http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.933333
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the invasive brown alga Sargassum muticum (Sargassaceae, Phaeophyceae) Feng Liu1,2 and Shaojun Pang1
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 08/22/14 For personal use only.
1
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China and 2Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, P. R. China Abstract
Keywords
Sargassum muticum (Yendo) Fensholt is an invasive canopy-forming brown alga, expanding its presence from Northeast Asia to North America and Europe. The complete mitochondrial genome of S. muticum is characterized as a circular molecule of 34,720 bp. The overall AT content of S. muticum mitogenome is 63.41%. This mitogenome contains 65 genes typically found in brown algae, including 3 ribosomal RNA genes, 25 transfer RNA genes, 35 proteincoding genes, and 2 conserved open reading frames (ORFs). The gene order of mitogenome for S. muticum is identical to that for Sargassum horneri, Fucus vesiculosus and Desmarestia viridis. Phylogenetic analyses based on 35 protein-coding genes reveal that S. muticum has a close evolutionary relationship with S. horneri and a distant relationship with Dictyota dichotoma, supporting current taxonomic systems. The present investigation provides new molecular data for studies of S. muticum population diversity as well as comparative genomics in the Phaeophyceae.
Brown alga, mitochondrial genome, Phaeophyceae, Sargassaceae, Sargassum muticum
Sargassum muticum (Yendo) Fensholt is a well-known invasive brown alga, introduced from its native habitats in Northeast Asia to the west coast of North America, to Europe, and to the Mediterranean Sea (Cheang et al., 2010; Liu et al., 2013). Its invasion has caused strongly negative action on native perennial seaweed and sea animals (Incera et al., 2011). Its large-scale appearance in invaded habitats has attracted lots of attention, but information on its genetics and molecular biology is scarce. Here, we sequenced and characterized the complete mitochondrial genome of S. muticum (collected from Sanggou Bay, China) via long PCR and primer walking techniques (Liu et al., 2014). The S. muticum mitogenome is a circular molecule of 34,720 bp (Figure 1; GenBank accession number KJ938301). The overall AT content is 63.41%, similar to other brown algae (62.01–67.47%). The percentage of the intergenic spacer (4.65%) in S. muticum is similar to Sargassum horneri (4.29%), but lower than other reported brown algae (5.62–6.81%) with the exception of Dictyota dichotoma (3.21%). The mitogenome size of S. muticum is 114 bp longer than that of S. horneri (34,606 bp. KJ938300). This difference was caused by increase of spacer size and reduction of overlap size. The average spacer size in
Correspondence: Feng Liu, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P. R. China. E-mail: [email protected] Shaojun Pang, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China. E-mail: [email protected]
History Received 5 June 2014 Accepted 7 June 2014 Published online 1 July 2014
S. muticum is 31.6 bp, longer than S. horneri (28.0 bp), and the average overlap size of 12.2 bp shorter than S. horneri (13.7 bp). In particular, the cox3-atp6 intergenic spacer for S. muticum is 105 bp, and longer than that for S. horneri (only 20 bp). The mitogenome of S. muticum contains 65 genes, including 3 ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes, as well as 2 conserved open reading frames (ORFs). Genes in S. muticum mitogenome are encoded on both strands, and only 6 genes (rpl2, rps19, rps3, rpl16, orf131 and tatC) are transcribed from the light strand. All protein-coding genes have a methionine (ATG) start codon. The frequency of stop-codon usage bias is 70.27% for TAA, higher than that for TAG (13.51%) and TGA (16.22%). Two tRNA clusters (MLHCNF and IQL) are well conserved in S. muticum as those of other brown algal mitogenomes. The gene order for S. muticum mitogenome is identical to that for S. horneri, Fucus vesiculosus and Desmarestia viridis, but differs from Laminariales by variation of trnA position (Li et al., 2014; Yotsukura et al., 2010), from Ectocarpales by variation of trnD and trnA positions, and from D. dichotoma by variation of nine gene positions (trnK, atp9, trnE, atp8, trnD, trnA, rps10, rpl31 and trnM3) (Oudot-Le Secq et al., 2006). Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 35 protein-coding genes indicate that S. muticum has a close evolutionary relationship with S. horneri and a distant relationship with D. dichotoma, supporting current taxonomic systems (Guiry & Guiry, 2014). The mitogenome of S. muticum determined herein augments the Sargassum mitogenome data, providing a rich resource of markers for systematic and population genetic investigation of Sargassum species.
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 08/22/14 For personal use only.
2
F. Liu & S. Pang
Mitochondrial DNA, Early Online: 1–2
Figure 1. Gene map of Sargassum muticum mitochondrial genome. Genes and ORFs are shown as solid blocks. The gene blocks shown inside and outside the circular map are transcribed in the clockwise and counter-clockwise directions, respectively. Number inside the circle indicates the mitogenome size.
Declaration of interest This work was supported by the 863 Hi-Tech Research and Development Program of China (No. 2012AA10A413), the National Natural Science Foundation of China (No. 41206146, 41176135), the Scientific Research Foundation for Outstanding Young Scientists of Shandong Province (No. BS2013HZ004), the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, State Oceanic Administration (No. MATHAB201408), and the Open Research Fund of Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, P. R. China (No. K201311). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Cheang CC, Chu KH, Fujita D, Yoshida G, Hiraoka M, Critchley A, Choi HG, et al. (2010). Low genetic variability of Sargassum muticum (Phaeophyceae) revealed by a global analysis of native and introduced populations. J Phycol 46:1063–74. Guiry MD, Guiry GM. (2014). AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. Available at: http://www.algaebase.org (Accessed 18 May 2014).
Incera M, Olabarria C, Cacabelos E, Ce´sar J, Troncoso JS. (2011). Distribution of Sargassum muticum on the NorthWest coast of Spain: Relationships with urbanization and community diversity. Cont Shelf Res 31:488–95. Li TY, Qu JQ, Feng YJ, Liu C, Chi S, Liu T. (2014). Complete mitochondrial genome of Undaria pinnatifida (Alariaceae, Laminariales, Phaeophyceae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.865172. Liu F, Pang SJ, Li X, Li J. (2014). Complete mitochondrial genome of the brown alga Sargassum horneri (Sargassaceae, Phaeophyceae): Genome organization and phylogenetic analyses. J Appl Phycol. [Epub ahead of print]. doi:10.1007/s10811-014-0295-5. Liu F, Pang SJ, Gao SQ, Shan TF. (2013). Intraspecific genetic analysis, gamete release performance and growth of Sargassum muticum (Fucales, Phaeophyta) from China. Chin J Oceanol Limnol 31: 1268–75. Oudot-Le Secq M-P, Loiseaux-De Goe¨r 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 49:47–58. 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 22:243–51.
Supplementary material available online Supplementary Figure
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the invasive brown alga Sargassum muticum (Sargassaceae, Phaeophyceae) Feng Liu1,2 and Shaojun Pang1
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 08/22/14 For personal use only.
1
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China and 2Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, P. R. China Abstract
Keywords
Sargassum muticum (Yendo) Fensholt is an invasive canopy-forming brown alga, expanding its presence from Northeast Asia to North America and Europe. The complete mitochondrial genome of S. muticum is characterized as a circular molecule of 34,720 bp. The overall AT content of S. muticum mitogenome is 63.41%. This mitogenome contains 65 genes typically found in brown algae, including 3 ribosomal RNA genes, 25 transfer RNA genes, 35 proteincoding genes, and 2 conserved open reading frames (ORFs). The gene order of mitogenome for S. muticum is identical to that for Sargassum horneri, Fucus vesiculosus and Desmarestia viridis. Phylogenetic analyses based on 35 protein-coding genes reveal that S. muticum has a close evolutionary relationship with S. horneri and a distant relationship with Dictyota dichotoma, supporting current taxonomic systems. The present investigation provides new molecular data for studies of S. muticum population diversity as well as comparative genomics in the Phaeophyceae.
Brown alga, mitochondrial genome, Phaeophyceae, Sargassaceae, Sargassum muticum
Sargassum muticum (Yendo) Fensholt is a well-known invasive brown alga, introduced from its native habitats in Northeast Asia to the west coast of North America, to Europe, and to the Mediterranean Sea (Cheang et al., 2010; Liu et al., 2013). Its invasion has caused strongly negative action on native perennial seaweed and sea animals (Incera et al., 2011). Its large-scale appearance in invaded habitats has attracted lots of attention, but information on its genetics and molecular biology is scarce. Here, we sequenced and characterized the complete mitochondrial genome of S. muticum (collected from Sanggou Bay, China) via long PCR and primer walking techniques (Liu et al., 2014). The S. muticum mitogenome is a circular molecule of 34,720 bp (Figure 1; GenBank accession number KJ938301). The overall AT content is 63.41%, similar to other brown algae (62.01–67.47%). The percentage of the intergenic spacer (4.65%) in S. muticum is similar to Sargassum horneri (4.29%), but lower than other reported brown algae (5.62–6.81%) with the exception of Dictyota dichotoma (3.21%). The mitogenome size of S. muticum is 114 bp longer than that of S. horneri (34,606 bp. KJ938300). This difference was caused by increase of spacer size and reduction of overlap size. The average spacer size in
Correspondence: Feng Liu, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P. R. China. E-mail: [email protected] Shaojun Pang, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China. E-mail: [email protected]
History Received 5 June 2014 Accepted 7 June 2014 Published online 1 July 2014
S. muticum is 31.6 bp, longer than S. horneri (28.0 bp), and the average overlap size of 12.2 bp shorter than S. horneri (13.7 bp). In particular, the cox3-atp6 intergenic spacer for S. muticum is 105 bp, and longer than that for S. horneri (only 20 bp). The mitogenome of S. muticum contains 65 genes, including 3 ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes, as well as 2 conserved open reading frames (ORFs). Genes in S. muticum mitogenome are encoded on both strands, and only 6 genes (rpl2, rps19, rps3, rpl16, orf131 and tatC) are transcribed from the light strand. All protein-coding genes have a methionine (ATG) start codon. The frequency of stop-codon usage bias is 70.27% for TAA, higher than that for TAG (13.51%) and TGA (16.22%). Two tRNA clusters (MLHCNF and IQL) are well conserved in S. muticum as those of other brown algal mitogenomes. The gene order for S. muticum mitogenome is identical to that for S. horneri, Fucus vesiculosus and Desmarestia viridis, but differs from Laminariales by variation of trnA position (Li et al., 2014; Yotsukura et al., 2010), from Ectocarpales by variation of trnD and trnA positions, and from D. dichotoma by variation of nine gene positions (trnK, atp9, trnE, atp8, trnD, trnA, rps10, rpl31 and trnM3) (Oudot-Le Secq et al., 2006). Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 35 protein-coding genes indicate that S. muticum has a close evolutionary relationship with S. horneri and a distant relationship with D. dichotoma, supporting current taxonomic systems (Guiry & Guiry, 2014). The mitogenome of S. muticum determined herein augments the Sargassum mitogenome data, providing a rich resource of markers for systematic and population genetic investigation of Sargassum species.
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 08/22/14 For personal use only.
2
F. Liu & S. Pang
Mitochondrial DNA, Early Online: 1–2
Figure 1. Gene map of Sargassum muticum mitochondrial genome. Genes and ORFs are shown as solid blocks. The gene blocks shown inside and outside the circular map are transcribed in the clockwise and counter-clockwise directions, respectively. Number inside the circle indicates the mitogenome size.
Declaration of interest This work was supported by the 863 Hi-Tech Research and Development Program of China (No. 2012AA10A413), the National Natural Science Foundation of China (No. 41206146, 41176135), the Scientific Research Foundation for Outstanding Young Scientists of Shandong Province (No. BS2013HZ004), the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, State Oceanic Administration (No. MATHAB201408), and the Open Research Fund of Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, P. R. China (No. K201311). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Cheang CC, Chu KH, Fujita D, Yoshida G, Hiraoka M, Critchley A, Choi HG, et al. (2010). Low genetic variability of Sargassum muticum (Phaeophyceae) revealed by a global analysis of native and introduced populations. J Phycol 46:1063–74. Guiry MD, Guiry GM. (2014). AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. Available at: http://www.algaebase.org (Accessed 18 May 2014).
Incera M, Olabarria C, Cacabelos E, Ce´sar J, Troncoso JS. (2011). Distribution of Sargassum muticum on the NorthWest coast of Spain: Relationships with urbanization and community diversity. Cont Shelf Res 31:488–95. Li TY, Qu JQ, Feng YJ, Liu C, Chi S, Liu T. (2014). Complete mitochondrial genome of Undaria pinnatifida (Alariaceae, Laminariales, Phaeophyceae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.865172. Liu F, Pang SJ, Li X, Li J. (2014). Complete mitochondrial genome of the brown alga Sargassum horneri (Sargassaceae, Phaeophyceae): Genome organization and phylogenetic analyses. J Appl Phycol. [Epub ahead of print]. doi:10.1007/s10811-014-0295-5. Liu F, Pang SJ, Gao SQ, Shan TF. (2013). Intraspecific genetic analysis, gamete release performance and growth of Sargassum muticum (Fucales, Phaeophyta) from China. Chin J Oceanol Limnol 31: 1268–75. Oudot-Le Secq M-P, Loiseaux-De Goe¨r 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 49:47–58. 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 22:243–51.
Supplementary material available online Supplementary Figure
