| dc.relation.references | Bardon, L., Sothers, C.A., Prance, G.T., Malé, P.G., Xi, Z., Davis, C.C., Murienne, J., GarcíaVillacorta, R., Coissac, E., Lavergne, S., Chave, J., 2016. Unravelling the biogeographical history
of Chrysobalanaceae from plastid genomes. American Journal of Botany 103: 1-14.
Bedoya, A., Ruhfel, B., Philbrick, T., Madriñán, S., Bove, C., Mesterhazy, A., Olmstead, R.., 2019.
Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and
Comparative Analysis in Malpighiales. Frontiers in Plant Science, 10, p.1035. DOI:
10.3389/fpls.2019.01035.
Blazier C.J., Guisinger, M.M., Jansen, R.K., 2011. Recent loss of plastid-encoded ndh genes within
Erodium (Geraniaceae). Plant molecular biology, 76(3-5): 263-72. doi: 10.1007/s11103-011-
9753-5.
Cai, L. et al. The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient
gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales. Syst. Biol. 70,
491–507 (2021).
Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T., 2009. trimAl: a tool for automated
alignment trimming in large-scale phylogenetic analyses, Bioinformatics 25(15): 1972–1973,
https://doi.org/10.1093/bioinformatics/btp348.
Cardoso, D.B.O.S. et al., 2017. Amazon plant diversity revealed by a taxonomically verified
species list. Proceedings of the National Academy of Science 114: 10695–10700.
Cauz-Santos, L.A., da Costa, Z.P., Callot, C., Cauet, S., Zucchi, M.I., Bergès, H., van den Berg, C.
and Vieira, M.L.C., 2020. A repertory of rearrangements and the loss of an inverted repeat region
in Passiflora chloroplast genomes. Genome biology and evolution, 12(10), pp.1841-1857.
Chave, J. et al., 2020. Rapid diversification rates in Amazonian Chrysobalanaceae inferred from
plastid genome phylogenetics. Botanical Journal of the Linnean Society 194(3): 271–289.
47
Csűös, M. 2010. Count: evolutionary analysis of phylogenetic profiles with parsimony and
likelihood. Bioinformatics 26: 1910–1912.
Caycho, E., La Torre R, O.G., 2023. Assembly, annotation and analysis of the chloroplast genome
of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae). BMC Plant Biol.
16;23(1):570. doi: 10.1186/s12870-023-04581-5.
Darling, A. E., Mau, B. & Perna, N. T. 2010. progressive Mauve: multiple genome alignment with
gene gain, loss and rearrangement. PLoS ONE 5: e11147.
Dong W, Liu J, Yu J, Wang L, Zhou S., 2012. Highly Variable Chloroplast Markers for Evaluating
Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding. PLOS ONE 7(4): e35071.
https://doi.org/10.1371/journal.pone.0035071
Dong, W., Xu, C., Li, C. et al., 2015. ycf1, the most promising plastid DNA barcode of land plants.
Sci Rep 5, 8348. https://doi.org/10.1038/srep08348
Emms, D. M., & Kelly, S. 2019. OrthoFinder: phylogenetic orthology inference for comparative
genomics. Genome biology 20: 1–14.
Feitosa, E.A., Xavier, H.S. & Randau, K.P., 2012. Chrysobalanaceae: traditional uses,
phytochemistry and pharmacology. Rev. Bras. Farmacogn. 22(5):1181–1186.
Firetti, F., Zuntini, A.R., Gaiarsa, J.W., Oliveira, R.S., Lohmann, L.G., Van Sluys. M.A., 2017.
Complete chloroplast genome sequences contribute to plant species delimitation: A case study of
the Anemopaegma species complex. Am J Bot. 104(10): 1493-1509. DOI: 10.3732/ajb.1700302.
Fonseca, L.H.M., Lohmann, L.G., 2017. Plastome Rearrangements in the "AdenocalymmaNeojobertia" Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications. Front Plant
Sci. 1(8): 1875. DOI: 10.3389/fpls.2017.01875.
Gastauer, M., Sarmento, P.S.M., Santos, V.C.A., Caldeira, C.F., Ramos, S.J., Teodoro, G.S. &
Siqueira, J.O., 2020. Functional traits guide plant species selection for initial mineland
rehabilitation. Ecological Engineering 148: 105763.
Iha, C., Grassa, C.J., Lyra, G.M., Davis, C.C., Verbruggen, H., Oliveira, M.C., 2018. Organellar
genomics: a useful tool to study evolutionary relationships and molecular evolution in
Gracilariaceae (Rhodophyta). J. Phycol. 54: 775-787.
48
Jansen, R.K., Cai, Z., Raubeson, L.A., Daniell, H., Depamphilis, C.W., Leebens-Mack, J., Müller,
K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., Chumley, T.W., Lee, S.B., Peery, R.,
McNeal, J.R., Kuehl, J.V., Boore, J.L., 2007. Analysis of 81 genes from 64 plastid genomes
resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl
Acad Sci USA, 104(49):19369-74.
Jesus, P.B., de Mattos Lyra, G., Zhang, H., Fujii, M.T., Nauer, F., de Castro Nunes, J.M., Davis,
C.C. and Oliveira, M.C., 2023. Phylogenomics and taxon-rich phylogenies of new and historical
specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta). Molecular
Phylogenetics and Evolution 183, p.107752.
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins,
S.E., Sánchez-Gracia, A., 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data
Sets, Molecular Biology and Evolution 34(2): 3299–3302,
https://doi.org/10.1093/molbev/msx248.
Katoh, K. and Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7:
improvements in performance and usability. Molecular biology and evolution 30(4), pp.772-780.
Lee, J., Cho, C.H., Park, S.I., Choi, J.W., Song, H.S., West, J.A., Bhattacharya, D. and Yoon, H.S.,
2016. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed
plants. BMC biology, 14, pp.1-16.
Long, L., Li, Y., Wang, S., Liu, Z., Wang, J. and Yang, M., 2023. Complete chloroplast genomes
and comparative analysis of Ligustrum species. Scientific Reports 13(1), p.212.
Malé, P.J.G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., Lhuillier, E., Scotti‐
Saintagne, C., Tinaut, A. and Chave, J., 2014. Genome skimming by shotgun sequencing helps
resolve the phylogeny of a pantropical tree family. Molecular ecology resources, 14(5), pp.966-
975.
Maréchal, A. and Brisson, N. (2010), Recombination and the maintenance of plant organelle
genome stability. New Phytologist, 186: 299-317. https://doi.org/10.1111/j.1469-
8137.2010.03195.x
49
Menezes, A.P.A., Resende-Moreira, L.C., Buzatti, R.S.O. et al. 2018. Chloroplast genomes of
Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence
sequences. Sci Rep 8, 2210. https://doi.org/10.1038/s41598-018-20189-4
Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for
Inference of Large Phylogenetic Trees. Gateway Computing Environments Workshop (GCE), 14
November, New Orleans, Louisiana. https://www.phylo.org/.
Mohanta, T.K., Mishra, A.K., Khan, A., Hashem, A., Abd_Allah, E.F. and Al-Harrasi, A., 2020.
Gene loss and evolution of the plastome. Genes, 11(10), p.1133.
Prance, G.T., 1972. Flora Neotropica - Chrysobalanaceae. Flora Neotropica Monograph 9. New
York: New York Botanical Garden. 410 p.
Prance, G.T. & White, F., 1988. The genera of Chrysobalanaceae: A study of practical and
theoretical taxonomy and its relevance to evolutionary biology. Philosophical Transactions of
the Royal Society of London B 320: 1-184.
Prance, G.T. & Sothers, C.A., 2003. Chrysobalanaceae 1: Chrysobalanus to Parinari. In: Species
plantarum: Flora of the World, Part 9. Canberra: Australian Biological Resources.
Prance, G.T., 2021. Sixty years with the Chrysobalanaceae. The Botanical Review, 87, pp.197-
232.
Puillandre, N., Brouillet, S., Achaz, G. 2020. ASAP: Assemble Species by Automatic Partitioning.
Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13281.
Rankin-de-Mérona, J.M. et al., 1992. Preliminary results of a large-scale inventory of upland rain
forest in the central Amazon. Acta Amazônica 22: 493–534.
Sanderson, M.J., Copetti, D., Burquez, A., Bustamante, E., Charboneau, J.L.M., Eguiarte, L.E.,
Kumar, S., Lee, H.O., Lee, J., McMahon, M., et al, 2015. Exceptional Reduction of the Plastid
Genome of Saguaro Cactus (Carnegiea Gigantea): Loss of the Ndh Gene Suite and Inverted Repeat.
Am. J. Bot., 102: 1115–1127. https://doi.org/10.3732/ajb.1500184.
Sothers, C., Prance, G.T., Buerki, S., Kok, R.D., Chase, M.W., 2014. Taxonomic novelties in
Neotropical Chrysobalanaceae: towards a monophyletic Couepia. Phytotaxa 172(2): 176-200.
50
Sothers, C., Prance, G.T., Chase, M.W., 2016. Towards a monophyletic Licania: a new generic
classification of the polyphyletic Neotropical genus Licania (Chrysobalanaceae). Kew Bulletin
71: 58.
Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large
phylogenies. Bioinformatics 30(9), pp.1312-1313.
Sun, J., Wang, S., Wang, Y., Wang, R., Liu, K., Li, E., Qiao, P., Shi, L., Dong, W., Huang, L., &
Guo, L., 2022. Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia,
Boraginaceae) in China. Frontiers in Plant Science, 13.
Thode, V.A., Lohmann, L.G., 2019. Comparative Chloroplast Genomics at Low Taxonomic
Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). Front Plant Sci. 19(10):
796. DOI: 10.3389/fpls.2019.00796.
Trad, R.J., Cabral, F.N., Bittrich, V. et al., 2021. Calophyllaceae plastomes, their structure and
insights in relationships within the clusioids. Sci Rep 11, 20712. https://doi.org/10.1038/s41598-
021-99178-z.
Turudić, A., Liber, Z., Grdiša, M., Jakše, J., Varga, F., Šatović, Z., 2022. Chloroplast Genome
Annotation Tools: Prolegomena to the Identification of Inverted Repeats. Int J Mol Sci.
16;23(18):10804. doi: 10.3390/ijms231810804.
Wang, R.N., Milne, R.I., Du, X.Y., Liu, J. and Wu, Z.Y., 2020. Characteristics and mutational
hotspots of plastomes in Debregeasia (Urticaceae). Frontiers in genetics, 11, p.729.
Wang, S., Gao, J., Chao, H., Li, Z., Pu, W., Wang, Y. and Chen, M., 2022. Comparative chloroplast
genomes of Nicotiana Species (Solanaceae): Insights into the genetic variation, phylogenetic
relationship, and polyploid speciation. Frontiers in plant science 13, p.899252.
Yakandawala, D.; Morton, C.M., Prance, G.T., 2010. Phylogenetic Relationships of the
Chrysobalanaceae Inferred from Chloroplast, Nuclear, and Morphological Data. Annals of the
Missouri Botanical Garden 97 (2): 259-281. | pt_BR |
