The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae).

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
Read Online Read More Add to Saved list
  • Additional Information
    • Source:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
    • Publication Information:
      Original Publication: San Francisco, CA : Public Library of Science
    • Subject Terms:
      Evolution, Molecular*; Arecaceae/*genetics ; Plastids/*genetics; Arecaceae/classification ; Comparative Genomic Hybridization ; DNA, Plant/chemistry ; DNA, Plant/genetics ; DNA, Plant/metabolism ; Genome, Plastid ; Phylogeny ; Plastids/classification ; Sequence Analysis, DNA
    • Abstract:
      The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.
      Competing Interests: The authors have declared that no competing interests exist.
    • References:
      PLoS One. 2012;7(2):e31468. (PMID: 22384027)
      Genet Mol Biol. 2020 Sep 11;43(4):e20200023. (PMID: 32926069)
      PLoS One. 2020 Jan 28;15(1):e0227991. (PMID: 31990943)
      Planta. 2016 Oct;244(4):927-38. (PMID: 27318823)
      Nat Ecol Evol. 2017 Dec;1(12):1903-1911. (PMID: 29062122)
      Front Plant Sci. 2015 Jul 30;6:586. (PMID: 26284102)
      Cladistics. 2015 Oct;31(5):509-534. (PMID: 34772273)
      BMC Genomics. 2008;9 Suppl 1:S25. (PMID: 18366615)
      Syst Biol. 2009 Apr;58(2):240-56. (PMID: 20525581)
      Am J Bot. 2007 Mar;94(3):275-88. (PMID: 21636401)
      PLoS One. 2020 Jul 23;15(7):e0235819. (PMID: 32701950)
      Mol Biol Evol. 2017 Dec 1;34(12):3299-3302. (PMID: 29029172)
      Ann Bot. 2011 Dec;108(8):1417-32. (PMID: 21325340)
      Am J Bot. 2014 Nov;101(11):1987-2004. (PMID: 25366863)
      Methods Mol Biol. 2014;1132:3-38. (PMID: 24599844)
      Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
      Genes Genomics. 2020 May;42(5):553-570. (PMID: 32200544)
      Gene. 2012 Jun 1;500(2):172-80. (PMID: 22487870)
      PLoS One. 2011;6(5):e19954. (PMID: 21637837)
      Bioinformatics. 2018 Sep 1;34(17):3030-3031. (PMID: 29659705)
      Nucleic Acids Res. 2012 May;40(10):e72. (PMID: 22323520)
      Planta. 2019 Oct;250(4):1229-1246. (PMID: 31222493)
      Planta. 2018 Apr;247(4):1011-1030. (PMID: 29340796)
      Front Plant Sci. 2020 Jul 03;11:799. (PMID: 32719690)
      PLoS One. 2013 Jun 18;8(6):e68180. (PMID: 23950788)
      Mol Biol Evol. 1990 Jul;7(4):303-14. (PMID: 1974691)
      PLoS One. 2010 Sep 15;5(9):e12762. (PMID: 20856810)
      Plant Mol Biol. 2011 Jul;76(3-5):273-97. (PMID: 21424877)
      Nucleic Acids Res. 2016 Jul 8;44(W1):W232-5. (PMID: 27084950)
      Chin Med. 2018 Feb 13;13:10. (PMID: 29449878)
      Ann Bot. 2011 Dec;108(8):1503-16. (PMID: 21831852)
      PLoS One. 2013 Aug 30;8(8):e74736. (PMID: 24023703)
      Genome Res. 2004 Jul;14(7):1394-403. (PMID: 15231754)
      New Phytol. 2016 Jan;209(2):855-70. (PMID: 26350789)
      Appl Plant Sci. 2017 May 8;5(5):. (PMID: 28529832)
      Mol Phylogenet Evol. 2020 Oct;151:106903. (PMID: 32628998)
      Mol Phylogenet Evol. 2002 May;23(2):189-204. (PMID: 12069550)
      PLoS One. 2014 Jan 02;9(1):e84792. (PMID: 24392157)
      Genome Biol Evol. 2016 Aug 25;8(8):2452-8. (PMID: 27401175)
    • Accession Number:
      0 (DNA, Plant)
    • Publication Date:
      Date Created: 20210824 Date Completed: 20211222 Latest Revision: 20240814
    • Publication Date:
      20240814
    • Accession Number:
      PMC8384209
    • Accession Number:
      10.1371/journal.pone.0256373
    • Accession Number:
      34428237