http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1028039
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Astatotilapia burtoni Xiao-Xiao Hu1,2, Jiang Lu1,3, Shi-Yang He1,3, Xiang-Feng Li1,2, Hong-Jie Liu1,2, and Li-Juan Han2 1
College of Life Science, University of Chinese Academy of Sciences, Beijing, China, 2BGI-tech, BGI-Shenzhen, Shenzhen, China, and BGI-Shenzhen, Shenzhen, China
Mitochondrial DNA Downloaded from informahealthcare.com by Fudan University on 05/13/15 For personal use only.
3
Abstract
Keywords
Astatotilapia burtoni is a species of fish in the Cichlidae family. Astatotilapia burtoni has been used as a model organism to research the behaviors and physical systems of cichlids. Here, we reported the complete mitogenome sequence of A. burtoni, which was 16,583 bp and composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region, with a base composition of lower G + C content (45.5%). Similar to Astatotilapia calliptera, all genes were located on H-strand except for eight tRNAs and ND6 genes. Most protein-coding genes started with an ATG codon except for COX1, ATP6 and ND3, which initiated with GTG or ATC instead, and terminated with the typical stop condon (TAA/TAG)or a single T. In this article, 12 protein-coding genes of other 10 closely species were used to construct the species phylogenetic tree to convince the mitogenome sequences. These results provided basic information for researching A. burtoni on genetics, phylogeny and adaptive evolution.
Astatotilapia burtoni, cichlid, mitogenome
Astatotilapia burtoni is a species of fish in the Cichlidae family. It is found in Rwanda, Tanzania, and Zambia (around Lake TanganyikaBurundi) (Brawand et al., 2014). It is a riverine species and its natural habitats are freshwater rivers, lakes, marshes and inland deltas. Astatotilapia burtoni has been used as a model organism to study the behaviors (Maruska et al., 2012) and physical systems (Parikh et al., 2006) of cichlids, including their development and embryogenesis. In addition, the phylogenetic position of this particular species makes it a perfect model system for comparative genomic research (Salzburger et al., 2008). Astatotilapia burtoni belongs under the haplochromines, which is the lineage of cichlids with the largest species. However, only the mitochondrial genome sequence of A. calliptera is available online (NC_018560.1). So, it is meaningful to research this species. We expected this study would contribute to the research of Astatotilapia. Tissue samples were isolated from a single female individual inbred for 60 generations in the
Correspondence: Li-Juan Han, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China. Tel: +86-13480602752. E-mail: [email protected]
History Received 4 February 2015 Revised 2 March 2015 Accepted 8 March 2015 Published online 12 May 2015
laboratory of Dr. Hans Hoffman (University of Texas at Austin, Austin, TX), and the DNA was extracted from 11 tissues (blood, brain, eye, embryo, heart, kidney, liver, muscle, ovary, skin and testis) and sequenced by Illumina Hiseq 2000 (Brawand et al., 2014). Its raw data can be downloaded from SRA database (SRX ID: SRX033044, SRX033029). We used the SPAdes-3.0.0 (Bankevich et al., 2012) to firstly completed mitochondrial genome sequence of A. burtoni (GenBank accession no. KP641358). The complete mitochondrial genome sequence of A. burtoni (16,583 bp) is consisted of 13 protein-coding genes, 2 rRNA genes , 22 tRNA genes and 1 putative control region. The order of all genes was identical to other vertebrate species. The overall base composition was C (30.1%)4A (27.8%)4T (26.7%)4G (15.4%), with an AT bias of 54.5%. To further validate the new sequences, we used 10 mitochondrial genome sequences of other closely cichlid species to construct the phylogenetic tree. Ten cichlid species were as follows. Astatotilapia burtoni and Astatotilapia calliptera come from Astatotilapia of cichlidae. And Oreochromis niloticus, Oreochromis variabilis and Oreochromis esculentus were from Oreochromis. The other species come from other different genus of cichlidae. Here we used RAxML program (Stamatakis et al., 2005) to produce the phylogenetic tree (Figure 1). The new phylogentic analysis results were consistent with the fact that the mitochondrial DNAs of same genus were more closely related to each other, such as Astatotilapia and Oreochromis. It was easily concluded that mitogenome sequences of A. burtoni could meet the demands.
2
X.-X. Hu et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Fudan University on 05/13/15 For personal use only.
Figure 1. (Drawing statement) The phylogenetic tree of A. burtoni and other 10 closely species which have reported mitogenome sequences. The phylogenetic tree inferred by RAxML. Red branches highlighted the study species. Accession numbers of analyzed species are as follows: A. burtoni, KP641358; A. calliptera, NC_018560.1; N. brichardi, NC_009062.1; O. niloticus, NC_013663.1; O. esculentus, NC_025555.1; O. variabilis, NC_026109.1; A. rivulatus, NC_025671.1; A. citrinellus, KJ562277.1; A. ocellatus, NC_009058.1; P. maculatus, NC_011177.1; P. polleni, NC_011170.1.
Acknowledgements We would like to thank Salzburger et al. for generating the sequencing data of A. burtoni used in this work and the anonymous reviewers for proving valuable comments on the manuscript.
Declaration of interest The authors have declared that no conflict of interest exists. The authors alone are responsible for the content and writing of the paper.
References Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–77.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, et al. (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature 513:375–81. Maruska KP, Ung US, Fernald RD. (2012). The African cichlid fish Astatotilapia burtoni uses acoustic communication for reproduction: Sound production, hearing, and behavioral significance. PLoS One 7: e37612. Parikh VN, Clement T, Fernald RD. (2006). Physiological consequences of social descent: Studies in Astatotilapia burtoni. J Endocrinol 190: 183–90. Salzburger W, Renn SC, Steinke D, Braasch I, Hofmann HA, Meyer A. (2008). Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genom 9:96. Stamatakis A, Ludwig T, Meier H. (2005). RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456–63.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Astatotilapia burtoni Xiao-Xiao Hu1,2, Jiang Lu1,3, Shi-Yang He1,3, Xiang-Feng Li1,2, Hong-Jie Liu1,2, and Li-Juan Han2 1
College of Life Science, University of Chinese Academy of Sciences, Beijing, China, 2BGI-tech, BGI-Shenzhen, Shenzhen, China, and BGI-Shenzhen, Shenzhen, China
Mitochondrial DNA Downloaded from informahealthcare.com by Fudan University on 05/13/15 For personal use only.
3
Abstract
Keywords
Astatotilapia burtoni is a species of fish in the Cichlidae family. Astatotilapia burtoni has been used as a model organism to research the behaviors and physical systems of cichlids. Here, we reported the complete mitogenome sequence of A. burtoni, which was 16,583 bp and composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region, with a base composition of lower G + C content (45.5%). Similar to Astatotilapia calliptera, all genes were located on H-strand except for eight tRNAs and ND6 genes. Most protein-coding genes started with an ATG codon except for COX1, ATP6 and ND3, which initiated with GTG or ATC instead, and terminated with the typical stop condon (TAA/TAG)or a single T. In this article, 12 protein-coding genes of other 10 closely species were used to construct the species phylogenetic tree to convince the mitogenome sequences. These results provided basic information for researching A. burtoni on genetics, phylogeny and adaptive evolution.
Astatotilapia burtoni, cichlid, mitogenome
Astatotilapia burtoni is a species of fish in the Cichlidae family. It is found in Rwanda, Tanzania, and Zambia (around Lake TanganyikaBurundi) (Brawand et al., 2014). It is a riverine species and its natural habitats are freshwater rivers, lakes, marshes and inland deltas. Astatotilapia burtoni has been used as a model organism to study the behaviors (Maruska et al., 2012) and physical systems (Parikh et al., 2006) of cichlids, including their development and embryogenesis. In addition, the phylogenetic position of this particular species makes it a perfect model system for comparative genomic research (Salzburger et al., 2008). Astatotilapia burtoni belongs under the haplochromines, which is the lineage of cichlids with the largest species. However, only the mitochondrial genome sequence of A. calliptera is available online (NC_018560.1). So, it is meaningful to research this species. We expected this study would contribute to the research of Astatotilapia. Tissue samples were isolated from a single female individual inbred for 60 generations in the
Correspondence: Li-Juan Han, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China. Tel: +86-13480602752. E-mail: [email protected]
History Received 4 February 2015 Revised 2 March 2015 Accepted 8 March 2015 Published online 12 May 2015
laboratory of Dr. Hans Hoffman (University of Texas at Austin, Austin, TX), and the DNA was extracted from 11 tissues (blood, brain, eye, embryo, heart, kidney, liver, muscle, ovary, skin and testis) and sequenced by Illumina Hiseq 2000 (Brawand et al., 2014). Its raw data can be downloaded from SRA database (SRX ID: SRX033044, SRX033029). We used the SPAdes-3.0.0 (Bankevich et al., 2012) to firstly completed mitochondrial genome sequence of A. burtoni (GenBank accession no. KP641358). The complete mitochondrial genome sequence of A. burtoni (16,583 bp) is consisted of 13 protein-coding genes, 2 rRNA genes , 22 tRNA genes and 1 putative control region. The order of all genes was identical to other vertebrate species. The overall base composition was C (30.1%)4A (27.8%)4T (26.7%)4G (15.4%), with an AT bias of 54.5%. To further validate the new sequences, we used 10 mitochondrial genome sequences of other closely cichlid species to construct the phylogenetic tree. Ten cichlid species were as follows. Astatotilapia burtoni and Astatotilapia calliptera come from Astatotilapia of cichlidae. And Oreochromis niloticus, Oreochromis variabilis and Oreochromis esculentus were from Oreochromis. The other species come from other different genus of cichlidae. Here we used RAxML program (Stamatakis et al., 2005) to produce the phylogenetic tree (Figure 1). The new phylogentic analysis results were consistent with the fact that the mitochondrial DNAs of same genus were more closely related to each other, such as Astatotilapia and Oreochromis. It was easily concluded that mitogenome sequences of A. burtoni could meet the demands.
2
X.-X. Hu et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Fudan University on 05/13/15 For personal use only.
Figure 1. (Drawing statement) The phylogenetic tree of A. burtoni and other 10 closely species which have reported mitogenome sequences. The phylogenetic tree inferred by RAxML. Red branches highlighted the study species. Accession numbers of analyzed species are as follows: A. burtoni, KP641358; A. calliptera, NC_018560.1; N. brichardi, NC_009062.1; O. niloticus, NC_013663.1; O. esculentus, NC_025555.1; O. variabilis, NC_026109.1; A. rivulatus, NC_025671.1; A. citrinellus, KJ562277.1; A. ocellatus, NC_009058.1; P. maculatus, NC_011177.1; P. polleni, NC_011170.1.
Acknowledgements We would like to thank Salzburger et al. for generating the sequencing data of A. burtoni used in this work and the anonymous reviewers for proving valuable comments on the manuscript.
Declaration of interest The authors have declared that no conflict of interest exists. The authors alone are responsible for the content and writing of the paper.
References Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–77.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, et al. (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature 513:375–81. Maruska KP, Ung US, Fernald RD. (2012). The African cichlid fish Astatotilapia burtoni uses acoustic communication for reproduction: Sound production, hearing, and behavioral significance. PLoS One 7: e37612. Parikh VN, Clement T, Fernald RD. (2006). Physiological consequences of social descent: Studies in Astatotilapia burtoni. J Endocrinol 190: 183–90. Salzburger W, Renn SC, Steinke D, Braasch I, Hofmann HA, Meyer A. (2008). Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genom 9:96. Stamatakis A, Ludwig T, Meier H. (2005). RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456–63.
