, U.; Mascher, M. MISA-web: A web server for microsatellite prediction. Bioinformatics, 2017, 33(16), 2583-2585.
[http://dx.doi.org/10.1093/bioinformatics/btx198] [PMID: 28398459]
[35]
Untergasser, A.; Cutcutache, I.; Koressaar, T.; Ye, J.; Faircloth, B.C.; Remm, M.; Rozen, S.G. Primer3-new capabilities and interfaces. Nucleic Acids Res., 2012, 40(15), e115.
[http://dx.doi.org/10.1093/nar/gks596] [PMID: 22730293]
[36]
Frazer, KA; Pachter, L; Poliakov, A; Rubin, EM; Dubchak, I VISTA: Computational tools for comparative genomics. Nucleic Acids Res., 2004, 32(((Web Server issue))), W273-W279.
[http://dx.doi.org/10.1093/nar/gkh458]
[37]
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol., 1990, 215(3), 403-410.
[http://dx.doi.org/10.1016/S0022-2836(05)80360-2] [PMID: 2231712]
[38]
Thompson, J.D.; Higgins, D.G.; Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 1994, 22(22), 4673-4680.
[http://dx.doi.org/10.1093/nar/22.22.4673] [PMID: 7984417]
[39]
Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 2018, 35(6), 1547-1549.
[http://dx.doi.org/10.1093/molbev/msy096] [PMID: 29722887]
[40]
Rozas, J.; Ferrer-Mata, A.; Sánchez-DelBarrio, J.C.; Guirao-Rico, S.; Librado, P.; Ramos-Onsins, S.E.; Sánchez-Gracia, A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol., 2017, 34(12), 3299-3302.
[http://dx.doi.org/10.1093/molbev/msx248] [PMID: 29029172]
[41]
Martin, G.E.; Rousseau-Gueutin, M.; Cordonnier, S.; Lima, O.; Michon-Coudouel, S.; Naquin, D.; de Carvalho, J.F.; Aïnouche, M.; Salmon, A.; Aïnouche, A. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: Evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Ann. Bot., 2014, 113(7), 1197-1210.
[http://dx.doi.org/10.1093/aob/mcu050] [PMID: 24769537]
[42]
Mader, M.; Pakull, B.; Blanc-Jolivet, C.; Paulini-Drewes, M.; Bouda, Z.; Degen, B.; Small, I.; Kersten, B. Complete chloroplast genome sequences of four meliaceae species and comparative analyses. Int. J. Mol. Sci., 2018, 19(3), 701.
[http://dx.doi.org/10.3390/ijms19030701] [PMID: 29494509]
[43]
Qian, J.; Song, J.; Gao, H.; Zhu, Y.; Xu, J.; Pang, X.; Yao, H.; Sun, C.; Li, X.; Li, C.; Liu, J.; Xu, H.; Chen, S. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One, 2013, 8(2), e57607.
[http://dx.doi.org/10.1371/journal.pone.0057607] [PMID: 23460883]
[44]
Guo, X.; Castillo-Ramírez, S.; González, V.; Bustos, P.; Luís Fernández-Vázquez, J.; Santamaría, R.; Arellano, J.; Cevallos, M.A.; Dávila, G. Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics, 2007, 8(1), 228.
[http://dx.doi.org/10.1186/1471-2164-8-228] [PMID: 17623083]
[45]
Saski, C.; Lee, S.B.; Daniell, H.; Wood, T.C.; Tomkins, J.; Kim, H.G.; Jansen, R.K. Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes. Plant Mol. Biol., 2005, 59(2), 309-322.
[http://dx.doi.org/10.1007/s11103-005-8882-0] [PMID: 16247559]
[46]
Liu, W.; Kong, H.; Zhou, J.; Fritsch, P.; Hao, G.; Gong, W. Complete chloroplast genome of cercis chuniana (fabaceae) with structural and genetic comparison to six species in caesalpinioideae. Int. J. Mol. Sci., 2018, 19(5), 1286.
[http://dx.doi.org/10.3390/ijms19051286] [PMID: 29693617]
[47]
Gao, X.; Zhang, X.; Meng, H.; Li, J.; Zhang, D.; Liu, C. Comparative chloroplast genomes of Paris Sect. Marmorata: Insights into repeat regions and evolutionary implications. BMC Genomics, 2018, 19(S10), 878.
[http://dx.doi.org/10.1186/s12864-018-5281-x] [PMID: 30598104]
[48]
Jansen, R.K.; Wojciechowski, M.F.; Sanniyasi, E.; Lee, S.B.; Daniell, H. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol. Phylogenet. Evol., 2008, 48(3), 1204-1217.
[http://dx.doi.org/10.1016/j.ympev.2008.06.013] [PMID: 18638561]
[49]
Keller, J.; Rousseau-Gueutin, M.; Martin, G.E.; Morice, J.; Boutte, J.; Coissac, E.; Ourari, M.; Aïnouche, M.; Salmon, A.; Cabello-Hurtado, F.; Aïnouche, A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res., 2017, 24(4), 343-358.
[http://dx.doi.org/10.1093/dnares/dsx006] [PMID: 28338826]
[50]
Tangphatsornruang, S.; Sangsrakru, D.; Chanprasert, J.; Uthaipaisanwong, P.; Yoocha, T.; Jomchai, N.; Tragoonrung, S. The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: Structural organization and phylogenetic relationships. DNA Res., 2010, 17(1), 11-22.
[http://dx.doi.org/10.1093/dnares/dsp025] [PMID: 20007682]
[51]
Li, J.; Su, Y.; Wang, T. The repeat sequences and elevated substitution rates of the chloroplast accd gene in cupressophytes. Front. Plant Sci., 2018, 9, 533.
[http://dx.doi.org/10.3389/fpls.2018.00533] [PMID: 29731764]
[52]
McKain, M.R.; Johnson, M.G.; Uribe-Convers, S.; Eaton, D.; Yang, Y. Practical considerations for plant phylogenomics. Appl. Plant Sci., 2018, 6(3), e1038.
[http://dx.doi.org/10.1002/aps3.1038] [PMID: 29732268]
[53]
Greiner, S.; Rauwolf, U.; Meurer, J.; Herrmann, R.G. The role of plastids in plant speciation. Mol. Ecol., 2011, 20(4), 671-691.
[http://dx.doi.org/10.1111/j.1365-294X.2010.04984.x] [PMID: 21214654]
[54]
Rocha, D.M.C. Aspectos taxonômicos, genéticos e reprodutivos de Pterodon pubescens (Benth) Benth e P. emarginatus Vog. (Leguminosae, Dipterygeae); PhD, Universidade Estadual de Campinas, 2006.

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