Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants.

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  • 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:
      DNA, Intergenic* ; Evolution, Molecular* ; Gene Rearrangement* ; Genome, Chloroplast* ; Open Reading Frames*; Diatoms/*genetics; Plants/genetics
    • Abstract:
      Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4-7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.
      Competing Interests: The authors have declared that no competing interests exist.
    • References:
      BMC Genomics. 2014 Aug 27;15:721. (PMID: 25159814)
      Protist. 2018 Dec;169(6):803-825. (PMID: 30448592)
      Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: 30016406)
      Mol Biol Evol. 2011 Jan;28(1):583-600. (PMID: 20805190)
      Mol Biol Evol. 2018 Aug 1;35(8):1869-1886. (PMID: 29688518)
      Mitochondrial DNA A DNA Mapp Seq Anal. 2019 Jan;30(1):43-51. (PMID: 29527965)
      Nucleic Acids Res. 2012 Apr;40(7):3152-8. (PMID: 22156163)
      Bioinformatics. 2004 Nov 22;20(17):3252-5. (PMID: 15180927)
      Genomics. 2015 Oct;106(4):221-31. (PMID: 26206079)
      Braz J Biol. 2014 Feb;74(1):257-63. (PMID: 25055112)
      Nat Methods. 2008 Jan;5(1):16-8. (PMID: 18165802)
      Mol Genet Genomics. 2007 Apr;277(4):427-39. (PMID: 17252281)
      Dokl Biochem Biophys. 2015;461:84-8. (PMID: 25937221)
      J Phycol. 2013 Dec;49(6):1207-22. (PMID: 27007638)
      J Phycol. 2019 Apr;55(2):352-364. (PMID: 30536677)
      Nucleic Acids Res. 2013 Jul;41(Web Server issue):W575-81. (PMID: 23609545)
      Plant J. 2012 Jun;70(6):1004-14. (PMID: 22332784)
      New Phytol. 2018 Jul;219(1):462-473. (PMID: 29624698)
      J Eukaryot Microbiol. 2013 Jul-Aug;60(4):414-20. (PMID: 23710621)
      PLoS One. 2014 Sep 18;9(9):e107854. (PMID: 25233465)
      Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
      Curr Biol. 2017 Jun 5;27(11):1677-1684.e4. (PMID: 28528908)
      J Phycol. 2019 Apr;55(2):442-456. (PMID: 30659609)
      Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
      Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
      Plant Mol Biol. 1992 Aug;19(5):759-70. (PMID: 1322740)
      EMBO J. 1986 Sep;5(9):2043-2049. (PMID: 16453699)
      J Bacteriol. 1991 Sep;173(18):5924-7. (PMID: 1885558)
      Sci Rep. 2018 Mar 19;8(1):4834. (PMID: 29556065)
      Am J Bot. 2018 Mar;105(3):330-347. (PMID: 29665021)
      Genome Biol Evol. 2014 Mar;6(3):644-54. (PMID: 24567305)
      Curr Genet. 2010 Jun;56(3):215-23. (PMID: 20309551)
      Protist. 2014 Mar;165(2):177-95. (PMID: 24646793)
      PLoS One. 2010 May 19;5(5):e10711. (PMID: 20502706)
      Protist. 2011 Jul;162(3):405-22. (PMID: 21239228)
      J Virol. 2009 Oct;83(20):10719-36. (PMID: 19640978)
      J Comput Biol. 2012 May;19(5):455-77. (PMID: 22506599)
      Genome Biol Evol. 2016 Sep 19;8(9):2789-805. (PMID: 27503298)
      Genome Res. 2004 Jul;14(7):1394-403. (PMID: 15231754)
      Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4430-5. (PMID: 11917101)
      BMC Genomics. 2010 Dec 20;11:718. (PMID: 21171997)
      Mol Phylogenet Evol. 2012 Sep;64(3):524-32. (PMID: 22659018)
      Mar Genomics. 2014 Aug;16:17-27. (PMID: 24365712)
      Mol Biol Evol. 2003 Sep;20(9):1499-505. (PMID: 12832641)
      Protist. 2011 Nov;162(5):723-37. (PMID: 21440497)
      Bioinformatics. 2002 Mar;18(3):492-3. (PMID: 11934753)
      Photosynth Res. 2011 Sep;109(1-3):223-9. (PMID: 21290260)
    • Accession Number:
      0 (DNA, Intergenic)
    • Publication Date:
      Date Created: 20190704 Date Completed: 20200217 Latest Revision: 20200309
    • Publication Date:
      20240829
    • Accession Number:
      PMC6608930
    • Accession Number:
      10.1371/journal.pone.0217824
    • Accession Number:
      31269054