Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) Feng Liu & Shaojun Pang To cite this article: Feng Liu & Shaojun Pang (2014): Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.953108
Published online: 04 Sep 2014.
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Date: 07 November 2015, At: 23:30
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.953108
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) Feng Liu and Shaojun Pang
Downloaded by [University of California, San Diego] at 23:30 07 November 2015
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
Abstract
Keywords
We determined the complete mitochondrial genome of Scytosiphon lomentaria (Lyngbye) Link, which is the first representative of the genus Scytosiphon C. Agardh. The circular mitogenome of S. lomentaria is 36,918 bp in length, with the overall A+T content of 65.86%. The genome contains 67 genes, including 3 ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes and 4 unidentified open reading frames (ORFs). The gene order of S. lomentaria mitogenome conforms to that of Ectocarpales mitogenomes (not including Pylaiella littoralis), i.e. Petalonia fascia, and Ectocarpus siliculosus, but differs from Laminariales, Desmarestiales, Fucales and Dictyotales with position variation of several genes. The S. lomentaria mitogenome has an overall nucleotide sequence identity of 80.4% with P. fascia, and 74.9% with E. siliculosus. The present data is of value to phylogenetic analyses of such a diverse Scytosiphonaceae family as well as to understanding of mitogenome evolution in brown algae.
Brown alga, mitochondrial genome, Phaeophyceae, Scytosiphonaceae, Scytosiphon lomentaria
Species in genus Scytosiphon C. Agardh are widespread in temperate coastal regions of the world, usually flourish in spring, and have a heteromorphic life history consisting of a large erect gametophyte and a small crustose sporophyte (Kogame et al., 2005; Tseng, 2009). Based on algaebase data, there are approximately 69 species names reported in Scytosiphon, only seven of which are currently accepted taxonomically (Guiry & Guiry, 2014). Scytosiphon lomentaria (Lyngbye) Link has been intensively studied owing to an ideal model species for life history and cytology researches (e.g. Nagasato & Motomura, 2002, 2004) and a popular economic seaweed as foodstaff under commercial cultivation in China (Xing et al., 2011; Zhang et al., 2013). We determined the complete mitochondrial genome of S. lomentaria (collected from Sanggou Bay, China), which is the first representative of Scytosiphon (GenBank accession number KJ995702). The circular S. lomentaria mitogenome is 36,918 bp in length with overall A+T content of 65.86%, and contains 67 genes including three ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes, and four unidentified open reading frames (ORFs) (Table 1). The 25 tRNA genes are interspersed in the genome and range in size from 72 to 88 bp.
Correspondence: Feng Liu, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P.R. China. E-mail: [email protected] Shaojun Pang, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P.R. China. E-mail: [email protected]
History Received 28 July 2014 Accepted 6 August 2014 Published online 26 December 2014
The 35 protein-coding genes include 17 ribosomal proteins (rps24, 7, 8, 10-14, and 19; rpl2, 5, 6, 14, 16, and 31), ten NADH dehydrogenase subunits (nad1-7, 4L, 9 and 11), apocytochrome b (cob), three cytochrome oxidase subunits (cox1-3), three ATPase subunits (atp6, 8 and 9) and a protein transporter component of the secY-independent pathway (tatC). Four ORFs contain three conserved ones (ORF40, ORF126 and ORF226) and one unique ORF43 located between trnD and trnV. All protein-coding genes start with the ATG codon with the exception of nad11, which starts with GTG codon. The majority of protein-coding genes (35 of 39 genes) use TAA as stop codon, while rps8 and nad3 use TGA, and rps12 and rpl2 use TAG. Thirteen pairs of genes overlap by 1 to 17 bp, and intergenic spacer regions range from 0 to 390 bp with the average size of 41.1 bp. Comparative analyses of brown algal mitogenomes from five different orders reveal that the gene order of S. lomentaria mitogenome conforms to that observed in Ectocarpales mitogenomes (not including Pylaiella littoralis), i.e. Petalonia fascia, and Ectocarpus siliculosus (Liu & Pang, 2014), but differs from Laminariales, Desmarestiales, Fucales and Dictyotales with position variation of several genes (Liu et al., 2014a,b; OudotLe Secq et al., 2006). Besides two conserved tRNA gene clusters (MLHCNF and MQL) identified in all known brown algal mitogenomes, another one, KAD, is only detected in Ectocarpales, which was arranged as KDA in P. littoralis. The S. lomentaria mitogenome has an overall nucleotide sequence identity of 80.4% with P. fascia, and 74.9% with E. siliculosus. The pairwise identities of 67 gene sequences among four species in Ectocarpales are summarized in Table 1. The present data is particularly useful in phylogenetic analyses of such a diverse Scytosiphonaceae family (Cho et al., 2006) and studies on mitogenome evolution in Phaeophyceae.
2
F. Liu & S. Pang
Mitochondrial DNA, Early Online: 1–3
Table 1. Mitochondrial genome organization of Scytosiphon lomentaria (Sl. KJ995702).
Downloaded by [University of California, San Diego] at 23:30 07 November 2015
% identity (nt/aa) Gene
Type
Location
Size (bp)
Sl/Pf
Sl/Es
Sl/Pl
Pf/Es**
Pf/Pl
Es/Pl
rnl (23S) trnK (uuu) trnA (ugc) trnD (guc) ORF43 trnV (uac) atp9 trnM (cau) trnL (uaa) trnH (gug) trnC (gca) trnN (guu) trnF (gaa) rps8 rpl6 rps2 rps4 nad1 tatC trnW (cca) ORF40* trnM (cau)* trnQ (uug) trnL (uag) rps12 rps7 nad4L trnL (caa) rpl14 rpl5 trnG (gcc) ORF126* rpl16 rps3 rps19 rpl2 rps13 rps11 trnY (gua) cox3 ORF226* atp6 trnR (ucu) nad2 cox1 trnI (gau) trnE (uuc) nad9 cob cox2 nad4 trnQ (cug)* nad5 nad6 nad11 nad3 rps14 atp8 trnS (gcu) rps10 trnS (uga) rpl31 rns (16S) rrn5 (5S) trnM (cau) nad7 trnP (ugg)
rRNA tRNA tRNA tRNA CDS tRNA CDS tRNA tRNA tRNA tRNA tRNA tRNA CDS CDS CDS CDS CDS CDS tRNA CDS tRNA tRNA tRNA CDS CDS CDS tRNA CDS CDS tRNA CDS CDS CDS CDS CDS CDS CDS tRNA CDS CDS CDS tRNA CDS CDS tRNA tRNA CDS CDS CDS CDS tRNA CDS CDS CDS CDS CDS CDS tRNA CDS tRNA CDS rRNA rRNA tRNA CDS tRNA
1–2710 2702–2775 2922–2994 2998–3070 3346–3477 3596–3667 3717–3944 4006–4078 4087–4169 4185–4258 4261–4333 4334–4406 4413–4485 4500–4871 4868–5359 5359–5940 5930–6727 6776–7756 7745–8467 8487–8559 8587–8709 8735–8807 8818–8889 8892–8973 8974–9360 9354–9854 9888–10,190 10,192–10,273 10,280–10,666 10,670–11,209 11,213–11,285 11,293–11,673 11,677–12,090 12,110–12,931 12,936–13,196 13,183–13,947 13,970–14,335 14,319–14,816 14,841–14,921 14,934–15,752 15,761–16,441 16,546–17,295 17,340–17,412 17,417–18,901 18,912–20,507 20,580–20,651 20,676–20,747 20,774–21,346 21,346–22,500 22,557–26,453 26,444–27,892 27,910–27,996 28,000–29,985 29,970–30,878 30,886–31,506 31,508–31,870 31,867–32,157 32,337–32,504 32,627–32,714 32,745–33,059 33,070–33,155 33,165–33,365 33,756–35,295 35,298–35,440 35,437–35,511 35,522–36,718 36,771–36,842
2710 74 73 73 132 72 228 73 83 74 73 73 73 372 492 582 798 981 723 73 123 73 72 82 387 501 303 82 387 540 73 381 414 822 261 765 366 498 81 819 681 750 73 1485 1596 72 72 573 1155 3897 1449 87 1986 909 621 363 291 168 88 315 86 201 1540 143 75 1197 72
94.8/– 100.0/– 93.1/– 95.8/– –/– 93.0/– 94.2/100.0 91.7/– 96.4/– 97.2/– 98.6/– 95.8/– 97.2/– 83.3/84.5 82.5/82.8 86.3/88.2 84.4/90.9 89.6/98.4 72.9/69.6 98.6/– 87.8/90.0 100.0/– 98.6/– 98.7/– 85.5/97.6 81.4/82.5 89.7/98.0 96.3/– 87.0/95.3 80.1/76.9 98.6/– 74.9/69.5 84.2/91.9 84.9/85.3 78.2/85.2 84.7/90.1 81.4/80.1 76.4/73.6 96.2/– 89.6/96.6 57.5/46.5 87.2/95.5 100.0/– 87.6/95.1 87.4/98.6 100.0/– 87.5/– 89.5/96.8 88.4/99.2 82.1/83.4 86.6/96.2 90.9/– 87.0/94.5 81.1/77.8 86.2/97.5 90.0/99.1 84.8/87.5 83.9/90.9 92.0/– 75.4/70.4 96.5/– 70.0/73.1 95.8/– 77.9/– 96.0/– 85.6/98.9 98.6/–
90.4/– 100.0/– 93.1/– 89.0/– –/– 93.0/– 91.2/100.0 94.5/– 96.4/– 97.2/– 91.7– 100.0/– 98.6/– 76.8/75.6 77.6/73.0 70.8/65.8 80.2/80.0 84.9/98.1 68.3/62.2 97.2/– 72.0/65.1 95.8/– 97.2/– 91.4/– 82.4/94.5 74.0/72.4 83.8/94.0 95.1/– 80.1/85.9 72.9/70.3 100.0/– 71.8/62.5 79.7/84.6 76.5/73.2 76.4/77.2 77.3/82.6 80.6/80.1 68.4/63.8 96.2/– 83.7/92.6 –/– 85.6/92.7 100.0/– 82.7/88.6 86.2/95.6 97.2/– 100.0/– 84.9/93.1 85.4/97.1 70.5/62.2 81.8/91.7 81.6/– 81.9/90.1 73.7/71.8 81.3/91.2 85.1/90.8 76.9/83.3 75.2/71.9 88.6/– 67.9/57.9 93.0/– 69.5/68.1 93.1/– 68.2/– 89.3/– 84.6/96.7 91.6/–
88.7/– 95.9/– 90.4/– 87.6/– –/– 94.4/– 91.2/100.0 93.1/– 97.5/– 96.0/– 89.0/– 97.2/– 97.2/– 72.7/65.6 72.9/65.6 71.7/72.4 73.1/78.8 83.8/96.0 68.1/63.5 97.2/– –/– 93.1/– 94.4/– 92.6/– 81.6/92.1 69.6/65.0 82.8/89.0 –/– 77.0/86.7 69.1/61.4 98.6/– 66.1/55.1 75.1/76.6 72.3/67.7 74.5/73.0 75.2/79.9 73.7/76.0 59.9/57.5 93.8/– 80.5/90.0 –/– 80.0/88.7 97.2/– 78.1/83.6 82.8/93.5 91.6/– 97.2/– 79.9/88.4 82.8/94.2 63.9/54.8 79.8/91.0 77.5/– 79.1/86.0 55.8/55.2 77.7/89.4 84.5/92.5 74.9/79.1 76.1/81.8 87.5/– 62.0/54.7 93.0/– 63.8/55.7 90.4/– 66.4/– 82.6/– 81.7/93.7 93.0/–
90.3/– 100.0/– 86.3/– 90.4/– –/– 88.8/– 92.1/100.0 91.7/– 100.0/– 97.2/– 90.4/– 95.8/– 95.8/– 78.2/78.8 77.6/78.5 73.6/66.8 80.4/82.6 86.6/97.2 72.9/64.1 95.8/– 73.6/64.2 95.8/– 95.8/– 92.6/– 83.2/92.9 74.8/72.4 85.8/96.0 96.3/– 78.2/87.5 74.3/69.7 98.6/– 70.5/64.8 80.1/83.9 77.6/76.1 75.7/77.0 79.4/84.2 83.8/86.5 71.6/61.3 92.5/– 85.9/91.5 –/– 84.5/92.3 100.0/– 82.0/89.0 84.6/96.2 97.2/– 87.5/– 87.7/95.2 86.1/97.3 70.6/63.5 81.6/91.9 84.0/– 83.3/90.3 75.1/73.3 82.1/91.3 85.3/91.6 78.0/77.0 75.8/71.9 90.9/– 69.7/62.6 93.0/– 66.8/62.3 93.3/– 80.1/– 93.3/– 85.2/96.7 90.2/–
88.2/– 95.9/– 89.0/– 91.7/– –/– 93.0/– 92.5/100.0 87.6/– 98.8/– 96.0/– 87.6/– 98.6/– 94.5/– 71.1/68.0 73.5/70.5 72.0/71.9 74.9/79.2 85.3/95.7 69.1/62.5 95.8/– –/– 93.1/– 93.0/– 92.6/– 81.6/90.6 72.6/66.8 83.8/91.0 –/– 75.4/87.5 69.6/62.5 97.2/– 66.6/57.8 79.7/79.5 72.8/68.1 75.2/75.0 75.8/81.1 75.8/81.5 68.7/61.2 92.5/– 81.9/90.8 –/– 80.0/87.1 97.2/– 77.4/83.1 82.4/94.1 91.6/– 90.2/– 83.0/88.9 84.5/94.2 65.0/55.1 80.5/90.8 79.7/– 81.3/87.5 55.5/55.5 78.8/90.4 83.4/93.3 79.3/80.2 77.9/83.6 90.9/– 61.3/56.0 94.1/– 60.9/55.0 90.4/– 73.6/– 86.6/– 82.1/93.9 91.6/–
87.9/– 95.9/– 94.5/– 87.6/– –/– 93.0/– 91.2/100.0 91.7/– 98.8/– 98.6/– 93.1/– 97.2/– 98.6/– 72.4/67.2 76.8/74.2 70.8/62.6 75.4/78.1 84.6/96.3 69.8/65.3 94.5/– –/– 97.2/– 94.4/– 95.1/– 83.4/95.3 71.4/70.6 84.1/90.0 –/– 78.2/85.1 71.1/64.1 98.6/– 68.9/62.5 76.3/72.2 72.1/69.9 81.2/78.4 76.6/82.2 75.8/77.3 68.6/62.0 92.5/– 84.0/90.8 –/– 80.6/89.5 97.2/– 79.1/82.1 82.5/94.3 91.6/– 95.8/– 85.5/87.8 85.1/95.5 67.5/58.9 80.3/90.2 79.5/– 80.6/87.8 57.6/57.3 81.8/88.0 84.2/90.0 74.2/75.0 77.0/73.6 87.5/– 61.2/53.4 95.3/– 63.8/54.9 91.3/– 80.9/– 88.0/– 82.6/95.4 94.4/–
It shows gene name, type, location and size of S. lomentaria, and pairwise identity (%) of nucleotide (nt) and/or amino acid (aa) sequences with comparison to Petalonia fascia (Pf. KJ957769), Ectocarpus siliculosus (Es. FP885846) and Pylaiella littoralis (Pl. AJ277126). Gene names in bold indicate genes transcribed on the light strand, whereas others on the heavy strand. *The gene identities were calculated between genes and their counterparts in different mitogenomes. **The gene identity (%) of nucleotide (nt) and/or amino acid (aa) sequences of Pf/Es was from Liu & Pang (2014).
DOI: 10.3109/19401736.2014.953108
Declaration of interest This work was supported by the National Natural Science Foundation of China (No. 41206146), the Scientific Research Foundation for Outstanding Young Scientists of Shandong Province (No. BS2013HZ004), the Open Reseach Fund of Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture (No. K201311), and the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, State Oceanic Administration (No. MATHAB201408). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Downloaded by [University of California, San Diego] at 23:30 07 November 2015
References Cho GY, Kogame K, Boo SM. (2006). Molecular phylogeny of the family Scytosiphonaceae (Phaeophyceae). Algae 21:175–83. Guiry MD, Guiry GM. (2014). AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. Available at: http://www.algaebase.org (Accessed 28 July 2014) Kogame K, Uwai S, Shimada S, Masuda M. (2005). A study of sexual and asexual populations of Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) in Hokkaido, northern Japan, using molecular marker. Eur J Phycol 40:313–22. Liu F, Pang SJ, Li X, Li J. (2014a). Complete mitochondrial genome of the brown alga Sargassum horneri (Sargassaceae, Phaeophyceae): Genome organization and phylogenetic analyses. J Appl Phycol doi:10.1007/s10811-014-0295-5.
Mitogenome of S. lomentaria
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Liu F, Pang SJ, Luo MB. (2014b). Complete mitochondrial genome of the brown alga Sargassum fusiforme (Sargassaceae, Phaeophyceae): Genome architecture and taxonomic consideration. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.936417. Liu F, Pang SJ. (2014). Mitochondrial phylogenomics reveals a close relationship between Petalonia fascia (Scytosiphonaceae, Phaeophyceae) and Ectocarpus siliculosus. J Appl Phycol doi:10.1007/s10811-014-0386-3. Nagasato C, Motomura T. (2002). Influence of the centrosome in cytokinesis of brown algae: Polyspermic zygotes of Scytosiphon lomentaria (Scytosiphonales, Phaeophyceae). J Cell Sci 115:2541–8. Nagasato C, Motomura T. (2004). Destruction of maternal centrioles during fertilization of the brown alga, Scytosiphon lomentaria (Scytosiphonales, Phaeophyceae). Cell Motil Cytoskel 59:109–18. 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. Tseng CK. (2009). Seaweeds in Yellow Sea and Bohai Sea of China. Beijing: Science Press (in Chinese). Xing YZ, Gong XZ, Gao W, Yin BS. (2011). Effect of ecological factors on growth and development of sporophytes of Scytosiphon lomentaria. Oceanologia et limnologia Sinica 42:101–6 (in Chinese with English abstract). Zhang WJ, Gong XZ, Gao W. (2013). Effect of environmental factors on spore attachment of Scytosiphon lomentaria. Oceanologia et limnologia Sinica 44:1661–6 (in Chinese with English abstract).
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) Feng Liu & Shaojun Pang To cite this article: Feng Liu & Shaojun Pang (2014): Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.953108
Published online: 04 Sep 2014.
Submit your article to this journal
Article views: 18
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 07 November 2015, At: 23:30
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.953108
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae) Feng Liu and Shaojun Pang
Downloaded by [University of California, San Diego] at 23:30 07 November 2015
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
Abstract
Keywords
We determined the complete mitochondrial genome of Scytosiphon lomentaria (Lyngbye) Link, which is the first representative of the genus Scytosiphon C. Agardh. The circular mitogenome of S. lomentaria is 36,918 bp in length, with the overall A+T content of 65.86%. The genome contains 67 genes, including 3 ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes and 4 unidentified open reading frames (ORFs). The gene order of S. lomentaria mitogenome conforms to that of Ectocarpales mitogenomes (not including Pylaiella littoralis), i.e. Petalonia fascia, and Ectocarpus siliculosus, but differs from Laminariales, Desmarestiales, Fucales and Dictyotales with position variation of several genes. The S. lomentaria mitogenome has an overall nucleotide sequence identity of 80.4% with P. fascia, and 74.9% with E. siliculosus. The present data is of value to phylogenetic analyses of such a diverse Scytosiphonaceae family as well as to understanding of mitogenome evolution in brown algae.
Brown alga, mitochondrial genome, Phaeophyceae, Scytosiphonaceae, Scytosiphon lomentaria
Species in genus Scytosiphon C. Agardh are widespread in temperate coastal regions of the world, usually flourish in spring, and have a heteromorphic life history consisting of a large erect gametophyte and a small crustose sporophyte (Kogame et al., 2005; Tseng, 2009). Based on algaebase data, there are approximately 69 species names reported in Scytosiphon, only seven of which are currently accepted taxonomically (Guiry & Guiry, 2014). Scytosiphon lomentaria (Lyngbye) Link has been intensively studied owing to an ideal model species for life history and cytology researches (e.g. Nagasato & Motomura, 2002, 2004) and a popular economic seaweed as foodstaff under commercial cultivation in China (Xing et al., 2011; Zhang et al., 2013). We determined the complete mitochondrial genome of S. lomentaria (collected from Sanggou Bay, China), which is the first representative of Scytosiphon (GenBank accession number KJ995702). The circular S. lomentaria mitogenome is 36,918 bp in length with overall A+T content of 65.86%, and contains 67 genes including three ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes, and four unidentified open reading frames (ORFs) (Table 1). The 25 tRNA genes are interspersed in the genome and range in size from 72 to 88 bp.
Correspondence: Feng Liu, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P.R. China. E-mail: [email protected] Shaojun Pang, Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P.R. China. E-mail: [email protected]
History Received 28 July 2014 Accepted 6 August 2014 Published online 26 December 2014
The 35 protein-coding genes include 17 ribosomal proteins (rps24, 7, 8, 10-14, and 19; rpl2, 5, 6, 14, 16, and 31), ten NADH dehydrogenase subunits (nad1-7, 4L, 9 and 11), apocytochrome b (cob), three cytochrome oxidase subunits (cox1-3), three ATPase subunits (atp6, 8 and 9) and a protein transporter component of the secY-independent pathway (tatC). Four ORFs contain three conserved ones (ORF40, ORF126 and ORF226) and one unique ORF43 located between trnD and trnV. All protein-coding genes start with the ATG codon with the exception of nad11, which starts with GTG codon. The majority of protein-coding genes (35 of 39 genes) use TAA as stop codon, while rps8 and nad3 use TGA, and rps12 and rpl2 use TAG. Thirteen pairs of genes overlap by 1 to 17 bp, and intergenic spacer regions range from 0 to 390 bp with the average size of 41.1 bp. Comparative analyses of brown algal mitogenomes from five different orders reveal that the gene order of S. lomentaria mitogenome conforms to that observed in Ectocarpales mitogenomes (not including Pylaiella littoralis), i.e. Petalonia fascia, and Ectocarpus siliculosus (Liu & Pang, 2014), but differs from Laminariales, Desmarestiales, Fucales and Dictyotales with position variation of several genes (Liu et al., 2014a,b; OudotLe Secq et al., 2006). Besides two conserved tRNA gene clusters (MLHCNF and MQL) identified in all known brown algal mitogenomes, another one, KAD, is only detected in Ectocarpales, which was arranged as KDA in P. littoralis. The S. lomentaria mitogenome has an overall nucleotide sequence identity of 80.4% with P. fascia, and 74.9% with E. siliculosus. The pairwise identities of 67 gene sequences among four species in Ectocarpales are summarized in Table 1. The present data is particularly useful in phylogenetic analyses of such a diverse Scytosiphonaceae family (Cho et al., 2006) and studies on mitogenome evolution in Phaeophyceae.
2
F. Liu & S. Pang
Mitochondrial DNA, Early Online: 1–3
Table 1. Mitochondrial genome organization of Scytosiphon lomentaria (Sl. KJ995702).
Downloaded by [University of California, San Diego] at 23:30 07 November 2015
% identity (nt/aa) Gene
Type
Location
Size (bp)
Sl/Pf
Sl/Es
Sl/Pl
Pf/Es**
Pf/Pl
Es/Pl
rnl (23S) trnK (uuu) trnA (ugc) trnD (guc) ORF43 trnV (uac) atp9 trnM (cau) trnL (uaa) trnH (gug) trnC (gca) trnN (guu) trnF (gaa) rps8 rpl6 rps2 rps4 nad1 tatC trnW (cca) ORF40* trnM (cau)* trnQ (uug) trnL (uag) rps12 rps7 nad4L trnL (caa) rpl14 rpl5 trnG (gcc) ORF126* rpl16 rps3 rps19 rpl2 rps13 rps11 trnY (gua) cox3 ORF226* atp6 trnR (ucu) nad2 cox1 trnI (gau) trnE (uuc) nad9 cob cox2 nad4 trnQ (cug)* nad5 nad6 nad11 nad3 rps14 atp8 trnS (gcu) rps10 trnS (uga) rpl31 rns (16S) rrn5 (5S) trnM (cau) nad7 trnP (ugg)
rRNA tRNA tRNA tRNA CDS tRNA CDS tRNA tRNA tRNA tRNA tRNA tRNA CDS CDS CDS CDS CDS CDS tRNA CDS tRNA tRNA tRNA CDS CDS CDS tRNA CDS CDS tRNA CDS CDS CDS CDS CDS CDS CDS tRNA CDS CDS CDS tRNA CDS CDS tRNA tRNA CDS CDS CDS CDS tRNA CDS CDS CDS CDS CDS CDS tRNA CDS tRNA CDS rRNA rRNA tRNA CDS tRNA
1–2710 2702–2775 2922–2994 2998–3070 3346–3477 3596–3667 3717–3944 4006–4078 4087–4169 4185–4258 4261–4333 4334–4406 4413–4485 4500–4871 4868–5359 5359–5940 5930–6727 6776–7756 7745–8467 8487–8559 8587–8709 8735–8807 8818–8889 8892–8973 8974–9360 9354–9854 9888–10,190 10,192–10,273 10,280–10,666 10,670–11,209 11,213–11,285 11,293–11,673 11,677–12,090 12,110–12,931 12,936–13,196 13,183–13,947 13,970–14,335 14,319–14,816 14,841–14,921 14,934–15,752 15,761–16,441 16,546–17,295 17,340–17,412 17,417–18,901 18,912–20,507 20,580–20,651 20,676–20,747 20,774–21,346 21,346–22,500 22,557–26,453 26,444–27,892 27,910–27,996 28,000–29,985 29,970–30,878 30,886–31,506 31,508–31,870 31,867–32,157 32,337–32,504 32,627–32,714 32,745–33,059 33,070–33,155 33,165–33,365 33,756–35,295 35,298–35,440 35,437–35,511 35,522–36,718 36,771–36,842
2710 74 73 73 132 72 228 73 83 74 73 73 73 372 492 582 798 981 723 73 123 73 72 82 387 501 303 82 387 540 73 381 414 822 261 765 366 498 81 819 681 750 73 1485 1596 72 72 573 1155 3897 1449 87 1986 909 621 363 291 168 88 315 86 201 1540 143 75 1197 72
94.8/– 100.0/– 93.1/– 95.8/– –/– 93.0/– 94.2/100.0 91.7/– 96.4/– 97.2/– 98.6/– 95.8/– 97.2/– 83.3/84.5 82.5/82.8 86.3/88.2 84.4/90.9 89.6/98.4 72.9/69.6 98.6/– 87.8/90.0 100.0/– 98.6/– 98.7/– 85.5/97.6 81.4/82.5 89.7/98.0 96.3/– 87.0/95.3 80.1/76.9 98.6/– 74.9/69.5 84.2/91.9 84.9/85.3 78.2/85.2 84.7/90.1 81.4/80.1 76.4/73.6 96.2/– 89.6/96.6 57.5/46.5 87.2/95.5 100.0/– 87.6/95.1 87.4/98.6 100.0/– 87.5/– 89.5/96.8 88.4/99.2 82.1/83.4 86.6/96.2 90.9/– 87.0/94.5 81.1/77.8 86.2/97.5 90.0/99.1 84.8/87.5 83.9/90.9 92.0/– 75.4/70.4 96.5/– 70.0/73.1 95.8/– 77.9/– 96.0/– 85.6/98.9 98.6/–
90.4/– 100.0/– 93.1/– 89.0/– –/– 93.0/– 91.2/100.0 94.5/– 96.4/– 97.2/– 91.7– 100.0/– 98.6/– 76.8/75.6 77.6/73.0 70.8/65.8 80.2/80.0 84.9/98.1 68.3/62.2 97.2/– 72.0/65.1 95.8/– 97.2/– 91.4/– 82.4/94.5 74.0/72.4 83.8/94.0 95.1/– 80.1/85.9 72.9/70.3 100.0/– 71.8/62.5 79.7/84.6 76.5/73.2 76.4/77.2 77.3/82.6 80.6/80.1 68.4/63.8 96.2/– 83.7/92.6 –/– 85.6/92.7 100.0/– 82.7/88.6 86.2/95.6 97.2/– 100.0/– 84.9/93.1 85.4/97.1 70.5/62.2 81.8/91.7 81.6/– 81.9/90.1 73.7/71.8 81.3/91.2 85.1/90.8 76.9/83.3 75.2/71.9 88.6/– 67.9/57.9 93.0/– 69.5/68.1 93.1/– 68.2/– 89.3/– 84.6/96.7 91.6/–
88.7/– 95.9/– 90.4/– 87.6/– –/– 94.4/– 91.2/100.0 93.1/– 97.5/– 96.0/– 89.0/– 97.2/– 97.2/– 72.7/65.6 72.9/65.6 71.7/72.4 73.1/78.8 83.8/96.0 68.1/63.5 97.2/– –/– 93.1/– 94.4/– 92.6/– 81.6/92.1 69.6/65.0 82.8/89.0 –/– 77.0/86.7 69.1/61.4 98.6/– 66.1/55.1 75.1/76.6 72.3/67.7 74.5/73.0 75.2/79.9 73.7/76.0 59.9/57.5 93.8/– 80.5/90.0 –/– 80.0/88.7 97.2/– 78.1/83.6 82.8/93.5 91.6/– 97.2/– 79.9/88.4 82.8/94.2 63.9/54.8 79.8/91.0 77.5/– 79.1/86.0 55.8/55.2 77.7/89.4 84.5/92.5 74.9/79.1 76.1/81.8 87.5/– 62.0/54.7 93.0/– 63.8/55.7 90.4/– 66.4/– 82.6/– 81.7/93.7 93.0/–
90.3/– 100.0/– 86.3/– 90.4/– –/– 88.8/– 92.1/100.0 91.7/– 100.0/– 97.2/– 90.4/– 95.8/– 95.8/– 78.2/78.8 77.6/78.5 73.6/66.8 80.4/82.6 86.6/97.2 72.9/64.1 95.8/– 73.6/64.2 95.8/– 95.8/– 92.6/– 83.2/92.9 74.8/72.4 85.8/96.0 96.3/– 78.2/87.5 74.3/69.7 98.6/– 70.5/64.8 80.1/83.9 77.6/76.1 75.7/77.0 79.4/84.2 83.8/86.5 71.6/61.3 92.5/– 85.9/91.5 –/– 84.5/92.3 100.0/– 82.0/89.0 84.6/96.2 97.2/– 87.5/– 87.7/95.2 86.1/97.3 70.6/63.5 81.6/91.9 84.0/– 83.3/90.3 75.1/73.3 82.1/91.3 85.3/91.6 78.0/77.0 75.8/71.9 90.9/– 69.7/62.6 93.0/– 66.8/62.3 93.3/– 80.1/– 93.3/– 85.2/96.7 90.2/–
88.2/– 95.9/– 89.0/– 91.7/– –/– 93.0/– 92.5/100.0 87.6/– 98.8/– 96.0/– 87.6/– 98.6/– 94.5/– 71.1/68.0 73.5/70.5 72.0/71.9 74.9/79.2 85.3/95.7 69.1/62.5 95.8/– –/– 93.1/– 93.0/– 92.6/– 81.6/90.6 72.6/66.8 83.8/91.0 –/– 75.4/87.5 69.6/62.5 97.2/– 66.6/57.8 79.7/79.5 72.8/68.1 75.2/75.0 75.8/81.1 75.8/81.5 68.7/61.2 92.5/– 81.9/90.8 –/– 80.0/87.1 97.2/– 77.4/83.1 82.4/94.1 91.6/– 90.2/– 83.0/88.9 84.5/94.2 65.0/55.1 80.5/90.8 79.7/– 81.3/87.5 55.5/55.5 78.8/90.4 83.4/93.3 79.3/80.2 77.9/83.6 90.9/– 61.3/56.0 94.1/– 60.9/55.0 90.4/– 73.6/– 86.6/– 82.1/93.9 91.6/–
87.9/– 95.9/– 94.5/– 87.6/– –/– 93.0/– 91.2/100.0 91.7/– 98.8/– 98.6/– 93.1/– 97.2/– 98.6/– 72.4/67.2 76.8/74.2 70.8/62.6 75.4/78.1 84.6/96.3 69.8/65.3 94.5/– –/– 97.2/– 94.4/– 95.1/– 83.4/95.3 71.4/70.6 84.1/90.0 –/– 78.2/85.1 71.1/64.1 98.6/– 68.9/62.5 76.3/72.2 72.1/69.9 81.2/78.4 76.6/82.2 75.8/77.3 68.6/62.0 92.5/– 84.0/90.8 –/– 80.6/89.5 97.2/– 79.1/82.1 82.5/94.3 91.6/– 95.8/– 85.5/87.8 85.1/95.5 67.5/58.9 80.3/90.2 79.5/– 80.6/87.8 57.6/57.3 81.8/88.0 84.2/90.0 74.2/75.0 77.0/73.6 87.5/– 61.2/53.4 95.3/– 63.8/54.9 91.3/– 80.9/– 88.0/– 82.6/95.4 94.4/–
It shows gene name, type, location and size of S. lomentaria, and pairwise identity (%) of nucleotide (nt) and/or amino acid (aa) sequences with comparison to Petalonia fascia (Pf. KJ957769), Ectocarpus siliculosus (Es. FP885846) and Pylaiella littoralis (Pl. AJ277126). Gene names in bold indicate genes transcribed on the light strand, whereas others on the heavy strand. *The gene identities were calculated between genes and their counterparts in different mitogenomes. **The gene identity (%) of nucleotide (nt) and/or amino acid (aa) sequences of Pf/Es was from Liu & Pang (2014).
DOI: 10.3109/19401736.2014.953108
Declaration of interest This work was supported by the National Natural Science Foundation of China (No. 41206146), the Scientific Research Foundation for Outstanding Young Scientists of Shandong Province (No. BS2013HZ004), the Open Reseach Fund of Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture (No. K201311), and the Open Research Fund of Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, State Oceanic Administration (No. MATHAB201408). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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