http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.905845
MITOGENOME ANNOUNCEMENT
Description and phylogenetic analysis of the mitochondrial genome of Pseudobagrus ondon Shaw (Siluriformes; Bagridae) Shoubao Yang, Chong Chen, Heng Wang, Liping He, Min Wei, and Chen Li
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 10/14/14 For personal use only.
College of life Sciences, Shaoxing University, Shaoxing, P.R. China
Abstract
Keywords
Pseudobagrus ondon is a small benthopelagic freshwater species of family Bagridae. In the present study, the complete mitochondrial genome of P. Ondon has been determined, and phylogenetic analysis with another individual and closely related species are preformed. The complete mitochondrial genome of P. ondon was 16,534 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: a control region (D-loop) and an L-strand replication origin (OL). It indicated that D-loop, ND1, ND2, ND4, ND5 and CYTB may be appropriate markers for studying population as well as conservation genetics.
Genetics, mitochondrial genome, Pseudobagrus ondon, sequencing
Pseudobagrus ondon is a benthopelagic freshwater species of family Bagridae (Fishbase, 2014). It is widely distributed in various water systems including Yellow River, Hanjiang River and Oujiang River in China, and is a species with high economic as well as nutritional value. Sequencing and determination of the complete mitochondrial genome shows the necessity of its phylogenetic relationships with the closely related species for its sustainable utilization. The primers for PCR amplification were designed based on the complete mitochondrial genome of P. ondon (GenBank accession no: KF514424, designated SU-PO2013) (Wang et al., 2013), a different individual of the
History Received 5 March 2014 Accepted 15 March 2014 Published online 4 April 2014
same species. All data were analyzed by DNASTAR 7.1 software (Madison, WI). The complete mitochondrial genome of P. ondon (designated SU-PO2014) was 16,534 bp in length, deposited in GenBank database with an accession number KJ530689. Its overall nucleotide base composition was 15.25% G, 31.06% A, 25.77% T and 27.92% C. The overall AT content was 56.83%, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: a control region (D-loop) and an L-strand replication origin (OL) (Table 1). Among these mitochondrial genes, eight tRNA genes (tRNAAsn, tRNAGln, tRNAAla, tRNACys,
Table 1. Organization of the mitochondrial genome of P. ondon. Position Gene
From Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1
1 71 1025 1097 2775 2850 3830 3901 3971 4041 5086 5159 5229 5302 5335 5402 5474
Size To 70 1024 1096 2774 2849 3824 3901 3971 4040 5085 5156 5227 5301 5334 5401 5472 7024
Nucleotide (bp) 70 954 72 1678 75 975 72 71 70 1045 71 69 73 33 67 71 1551
Codon AA
Start
Stop
Anti codon GAA TAC TAA
324
ATG
TAG GAT TTG CAT
348
ATG
T- TCA TGC GTT GCA GTA
516
GTG
TAA
Intergenic nucleotides 0 0 0 0 0 5 1 1 0 0 2 1 0 0 0 1 0
Strand H H H H H H H L H H H L L L L H (continued )
Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, P.R. China. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
S. Yang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 10/14/14 For personal use only.
Ser(UCN)
tRNA tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control region
Size
From
To
Nucleotide (bp)
7025 7100 7187 7878 7953 8111 8794 9578 9651 10,000 10,071 10,361 11,742 11,812 11,882 11,955 13,778 14,294 14,365 15,503 15,574 15,644
7095 7172 7877 7951 8120 8794 9577 9650 9999 10,070 10,367 11,741 11,811 11,878 11,954 13,781 14,293 14,362 15,502 15,575 15,643 16,534
71 73 691 74 168 684 784 73 349 71 297 1381 70 67 73 1827 516 69 1138 73 70 891
Codon AA
Start
Stop
Anti codon TGA GTC
230
ATG
T- -
55 227 261
ATG ATG ATG
TAA TAA T- -
116
ATG
T- -
98 460
ATG ATG
TAA T- -
TTT
TCC TCG GTG GCT TAG 608 171
ATG ATG
TAA TAA
379
ATG
T- -
TTC
tRNATyr, tRNASer(UCN), tRNAPro and tRNAGlu) and a proteincoding gene (ND6) were encoded on the L-strand, while other genes were encoded on the H-strand. All genes showed typical gene arrangement conforming to the vertebrate consensus (Jondeung & Karinthanyakit, 2010). After the pairwise analysis, 105 variable sites (103 base substitutions and 2 indels) were determined between P. ondon (SU-PO2013) and P. ondon (SU-PO2014), accounted for 0.64% of the complete mitogenome sites, these base substitutions were distributed in most of the protein-coding genes (except for ATP8 and ND3), four tRNA genes (tRNAVal, tRNAGln, tRNASer(UCN) and tRNAGly) and a non-coding region (D-loop). Among them, five protein-coding genes (ND1, ND2, ND4, ND5 and CYTB) had relatively higher variable sites with 15, 9, 8, 14 and 13, respectively. Furthermore, two indels were only detected in the D-loop which had 14 variable sites, indicating D-Loop is the fastest variable region in mitogenome (Wan et al., 2014). All data reveal that protein-coding genes (ND1, ND2, ND4, ND5 and CYTB) and control region may be appropriate markers for studying population as well as conservation genetics. Phylogenetic tree of genus Pseudobagrus was constructed based on the complete mitochondrial genome sequences of P. ondon (SU-PO2013 and SU-PO2014), Pseudobagrus ussuriensis (KC188782), Pseudobagrus albomarginatus (KF514425), Pseudobagrus truncates (JX867259), Pseudobagrus trilineatus (KF356196), Pseudobagrus tokiensis (AB054127), Pseudobagrus brevicorpus (HM355585) and Pseudobagrus brevicaudatus (JX867256) using the neighbor-joining method (figure not
TGT TGG
Intergenic nucleotides 4 14 0 1 10 1 0 0 0 0 7 0 0 3 0 4 0 2 0 2 0
Strand L H H H H H H H H H H H H H H H L L H H L H
shown and is available on request). It shows that P. ondon, P. ussuriensis, P. truncates, P. tokiensis and P. trilineatus are more closely related species, which formed a monophyletic group with high bootstrap support value while P. brevicaudatus, P. albomarginatus and P. brevicorpus formed the other monophyletic group.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang province (2011C22084).
References Fishbase. (2014). Pseudobagrus ondon. [Online] Available at: http:// www.fishbase.org (Accessed 3 March 2014). Jondeung A, Karinthanyakit W. (2010). The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47. Wan Q, Qiao HY, Cheng QQ, Chen Y. (2014). Complete mitochondrial genome of Pelteobagrus fulvidraco (Siluriformes: Bagridae): Genome description and related phylogenetic analyses. Mitochondrial DNA 25: 39–41. Wang H, Li C, Yang XX, Yang SB, Han JW, He LP, Wei M, et al. (2013). Complete mitochondrial genome of Pseudobagrus ondon Shaw. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.834437.
MITOGENOME ANNOUNCEMENT
Description and phylogenetic analysis of the mitochondrial genome of Pseudobagrus ondon Shaw (Siluriformes; Bagridae) Shoubao Yang, Chong Chen, Heng Wang, Liping He, Min Wei, and Chen Li
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 10/14/14 For personal use only.
College of life Sciences, Shaoxing University, Shaoxing, P.R. China
Abstract
Keywords
Pseudobagrus ondon is a small benthopelagic freshwater species of family Bagridae. In the present study, the complete mitochondrial genome of P. Ondon has been determined, and phylogenetic analysis with another individual and closely related species are preformed. The complete mitochondrial genome of P. ondon was 16,534 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: a control region (D-loop) and an L-strand replication origin (OL). It indicated that D-loop, ND1, ND2, ND4, ND5 and CYTB may be appropriate markers for studying population as well as conservation genetics.
Genetics, mitochondrial genome, Pseudobagrus ondon, sequencing
Pseudobagrus ondon is a benthopelagic freshwater species of family Bagridae (Fishbase, 2014). It is widely distributed in various water systems including Yellow River, Hanjiang River and Oujiang River in China, and is a species with high economic as well as nutritional value. Sequencing and determination of the complete mitochondrial genome shows the necessity of its phylogenetic relationships with the closely related species for its sustainable utilization. The primers for PCR amplification were designed based on the complete mitochondrial genome of P. ondon (GenBank accession no: KF514424, designated SU-PO2013) (Wang et al., 2013), a different individual of the
History Received 5 March 2014 Accepted 15 March 2014 Published online 4 April 2014
same species. All data were analyzed by DNASTAR 7.1 software (Madison, WI). The complete mitochondrial genome of P. ondon (designated SU-PO2014) was 16,534 bp in length, deposited in GenBank database with an accession number KJ530689. Its overall nucleotide base composition was 15.25% G, 31.06% A, 25.77% T and 27.92% C. The overall AT content was 56.83%, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: a control region (D-loop) and an L-strand replication origin (OL) (Table 1). Among these mitochondrial genes, eight tRNA genes (tRNAAsn, tRNAGln, tRNAAla, tRNACys,
Table 1. Organization of the mitochondrial genome of P. ondon. Position Gene
From Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1
1 71 1025 1097 2775 2850 3830 3901 3971 4041 5086 5159 5229 5302 5335 5402 5474
Size To 70 1024 1096 2774 2849 3824 3901 3971 4040 5085 5156 5227 5301 5334 5401 5472 7024
Nucleotide (bp) 70 954 72 1678 75 975 72 71 70 1045 71 69 73 33 67 71 1551
Codon AA
Start
Stop
Anti codon GAA TAC TAA
324
ATG
TAG GAT TTG CAT
348
ATG
T- TCA TGC GTT GCA GTA
516
GTG
TAA
Intergenic nucleotides 0 0 0 0 0 5 1 1 0 0 2 1 0 0 0 1 0
Strand H H H H H H H L H H H L L L L H (continued )
Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, P.R. China. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
S. Yang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 10/14/14 For personal use only.
Ser(UCN)
tRNA tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro Control region
Size
From
To
Nucleotide (bp)
7025 7100 7187 7878 7953 8111 8794 9578 9651 10,000 10,071 10,361 11,742 11,812 11,882 11,955 13,778 14,294 14,365 15,503 15,574 15,644
7095 7172 7877 7951 8120 8794 9577 9650 9999 10,070 10,367 11,741 11,811 11,878 11,954 13,781 14,293 14,362 15,502 15,575 15,643 16,534
71 73 691 74 168 684 784 73 349 71 297 1381 70 67 73 1827 516 69 1138 73 70 891
Codon AA
Start
Stop
Anti codon TGA GTC
230
ATG
T- -
55 227 261
ATG ATG ATG
TAA TAA T- -
116
ATG
T- -
98 460
ATG ATG
TAA T- -
TTT
TCC TCG GTG GCT TAG 608 171
ATG ATG
TAA TAA
379
ATG
T- -
TTC
tRNATyr, tRNASer(UCN), tRNAPro and tRNAGlu) and a proteincoding gene (ND6) were encoded on the L-strand, while other genes were encoded on the H-strand. All genes showed typical gene arrangement conforming to the vertebrate consensus (Jondeung & Karinthanyakit, 2010). After the pairwise analysis, 105 variable sites (103 base substitutions and 2 indels) were determined between P. ondon (SU-PO2013) and P. ondon (SU-PO2014), accounted for 0.64% of the complete mitogenome sites, these base substitutions were distributed in most of the protein-coding genes (except for ATP8 and ND3), four tRNA genes (tRNAVal, tRNAGln, tRNASer(UCN) and tRNAGly) and a non-coding region (D-loop). Among them, five protein-coding genes (ND1, ND2, ND4, ND5 and CYTB) had relatively higher variable sites with 15, 9, 8, 14 and 13, respectively. Furthermore, two indels were only detected in the D-loop which had 14 variable sites, indicating D-Loop is the fastest variable region in mitogenome (Wan et al., 2014). All data reveal that protein-coding genes (ND1, ND2, ND4, ND5 and CYTB) and control region may be appropriate markers for studying population as well as conservation genetics. Phylogenetic tree of genus Pseudobagrus was constructed based on the complete mitochondrial genome sequences of P. ondon (SU-PO2013 and SU-PO2014), Pseudobagrus ussuriensis (KC188782), Pseudobagrus albomarginatus (KF514425), Pseudobagrus truncates (JX867259), Pseudobagrus trilineatus (KF356196), Pseudobagrus tokiensis (AB054127), Pseudobagrus brevicorpus (HM355585) and Pseudobagrus brevicaudatus (JX867256) using the neighbor-joining method (figure not
TGT TGG
Intergenic nucleotides 4 14 0 1 10 1 0 0 0 0 7 0 0 3 0 4 0 2 0 2 0
Strand L H H H H H H H H H H H H H H H L L H H L H
shown and is available on request). It shows that P. ondon, P. ussuriensis, P. truncates, P. tokiensis and P. trilineatus are more closely related species, which formed a monophyletic group with high bootstrap support value while P. brevicaudatus, P. albomarginatus and P. brevicorpus formed the other monophyletic group.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang province (2011C22084).
References Fishbase. (2014). Pseudobagrus ondon. [Online] Available at: http:// www.fishbase.org (Accessed 3 March 2014). Jondeung A, Karinthanyakit W. (2010). The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47. Wan Q, Qiao HY, Cheng QQ, Chen Y. (2014). Complete mitochondrial genome of Pelteobagrus fulvidraco (Siluriformes: Bagridae): Genome description and related phylogenetic analyses. Mitochondrial DNA 25: 39–41. Wang H, Li C, Yang XX, Yang SB, Han JW, He LP, Wei M, et al. (2013). Complete mitochondrial genome of Pseudobagrus ondon Shaw. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.834437.
