Journal of Applied Phycology

, Volume 30, Issue 4, pp 2715–2722 | Cite as

Organelle genomes of Sargassum confusum (Fucales, Phaeophyceae): mtDNA vs cpDNA

  • Feng LiuEmail author
  • Jun Pan
  • Zhongshan Zhang
  • Fiona Wanjiku Moejes


The drifting biomass of golden tide in the Yellow Sea of China mainly consisted of Sargassum horneri with a small fraction composed of Sargassum confusum thalli. In this study, the circular-mapping organelle genomes (mtDNA and cpDNA) of S. confusum were sequenced and coupled with comparative genomic and phylogenomic analyses within the Sargassum genus. This revealed 34,721-bp mitochondrial and 124,375-bp chloroplast genomes of S. confusum harboring 65 and 173 genes, respectively, figures which are highly comparable to those reported in other Sargassum species. The mtDNA of S. confusum displayed lower values in A+T and intergenic spacer contents than cpDNA. Mitochondrial phylogenomics revealed a close relationship between Sargassum muticum and S. confusum. The Sargassum mtDNAs had an approximately three-fold greater mutation rate than cpDNAs indicating a higher evolution rate in mtDNAs than cpDNAs for Sargassum species. Therefore, mtDNA is a more effective molecular marker and could aid in tracking the source of the golden tides.


Organelle genomes Golden tide Phaeophyceae Evolution Sargassum Phylogenomics 



The authors wish to thank Wei Luan and Zhe Jin for their assistance in algal collection and data analysis.

Funding information

This work was supported by the Scientific and Technological Innovation Project Financially Supported by Qingdao National Laboratory for Marine Science and Technology (no. 2016ASKJ02), the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (no. QYZDB-SSW-DQC023), the Strategic Priority Research Program, Chinese Academy of Sciences (no. XDA11020304), the Key Research and Development Project of Shandong Province, China (no. 2016GSF115041), the National Natural Science Foundation of China (no. 31700307), the Youth Innovation Promotion Association, Chinese Academy of Sciences (no. 2015164), the Foundation for Huiquan Young Scholar of Institute of Oceanology, Chinese Academy of Sciences (no. 2015), and the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A. (no. MATHAB201701).

Supplementary material

10811_2018_1461_MOESM1_ESM.pptx (673 kb)
Fig. S1 Circular gene map of mitochondrial genome of S. confusum. Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counter-clockwise. Genes are colour-coded according to their functional groups. Inner circle indicates the GC content. (PPTX 672 kb)
10811_2018_1461_MOESM2_ESM.pptx (841 kb)
Fig. S2 Circular gene map of chloroplast genome of S. confusum. Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counter-clockwise. Genes are colour-coded according to their functional groups. Inner circle indicates the GC content. (PPTX 841 kb)
10811_2018_1461_MOESM3_ESM.pdf (22 kb)
Table S1 The known mitochondrial and chloroplast genomes (mtDNAs and cpDNAs) in the order Fucales. (PDF 22 kb)
10811_2018_1461_MOESM4_ESM.pdf (8 kb)
Table S2 Genetic distance between S. confusum (Sco) and other Sargassum species including S. muticum (Smu), S. hemiphyllum (She), S. thunbergii (Sth), S. fusiforme (Sfu), S. horneri (Sho), S. aquifolium (Saq), S. polycystum (Spo), S. ilicifolium (Sil), S. spinuligerum (Ssp), S. vachellianum (Sva), S. fluitans (Sfl), and S. natans (Sna) based on the mitochondrial genome sequences. (PDF 8 kb)


  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  2. Amaral-Zettler LA, Dragone NB, Schell J, Slikas B, Murphy LG, Morrall CE, Zettler ER (2017) Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic. Ecol Evol 7:516–525CrossRefPubMedGoogle Scholar
  3. Bi YH, Zhou ZG (2016) Complete mitochondrial genome of the brown alga Sargassum vachellianum (Sargassaceae, Phaeophyceae). Mitochondrial DNA A 27:2796–2797Google Scholar
  4. Bi YH, Li JL, Zhou ZG (2017) Complete sequence of chloroplast genome from Sargassum vachellianum (Sargassaceae, Phaeophyceae): genome structure and comparative analysis. Aquac Fish 2:157–164CrossRefGoogle Scholar
  5. Boo GH, Lindstrom SC, Klochkova NG, Yotsukura N, Yang EC, Kim HG, Waaland JR, Cho GY, Miller KA, Boo SM (2011) Taxonomy and biogeography of the genus Agarum (Laminariales, Phaeophyceae) based on nuclear, mitochondrial, and plastid gene sequences. Taxon 60:831–840Google Scholar
  6. Cheng S, Chang SY, Gravitt P, Respess R (1994) Long PCR. Nature 369:684–685CrossRefPubMedGoogle Scholar
  7. Duncan RS (2013) Southern wonder: Alabama’s surprising biodiversity. The University of Alabama Press, Tuscaloosa, p 459Google Scholar
  8. Engel CR, Billard E, Voisin M, Viard F (2008) Conservation and polymorphism of mitochondrial intergenic sequences in brown algae (Phaeophyceae). Eur J Phycol 43:195–205CrossRefGoogle Scholar
  9. Graf L, Kim YJ, Cho GY, Miller KA, Yoon HS (2017) Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers. PLoS One 12(11):e0187104CrossRefPubMedPubMedCentralGoogle Scholar
  10. Guiry MD, Guiry GM (2018) AlgaeBase. World-wide electronic publication. National University of Ireland, Galway; searched on 7 February 2018Google Scholar
  11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95–98Google Scholar
  12. Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  13. Hughey JR, Gabrielson PW (2017) The complete mitogenome of the rockweed Fucus distichus (Fucaceae, Phaeophyceae). Mitochondrial DNA P B 2:203–204CrossRefGoogle Scholar
  14. Keeling PJ (2010) The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc B 365:729–748CrossRefGoogle Scholar
  15. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  16. Komatsu T, Matsunaga D, Mikami A, Sagawa T, Boisnier E, Tatsukawa K, Aoki M, Ajisaka T, Uwai S, Tanaka K, Ishida K, Tanoue H, Sugimoto T (2008) Abundance of drifting seaweeds in eastern East China Sea. J Appl Phycol 20:801–809CrossRefGoogle Scholar
  17. Komatsu T, Fukuda M, Mikami A, Mizuno S, Kantachumpoo A, Tanoue H, Kawamiya M (2014) Possible change in distribution of seaweed, Sargassum horneri, in Northeast Asia under A2 scenario of global warming and consequent effect on some fish. Mar Pollut Bull 85:317–324CrossRefPubMedGoogle Scholar
  18. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  19. Laffoley D’A, Roe HSJ, Angel MV, Ardron J, Bates NR, Boyd LLL, Brooke S, Buck KN, Carlson CA, Causey B, Conte MH, Christiansen S, Cleary J, Donnelly J, Earle SA, Edwards R, Gjerde KM, Giovannoni SJ, Gulick S, Gollock M, Hallett J, Halpin P, Hanel R, Hemphill A, Johnson RJ, Knap AH, Lomas MW, McKenna SA, Miller MJ, Miller PI, Ming FW, Moffitt R, Nelson NB, Parson L, Peters AJ, Pitt J, Rouja P, Roberts J, Roberts J, Seigel DA, Siuda ANS, Steinberg DK, Stevenson A, Sumaila VR, Swartz W, Thorrold S, Trott TM, Vats V (2011) The protection and management of the Sargasso Sea: the golden floating rainforest of the Atlantic Ocean: summary science and supporting evidence case. Sargasso Sea Alliance, St. George’sGoogle Scholar
  20. Lane CE, Lindstrom SC, Saunders GW (2007) A molecular assessment of Northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding. Mol Phylogenet Evol 44:634–648CrossRefPubMedGoogle Scholar
  21. Le Corguillé G, Pearson G, Valente M, Viegas C, Gschloessl B, Corre E, Bailly X, Peters AF, Jubin C, Vaccherie B, Cock JM, Leblanc C (2009) Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids. BMC Evol Biol 9:253CrossRefPubMedPubMedCentralGoogle Scholar
  22. Liu F, Pang SJ (2015) Mitochondrial genome of Turbinaria ornata (Sargassaceae, Phaeophyceae): comparative mitogenomics of brown algae. Curr Genet 61:621–631CrossRefPubMedGoogle Scholar
  23. Liu F, Pang SJ (2016a) Chloroplast genome of Sargassum horneri (Sargassaceae, Phaeophyceae): comparative chloroplast genomics of brown algae. J Appl Phycol 28:1419–1426CrossRefGoogle Scholar
  24. Liu F, Pang SJ (2016b) Complete mitochondrial genome of the invasive brown alga Sargassum muticum (Sargassaceae, Phaeophyceae). Mitochondrial DNA A 27:1129–1130CrossRefGoogle Scholar
  25. Liu F, Pang SJ (2016c) Mitochondrial genome of Sargassum thunbergii: conservation and variability of mitogenomes within the subgenus Bactrophycus. Mitochondrial DNA A 27:3186–3188Google Scholar
  26. Liu F, Pang SJ, Gao SQ, Shan TF (2013) Intraspecificgenetic analysis, gamete release performance and growth of Sargassum muticum (Fucales, Phaeophyta) from China. Chin J Oceanol Limnol 31:1268–1275CrossRefGoogle Scholar
  27. Liu F, Pang SJ, Li X, Li J (2015) Complete mitochondrial genome of the brown alga Sargassum horneri (Sargassaceae, Phaeophyceae): genome organization and phylogenetic analyses. J Appl Phycol 27:469–478CrossRefGoogle Scholar
  28. Liu F, Pang SJ, Chen WZ (2016a) Complete mitochondrial genome of the brown alga Sargassum hemiphyllum (Sargassaceae, Phaeophyceae): comparative analyses. Mitochondrial DNA A 27:1468–1470CrossRefGoogle Scholar
  29. Liu F, Pang SJ, Luo MB (2016b) Complete mitochondrial genome of the brown alga Sargassum fusiforme (Sargassaceae, Phaeophyceae): genome architecture and taxonomic consideration. Mitochondrial DNA A 27:1158–1160CrossRefGoogle Scholar
  30. Liu F, Jin Z, Wang Y, Bi YP, Melton JT (2017a) Plastid genome of Dictyopteris divaricata (Dictyotales, Phaeophyceae): understanding the evolution of plastid genomes in brown algae. Mar Biotechnol 19:627–637CrossRefPubMedGoogle Scholar
  31. Liu F, Li XD, Che ZW (2017b) Mitochondrial genome sequences uncover evolutionary relationships of two Sargassum subgenera, Bactrophycus and Sargassum. J Appl Phycol 29:3261–3270CrossRefGoogle Scholar
  32. Liu F, Liu XF, Wang Y, Jin Z, Moejes FW, Sun S (2018) Insights on the Sargassum horneri golden tides in the Yellow Sea inferred from morphological and molecular data. Limnol Oceanogr.
  33. Lowe TM, Chan PP (2016) tRNAscan-SE On-line Search and contextual analysis of transfer RNA genes. Nucleic Acids Res 44:54–57CrossRefGoogle Scholar
  34. Mattio L, Payri CE (2011) 190 years of Sargassum taxonomy, facing the advent of DNA phylogenies. Bot Rev 77:31–70CrossRefGoogle Scholar
  35. Milledge JJ, Harvey PJ (2017) Golden tides: problem or golden opportunity? The valorization of Sargassum from beach inundations. J Mar Sci Eng 4:2–19Google Scholar
  36. Oudot-Le Secq MP, Loiseaux-De Goër S, Stam WT, Olsen JL (2006) Complete mitochondrial genome of the three brown algae (Heterokonta: Phaeophyceae) Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis. Curr Genet 49:47–58CrossRefPubMedGoogle Scholar
  37. Phillips NE, Smith CM, Morden CW (2005) Testing systematic concepts of Sargassum (Fucales, Phaeophyceae) using portions of the rbcL-S operon. Phycol Res 53:1–10CrossRefGoogle Scholar
  38. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574CrossRefPubMedGoogle Scholar
  39. Silberfeld T, Rousseau F, Reviers B d (2014) An updated classification of brown algae (Ochrophyta, Phaeophyceae). Cryptogam Algol 35:117–156CrossRefGoogle Scholar
  40. Smetacek V, Zingone A (2013) Green and golden seaweed tides on the rise. Nature 504:84–88CrossRefPubMedGoogle Scholar
  41. Smith DR (2015) Mutation rates in plastid genomes: they are lower than you might think. Genome Biol Evol 7:1227–1234CrossRefPubMedPubMedCentralGoogle Scholar
  42. Smith DR, Keeling PJ (2015) Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci U S A 112:10177–10184CrossRefPubMedPubMedCentralGoogle Scholar
  43. Tseng CK (2009) Seaweeds in Yellow Sea and Bohai Sea of China. Science Press, Beijing, pp 363–372 (in Chinese)Google Scholar
  44. Witherington B, Hirama S, Hardy R (2012) Young sea turtles of the pelagic Sargassum dominated drift community: habitat use, population density, and threats. Mar Ecol Prog Ser 463:1–22CrossRefGoogle Scholar
  45. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A 84:9054–9058CrossRefPubMedPubMedCentralGoogle Scholar
  46. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255CrossRefPubMedGoogle Scholar
  47. Yang EC, Boo GH, Kim HJ, Cho SM, Boo SM, Andersen RA, Yoon HS (2012) Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles. Protist 163:217–231CrossRefPubMedGoogle Scholar
  48. Yang JH, Graf L, Cho CH, Jeon BH, Kim JH, Yoon HS (2016) Complete plastid genome of an ecologically important brown alga Sargassum thunbergii (Fucales, Phaeophyceae). Mar Genomics 28:17–20CrossRefPubMedGoogle Scholar
  49. Yotsukura N, Shimizu T, Katayama T, Druehl LD (2010) Mitochondrial DNA sequence variation of four Saccharina species (Laminariales, Phaeophyceae) growing in Japan. J Appl Phycol 22:243–251CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Feng Liu
    • 1
    • 2
    Email author
  • Jun Pan
    • 3
    • 4
  • Zhongshan Zhang
    • 5
  • Fiona Wanjiku Moejes
    • 6
  1. 1.CAS Key Laboratory of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoPeople’s Republic of China
  2. 2.Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoPeople’s Republic of China
  3. 3.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  4. 4.Center for Marine Environmental Engineering, Institute of OceanologyChinese Academy of SciencesQingdaoPeople’s Republic of China
  5. 5.Department of MedicineHuzhou UniversityHuzhouPeople’s Republic of China
  6. 6.Bantry Marine Research StationCorkIreland

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