Abstract
The aim of this study was to determine the sequence of the plastome of Syagrus coronata Mart. Becc using NGS data and to construct a phylogeny using complete chloroplast genomes for the subfamily Arecoideae. Seventy-seven million Illumina 100 nt single-end reads were used and mapped using the Cocos nucifera L. genome as a reference for obtaining the genome of S. coronata. The complete genome of S. coronata and other genomes of Arecoideae available in NCBI were used to obtain the phylogeny of Arecoideae using maximum likelihood and Bayesian approaches. The genome of S. coronata showed 155,053 bp, with inverted repeat A having 26,476 bp, inverted repeat B with 26,647 bp, large single copy with 84,410 bp and small single copy with 17,520 bp. Ninety genes were identified, eight rRNAs, 39 tRNAs and 30 repetitive regions. The phylogenetics analyses showed C. nucifera as the closest relative to S. coronata and Chamaedorea seifrizii Burre as the most divergent. The phylogenie analyzed using complete chloroplast genomes showed a similar topology when compared with phylogenies using small plastome regions and nuclear genes, indicating high consistency in terms of phylogenetic inferences.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genom 12:402. https://doi.org/10.1186/1471-2164-12-402
Asmussen CBEA (2006) A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny. Bot J Linn Soc 151:15–38. https://doi.org/10.1111/j.1095-8339.2006.00521.x
Baker WJ, Norup MV, Clarkson JJ, Couvreur TLP, Dowe JL, Lewis CE, Pintaud JC, Savolainen V, Wilmot T, Chase MW (2011) Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae). Ann Bot 108:1417–1432. https://doi.org/10.1093/aob/mcr020
Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L et al (2016) Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytol 209:855–870. https://doi.org/10.1111/nph.13617
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J (2012) Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13:R122. https://doi.org/10.1186/gb-2012-13-12-r122
CBOL (2009) A DNA barcode for land plants. PNAS 106:794–797
Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, Leebens-Mack JH (2015) Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing. Am J Bot 102:888–899. https://doi.org/10.3732/ajb.1500057
Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH (2016) Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 97:32–42. https://doi.org/10.1016/j.ympev.2015.12.015
Crepaldi IC, De Almeida-Muradian LB, Rios MDG, Penteado MDVC, Salatino A (2001) Composição nutricional do fruto de licuri (Syagrus coronata (Martius) Beccari). Rev Bras Bot 24:155–159. https://doi.org/10.1590/S0100-84042001000200004
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Dransfield J, Uhl NW, Asmussen-Lange CB, Baker WJ, Harley MM, Lewis CE (2005) A new phylogenetic classification of the palm family. Kew Bull 60:559–569. https://doi.org/10.2307/25070242
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
Green BR (2011) Chloroplast genomes of photosynthetic eukaryotes. Plant J 66:34–44. https://doi.org/10.1111/j.1365-313X.2011.04541.x
Huang YY, Matzke AJM, Matzke M (2013) Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS ONE 8:1–12. https://doi.org/10.1371/journal.pone.0074736
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
La Salles KTS, Meneghetti SMP, La Salles WF, Meneghetti MR, Santos ICF, Silva JPV, Carvalho SHV, Soletti JI (2010) Characterization of Syagrus coronata ( Mart .) Becc. oil and properties of methyl esters for use as biodiesel. Ind Crop Prod 32:518–521. https://doi.org/10.1016/j.indcrop.2010.06.026
Mayer, Christoph, Phobos 3.3.11, 2006−2010, http://www.rub.de/spezzoo/cm/cm_phobos.htm
Meerow AW, Noblick L, Borrone JW, Couvreur TLP, Mauro-Herrera M, Hahn WJ, Kuhn DN, Nakamura K, Oleas NH, Schnell RJ (2009) Phylogenetic analysis of seven WRKY genes across the palm subtribe attaleinae (Arecaceae) identifies Syagrus as sister group of the coconut. PLoS ONE 4:10–13. https://doi.org/10.1371/journal.pone.0007353
Môro J, Silva MAS, Geraldo JS (1999) Methodology for kariological study of Brazilian palms. Acta Hortic. 486:225–228. https://doi.org/10.17660/ActaHortic.1999.486.33
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
Rambaut DA (2009) Tracer v1.5. http://tree.bio.ed.ac.uk/software/tracer/
Scarcelli N, Barnaud A, Eiserhardt W, Treier UA, Seveno M, d’Anfray A, Vigouroux Y, Pintaud J-C (2011) A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PLoS ONE 6(5):e19954. https://doi.org/10.1371/journal.pone.0019954
Simpson JT, Wong K, Jackman SD, Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM (2009) ABySS: a parallel assembler for short read sequence data ABySS : A parallel assembler for short read sequence data. https://doi.org/10.1101/gr.089532.108
Uthaipaisanwong P, Chanprasert J, Shearman JR, Sangsrakru D, Yoocha T, Jomchai N, Jantasuriyarat C, Tragoonrung S, Tangphatsornruang S (2012) Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene 500:172–180. https://doi.org/10.1016/j.gene.2012.03.061
Acknowledgements
Federal University of Alagoas for laboratories and scientific support and the Fundação de Apoio à Pesquisa de Alagoas (FAPEAL) for funding this project.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Áquila, R., Silva, J., Silva, J.V. et al. The first complete chloroplast genome sequence of Syagrus coronata: comparative analysis in Arecoideae (Arecaceae). Braz. J. Bot 41, 393–401 (2018). https://doi.org/10.1007/s40415-018-0462-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s40415-018-0462-z