ࡱ> dfca pXbjbjڥڥ 0\R\R\`      4448l,4)2~D(llll  1111111$4]7b19  1  llH1D)D)D)  l l1D) 1D)D)D)ll'D)p110)2D)7'7D)D)7 +h D) 11D) )2 7 > : The complete organellar genomes of the rockweed Fucus distichus (Fucaceae, Phaeophyceae) *91Ů Genomics Group, 1print name here, 1print name here, 1print name here, 1, 2Jeffery R. Hughey 1 Division of Mathematics, Science, and Engineering, 91Ů, Salinas, California, USA 2 Corresponding author- Jeffery R. Hughey, HYPERLINK "mailto:jhughey@hartnell.edu"jhughey@hartnell.edu, 831-770-7054, no fax available *All authors contributed equally to the analysis and writing of this paper KeyWords: Alaska, British Columbia, cox1, Fucus vesiculosus, Oregon The complete organellar genomes of the rockweed Fucus distichus (Fucaceae, Phaeophyceae) Abstract The rockweed F. distichus is a one of the most common intertidal seaweeds in the northern hemisphere. The systematics of F. distichus however remains open to discussion. Here, we contribute to the bioinformatics and systematics of F. distichus by deciphering its complete mitogenome. The F. distichus mitogenome is 36,400 bp in length and contains 67 genes. The plastid genome of F. spiralis is 125,066 bp in length and contains 171 genes. The two organellar genomes share the same gene content and organization as the generitype, F. vesiculusus. This data supports the continued recognition of F. distichus as a polymorphic entity with a broad distribution and high degree of ecological diversity. Fucus L. is one of the three original genera proposed by Linnaeus (1753) to accommodate macroscopic marine algae. Since then more than 1,000 names have been assigned to the genus (Guiry & Guiry 2017), but nearly all have been reclassified. Based on genetic analyses, three or four species are recognized: F. distichus L., F. serratus L., F. spiralis L., and F. vesiculosus L. (Serrao et al. 1999; Coyer et al. 2006, 2011; Kucera & Saunders 2008; Laughinghouse et al. 2015). This classification remains problematic however, as exemplified by F. distichus, which displays a high degree of morphological, ecological, geographical, and reproductive variation (Gardner 1922; Kucera & Saunders 2008; Coyer et al. 2011; Laughinghouse et al. 2015). Herein we characterize the mitogenome of F. distichus to clarify its systematics. Fucus spiralis (voucher specimen- UC2050586) was collected from Pacific Grove, California (3638'02.0"N 12156'19.7"W) and its DNA isolated following Lindstrom et al. (2011). The 150 bp paired-end library construction and sequencing was performed by myGenomics, LLC (Alpharetta, Georgia, USA). The genomes were assembled by mapping the reads against F. vesiculosus (GenBanks- FM957154, AY494079) with the Low Sensitivity/Fast setting in Geneious R11 (Biomatters Limited, Auckland, New Zealand) and annotated using blastx and NCBI ORF-finder. The mitogenome was aligned to other Phaeophyceae with MAFFT (Katoh & Standley 2013). The RaxML analysis was executed using complete mitogenome sequences at Trex-online (Boc & Makarenkov 2012) with the GTR + gamma model and 1,000 fast bootstraps, then visualized with TreeDyn 198.3 at Phylogeny.fr (Dereeper et al. 2008). The F. distichus mitogenome (GenBank MG922856) is 36,400 bp in length and contains cob and tatC, 3 rRNA, 3 open reading frames, 3 ATP synthase, 3 cox, 6 rpl, 10 NADH, 11 rps, and 26 tRNA genes (trnL occurs in triplicate and trnI, trnM, trnS, trnY in duplicate). Gene content, organization, and length are nearly identical to F. vesiculosus (36,392 bp) (Oudot-Le Secq et al. 2006). The genetic distance between these two species is 2.0%. Phylogenetic analysis of F. distichus supports this close relationship, positioning it in a clade with F. vesiculosus (Figure 1). The plastid genome (GenBank- MG922855) is 125,066 bp in length and contains duplicate copies of 16S, 23S and 5S rRNAs, 26 tRNAs, and 139 protein-coding genes. It is also highly similar in chromosomal content and structure to F. vesiculosus (Le Corguill et al. 2009). The plastid genome of F. spiralis differs from F. vesiculosus by only 301 SNPs and 67 gaps, and shows 168 amino acid substitutions out of 31,893 total amino acids, of which only 32 were not conservative. On the basis of the biological, marker, and phylogenetic species concepts, and this genomic evidence, we conclude that the name F. spiralis should be reduced to a subspecies of F. vesiculosus, F. vesiculosus var. spiralis (Linnaeus) Roth. Disclosure statement The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article. Acknowledgments We wish to thank Long Nguyen for technical support with the Geneious software. This work was partly funded by a 2017-2018 Innovation Grant from 91Ů to Jeffery R. Hughey. REFERENCES Boc A, Makarenkov V. 2012. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 40:W573W579. Coyer JA, Hoarau G, Oudot-Le Secq MP, Stam WT, Olsen JL. 2006. A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta). Mol Phylogenet Evol. 39:209222. Coyer JA, Hoarau G, Van Schaik J, Luijckx P, Olsen JL. 2011. Trans Pacific and trans Arctic pathways of the intertidal macroalga Fucus distichus L. reveal multiple glacial refugia and colonizations from the North Pacific to the North Atlantic. J Biogeogr. 38:756 771. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:W465W469. Gardner NL. 1922. The genus Fucus on the Pacific coast of North America. Univ Calif publ bot. 10:1180. Guiry MD, Guiry GM. 2017. AlgaeBase. [Internet]. Galway: World-wide electronic publication, National University of Ireland; [cited 2017 Feb 16]. Available from: HYPERLINK "http://www.algaebase.org"http://www.algaebase.org Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol Biol Evol. 30:772780. Kucera H, Saunders GW. 2008. Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. Botany. 86:10651079. Laughinghouse IV HD, Mller KM, Adey WH, Lara Y, Young R, Johnson G. 2015. Evolution of the northern rockweed, Fucus distichus, in a regime of glacial cycling: implications for benthic algal phylogenetics. PloS One. 10:e0143795. Lindstrom SC, Hughey JR, Martone PT. 2011. New, resurrected and redefined species of Mastocarpus (Phyllophoraceae, Rhodophyta) from the northeast Pacific. Phycologia. 50:661683. Linnaeus C. 1753. Species plantarum, exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas. Holmiae (Stockholm): Impensis Laurentii Salvii. Oudot-Le Secq MP, Loiseaux-de Goer S, Stam WT, Olsen JL. 2006. Complete mitochondrial genomes of the three brown algae (Heterokonta: Phaeophyceae) Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis. Curr Genet. 49:4758. Serrao EA, Alice LA, Brawley SH. 1999. Evolution of the Fucaceae (Phaeophyceae) inferred from nrDNA-ITS. J Phycol. 35:382394. Figure 1. Maximum likelihood phylogram of Fucus distichus (bold letters) and related Phaeophyceae mitogenomes. 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