http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982570
MITOGENOME ANNOUNCEMENT
Next-generation sequencing of the yellowfin tuna mitochondrial genome reveals novel phylogenetic relationships within the genus Thunnus Liang Guo1, Mingming Li1, Heng Zhang2, Sen Yang1, Xinghan Chen1, Zining Meng1, and Haoran Lin1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/26/15 For personal use only.
1
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and 2Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China Abstract
Keywords
Recently, the next-generation sequencing (NGS) technology has become a powerful tool for sequencing the teleost mitochondrial genome (mitogenome). Here, we used this technology to determine the mitogenome of the yellowfin tuna (Thunnus albacares). A total of 41,378 reads were generated by Illumina platform with an average depth of 250. The mitogenome (16,528 bp in length) contained 37 mitochondrial genes with the similar gene order to other typical teleosts. These mitochondrial genes were encoded on the heavy strand except for ND6 and eight tRNA genes. The result of phylogenetic analysis supported two distinct clades dividing the genus Thunnus, but the tuna species of these two genetic clades were different from that of two recognized subgenus based on anatomical characters and geographical distribution. Our results might help to understand the structure, function, and evolutionary history of the yellowfin tuna mitogenome and also provide valuable new insights for phylogenetic affinity of tuna species.
Mitochondrial genome, phylogeny, thunnus albacares
Yellowfin tuna, Thunnus albacares, is a highly migratory species and widely distributed in tropical and subtropical seas. As one of the most important fishery species around the world, T. albacares is considered fully to be overexploited and has been listed as Near Threatened (IUCN, 2014). An understanding of phylogenetic relationship and historical evolutionary process is essential for effective conservation and management of the fishery resources. Traditionally, eight tuna species of the genus Thunnus are classified into two subgenera: Thunnus (T. alalunga, T. maccoyii, T. obesus, T. orientalis and T. thynnus) and Neothunnus (T. albacares, T. tonggol and T. atlanticus) based on anatomical characters and geographical distribution (Collette, 1978). Recently, the next-generation sequencing (NGS) technology has become a powerful tool for sequencing the teleost mitochondrial genome (mitogenome) (Cui et al., 2009; Xie et al., 2014), while mitochondrial DNA sequences are commonly used in phylogenetic and population structure studies. In this study, we used the NGS technology to determine the mitogenome of T. albacares, and then preformed a phylogenetic analysis to reveal true relationships within the genus Thunnus. The specimen of T. albacares was caught from the South China Sea near the Subi Reef and muscular tissue was preserved
Correspondence: Zining Meng, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. E-mail: [email protected]
History Received 8 October 2014 Revised 27 October 2014 Accepted 27 October 2014 Published online 24 November 2014
in 95% alcohol for DNA extraction. Through guided assemble, Illumina next-generation sequencing platform generated 41,378 reads for the mitogenome of T. albacares with an average depth of 250. The entire sequence of mitogenome is 16,528 bp (GenBank Accession No. KM588080; Figure 1) containing one control region (D-loop) and 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes) with the similar gene order to other typical teleosts. All the proteinscoding genes use typical ATG as the start codon except for COX I, whose start code is GTG. Accordingly, TAA, TA and T are used as the stop codon by protein-coding genes except for ND6, whose terminal code is TAG. The two rRNA genes are located between tRNA-Phe and tRNA-Leu, separated by tRNA-Val. The tRNA genes, ranging from 68 to 74 bp in length, have the potential to fold into the typical clover-leaf secondary structures, except that tRNA-Ser2 loses the dihydrouridine arm and forms one loop. ND6 and other 8 tRNA (for Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) are coded by the L-strand. The control region (865 bp) are located between tRNA-Pro gene and tRNA-Phe gene. We used the mitogenome sequence of T. albacares obtained in this study, together with the sequence data of other tuna species retrieved from NCBI database (missing data for T. atlanticus), to perform a neighbor-joining phylogenic analysis in the MEGA6.06 program with Katsuwonus pelamis as outgroup. The result suggests two distinct clades divide the genus Thunnus. The first clade comprises T. albacares, T. tonggol, T. obesus, T. maccoyii and T. thynnus, and the second includes T. orientalis and T. alalunga. Obviously, these tuna species of two genetic clades are different from that of two recognized subgenus mentioned above.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/26/15 For personal use only.
2
L. Guo et al.
Mitochondrial DNA, Early Online: 1–2
Figure1. Genes map of yellowfin tuna (Thunnus albacares) mitochondrial genome (accession number KM588080). Genes shown at the outer circle are encoded by the H-strand and those at the inner circle are encoded by the L-strand. ND1-6 indicate genes of the NADH dehydrogenase subunits 1–6; COXI-III, cytochrome c oxidase subunits I–III; ATP6 and ATP8, ATPase subunits 6 and 8; Cytb, cytochrome b. The inner ring indicates the GC content with the window size 4 nucleotides.
Declaration of interest This work was supported by the National High Technology R & D Program 863 of China (2012AA10A414) and the National Natural Science Foundation of China (grant 31370047 & 31001112). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Collette B. (1978). Adaptations and systematics of the mackerels and tunas. In: Sharp GD, Dizon AE, editors. The physiological ecology of tunas New York: Academic Press. p 7–39.
Cui Z, Liu Y, Li CP, You F, Chu H. (2009). The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae. Gene 432: 33–43. IUCN. (2014).The IUCN Red List of Threatened Species. Cambridge, UK, Version 2014.2. Available at: www.iucnredlist.org (Accessed 15 September 2014). Xie Z, Yu C, Guo L, Li M, Zhang Y, Liu X, Meng Z, Lin H. (2014). Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of black and reddish morphs of the Coral Trout Plectropomus leopardus. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.908369.
MITOGENOME ANNOUNCEMENT
Next-generation sequencing of the yellowfin tuna mitochondrial genome reveals novel phylogenetic relationships within the genus Thunnus Liang Guo1, Mingming Li1, Heng Zhang2, Sen Yang1, Xinghan Chen1, Zining Meng1, and Haoran Lin1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/26/15 For personal use only.
1
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and 2Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China Abstract
Keywords
Recently, the next-generation sequencing (NGS) technology has become a powerful tool for sequencing the teleost mitochondrial genome (mitogenome). Here, we used this technology to determine the mitogenome of the yellowfin tuna (Thunnus albacares). A total of 41,378 reads were generated by Illumina platform with an average depth of 250. The mitogenome (16,528 bp in length) contained 37 mitochondrial genes with the similar gene order to other typical teleosts. These mitochondrial genes were encoded on the heavy strand except for ND6 and eight tRNA genes. The result of phylogenetic analysis supported two distinct clades dividing the genus Thunnus, but the tuna species of these two genetic clades were different from that of two recognized subgenus based on anatomical characters and geographical distribution. Our results might help to understand the structure, function, and evolutionary history of the yellowfin tuna mitogenome and also provide valuable new insights for phylogenetic affinity of tuna species.
Mitochondrial genome, phylogeny, thunnus albacares
Yellowfin tuna, Thunnus albacares, is a highly migratory species and widely distributed in tropical and subtropical seas. As one of the most important fishery species around the world, T. albacares is considered fully to be overexploited and has been listed as Near Threatened (IUCN, 2014). An understanding of phylogenetic relationship and historical evolutionary process is essential for effective conservation and management of the fishery resources. Traditionally, eight tuna species of the genus Thunnus are classified into two subgenera: Thunnus (T. alalunga, T. maccoyii, T. obesus, T. orientalis and T. thynnus) and Neothunnus (T. albacares, T. tonggol and T. atlanticus) based on anatomical characters and geographical distribution (Collette, 1978). Recently, the next-generation sequencing (NGS) technology has become a powerful tool for sequencing the teleost mitochondrial genome (mitogenome) (Cui et al., 2009; Xie et al., 2014), while mitochondrial DNA sequences are commonly used in phylogenetic and population structure studies. In this study, we used the NGS technology to determine the mitogenome of T. albacares, and then preformed a phylogenetic analysis to reveal true relationships within the genus Thunnus. The specimen of T. albacares was caught from the South China Sea near the Subi Reef and muscular tissue was preserved
Correspondence: Zining Meng, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. E-mail: [email protected]
History Received 8 October 2014 Revised 27 October 2014 Accepted 27 October 2014 Published online 24 November 2014
in 95% alcohol for DNA extraction. Through guided assemble, Illumina next-generation sequencing platform generated 41,378 reads for the mitogenome of T. albacares with an average depth of 250. The entire sequence of mitogenome is 16,528 bp (GenBank Accession No. KM588080; Figure 1) containing one control region (D-loop) and 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes) with the similar gene order to other typical teleosts. All the proteinscoding genes use typical ATG as the start codon except for COX I, whose start code is GTG. Accordingly, TAA, TA and T are used as the stop codon by protein-coding genes except for ND6, whose terminal code is TAG. The two rRNA genes are located between tRNA-Phe and tRNA-Leu, separated by tRNA-Val. The tRNA genes, ranging from 68 to 74 bp in length, have the potential to fold into the typical clover-leaf secondary structures, except that tRNA-Ser2 loses the dihydrouridine arm and forms one loop. ND6 and other 8 tRNA (for Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) are coded by the L-strand. The control region (865 bp) are located between tRNA-Pro gene and tRNA-Phe gene. We used the mitogenome sequence of T. albacares obtained in this study, together with the sequence data of other tuna species retrieved from NCBI database (missing data for T. atlanticus), to perform a neighbor-joining phylogenic analysis in the MEGA6.06 program with Katsuwonus pelamis as outgroup. The result suggests two distinct clades divide the genus Thunnus. The first clade comprises T. albacares, T. tonggol, T. obesus, T. maccoyii and T. thynnus, and the second includes T. orientalis and T. alalunga. Obviously, these tuna species of two genetic clades are different from that of two recognized subgenus mentioned above.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/26/15 For personal use only.
2
L. Guo et al.
Mitochondrial DNA, Early Online: 1–2
Figure1. Genes map of yellowfin tuna (Thunnus albacares) mitochondrial genome (accession number KM588080). Genes shown at the outer circle are encoded by the H-strand and those at the inner circle are encoded by the L-strand. ND1-6 indicate genes of the NADH dehydrogenase subunits 1–6; COXI-III, cytochrome c oxidase subunits I–III; ATP6 and ATP8, ATPase subunits 6 and 8; Cytb, cytochrome b. The inner ring indicates the GC content with the window size 4 nucleotides.
Declaration of interest This work was supported by the National High Technology R & D Program 863 of China (2012AA10A414) and the National Natural Science Foundation of China (grant 31370047 & 31001112). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Collette B. (1978). Adaptations and systematics of the mackerels and tunas. In: Sharp GD, Dizon AE, editors. The physiological ecology of tunas New York: Academic Press. p 7–39.
Cui Z, Liu Y, Li CP, You F, Chu H. (2009). The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae. Gene 432: 33–43. IUCN. (2014).The IUCN Red List of Threatened Species. Cambridge, UK, Version 2014.2. Available at: www.iucnredlist.org (Accessed 15 September 2014). Xie Z, Yu C, Guo L, Li M, Zhang Y, Liu X, Meng Z, Lin H. (2014). Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of black and reddish morphs of the Coral Trout Plectropomus leopardus. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.908369.
