http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945541
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Caridina nilotica gracilipes Gangchun Xu, Fukuan Du, Zhijuan Nie, Pao Xu, and Ruobo Gu
Mitochondrial DNA Downloaded from informahealthcare.com by Universite De Sherbrooke on 04/11/15 For personal use only.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People’s Republic of China Abstract
Keywords
In this study, we sequenced the complete mitochondrial genome of Caridina nilotica gracilipes. This mitochondrial genome, consisting of 15,550 base pairs, encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other Decapoda, with the gene synteny identical to that of typical invertebrates. Control region (D-Loop), of 673 bp in length, is located between 12S rRNA and tRNAIle. The overall base composition of the heavy strand shows T 30.4%, C 22.0%, A 33.0% and G 14.6%, with an AT bias of 63.4%.
Atyidae, Caridina nilotica gracilipes, mitochondrial genome
Caridina nilotica gracilipes (Decapoda: Atyidae) is a commercially important aquaculture species due to its ornamental value (Kenny et al., 2014). They are widely distributed in Fujian, Zhejiang, Jiangsu, Hunan and Hubei province in China. Caridina nilotica gracilipes is a small-sized, demersal, and was an endemic species to China. Previous studies of C. nilotica gracilipes gave only the characterization of morphological data, and no molecular data were reported. In this study, the complete mitochondrial genome of C. nilotica gracilipes was first determined (KM023648). The complete mitochondrial genome of Caridina nilotica gracilipes (15,550 bp in length) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR) (Table 1). The arrangement of all genes was identical to other Atyidae (Lavrov et al., 2000; Yang et al., 2008). Most of the genes were encoded on the heavy strand (H-strand), except for four protein-coding genes (NAD 1, NAD 4, NAD 4L and NAD 5), eight tRNA genes (tRNA-Phe, -His, -Thr, -Pro, -Leu, -Val, -Gln, and -Cys) and two rRNA (16S rRNA and 12S rRNA) encoded on the L-strand. The overall base composition values for the H-strand were 30.4% for T, 22.0% for C, 33.0% for A, and 14.6% for G, with a A + T bias of 63.4%. Except for COXI, NAD3, NAD5, NAD6, NAD2 start with CTG, ATA, ATT, ATT and ATT, the remaining 12 protein-coding genes started with ATG. Within stop codons of 13 protein-coding genes, three kinds of codon were found in C. nilotica gracilipes: TAA (COXI, COXII, ATPase 8, ATPase 6, COXIII, NAD3, ND4L, NAD6, NAD2); TAG (Cytb); and incomplete stop codon T (NAD5, NAD4, NAD1). This feature is common among invertebrate mitochondrial proteincoding genes, and these incomplete stop codons were presumably completed as TAA via post-transcriptional polyadenylation (Ojala et al., 1981). The two ribosomal RNA genes, 12srR NA (797 bp) Correspondence: Ruobo Gu, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, People’s Republic of China. Tel: +86-510-85390029. Fax: +86510-85390026. E-mail: [email protected]
History Received 19 June 2014 Accepted 27 June 2014 Published online 4 August 2014
and 16SrR NA (1329 bp), were located between D-loop and tRNALeu and are separated by tRNAVal gene. As in vertebrates (Chang et al., 2014; Li et al., 2014; Zhou et al., 2014), C. nilotica gracilipes has a non-coding regions within its mitogenome: a CR (673 bp) located between 12S rRNA and tRNAIle. Table 1. Characteristics of the mitochondrial genome of C. nilotica gracilipes.
Gene/Elemen
From
To
COXI tRNALeu COXII tRNALys tRNAAsp ATPase8 ATPase6 COXIII tRNAGly NAD3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe NAD5 tRNAHis NAD4 ND4L tRNAThr tRNAPro NAD6 Cyt b tRNASer NAD1 tRNALeu 16S rRNA tRNAVal 12S rRNA
1 1538 1604 2299 2382 2449 2601 3275 4061 4126 4482 4546 4609 4676 4743 4810 4880 6606 6672 8004 8309 8369 8443 8958 10,087 10,182 11,150 11,216 12,545 12,613
1536 1601 2284 2381 2448 2607 3275 4060 4128 4482 4547 4610 4675 4742 4811 4874 6587 6671 8010 8306 8374 8440 8958 10,094 10,164 11,123 11,215 12,544 12,612 13,409
Length Intergenic (bp) Start Stop nucleotides* Strand# 1536 64 681 83 67 159 675 786 67 357 66 65 67 67 69 65 1705 66 1339 303 66 72 515 1137 78 942 66 1329 68 797
CTG TAA ATG TAA ATC TAA ATG TAA ATG TAA ATA TAA
ATT
T
ATG T ATG TAA ATT TAA ATG TAG ATG
T
0 1 2 14 0 0 7 1 1 3 1 2 2 0 0 2 5 21 0 7 2 6 2 1 8 17 26 0 0 0
H H H H H H H H H H H H H H H L L L L L L L H H H L L L L L (continued )
2
G. Xu et al.
Mitochondrial DNA, Early Online: 1–2
References
Table 1. Continued
Gene/Elemen
From
To
D-Loop tRNAIle tRNAGln tRNAMet NAD2 tRNATrp tRNACys tRNATyr
13,410 14,083 14,152 14,237 14,304 15,306 15,375 15,509
14,082 14,154 14,231 14,303 15,308 15,376 15,442 15,550
Length Intergenic (bp) Start Stop nucleotides* Strand# 673 72 80 67 1005 71 67 42
ATT TAA
0 0 3 5 0 3 1 66
H H L H H H L H
Mitochondrial DNA Downloaded from informahealthcare.com by Universite De Sherbrooke on 04/11/15 For personal use only.
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. #H and L indicate genes transcribed on the heavy and light strand, respectively.
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 a grant from the National Key Technology R&D Program of China (2012BAD26B05) and Three New Projects of Agricultural Aquaculture Program of Jiangsu Province (DZ2012-1).
Chang CH, Jabado RW, Lin YS, Shao KT. (2014). The complete mitochondrial genome of the sand tiger shark, Carcharias taurus (Chondrichthyes, Odontaspididae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2013.845761. Kenny NJ, Sin YW, Shen X, Zhe Q, Wang W, Chan TF, Tobe SS, et al. (2014). Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Mar Drugs 12: 1419–37. Lavrov DV, Boore JL, Brown WM. (2000). The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Mol Biol Evol 17:813–24. Li Q, Xu R, Shu H, Chen Q, Huang J. (2014). The complete mitochondrial genome of the Zig-zag eel Mastacembelus armatus (Teleostei, Mastacembelidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892102. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ. (2008). The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): A novel arrangement and incomplete tRNA suite. BMC Genomics 9:257. Zhou C, Wang X, Guan L, He S. (2014). The complete mitochondrial genome of Clarias fuscus (Teleostei, Siluriformes: Clariidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.823177.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Caridina nilotica gracilipes Gangchun Xu, Fukuan Du, Zhijuan Nie, Pao Xu, and Ruobo Gu
Mitochondrial DNA Downloaded from informahealthcare.com by Universite De Sherbrooke on 04/11/15 For personal use only.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, People’s Republic of China Abstract
Keywords
In this study, we sequenced the complete mitochondrial genome of Caridina nilotica gracilipes. This mitochondrial genome, consisting of 15,550 base pairs, encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other Decapoda, with the gene synteny identical to that of typical invertebrates. Control region (D-Loop), of 673 bp in length, is located between 12S rRNA and tRNAIle. The overall base composition of the heavy strand shows T 30.4%, C 22.0%, A 33.0% and G 14.6%, with an AT bias of 63.4%.
Atyidae, Caridina nilotica gracilipes, mitochondrial genome
Caridina nilotica gracilipes (Decapoda: Atyidae) is a commercially important aquaculture species due to its ornamental value (Kenny et al., 2014). They are widely distributed in Fujian, Zhejiang, Jiangsu, Hunan and Hubei province in China. Caridina nilotica gracilipes is a small-sized, demersal, and was an endemic species to China. Previous studies of C. nilotica gracilipes gave only the characterization of morphological data, and no molecular data were reported. In this study, the complete mitochondrial genome of C. nilotica gracilipes was first determined (KM023648). The complete mitochondrial genome of Caridina nilotica gracilipes (15,550 bp in length) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR) (Table 1). The arrangement of all genes was identical to other Atyidae (Lavrov et al., 2000; Yang et al., 2008). Most of the genes were encoded on the heavy strand (H-strand), except for four protein-coding genes (NAD 1, NAD 4, NAD 4L and NAD 5), eight tRNA genes (tRNA-Phe, -His, -Thr, -Pro, -Leu, -Val, -Gln, and -Cys) and two rRNA (16S rRNA and 12S rRNA) encoded on the L-strand. The overall base composition values for the H-strand were 30.4% for T, 22.0% for C, 33.0% for A, and 14.6% for G, with a A + T bias of 63.4%. Except for COXI, NAD3, NAD5, NAD6, NAD2 start with CTG, ATA, ATT, ATT and ATT, the remaining 12 protein-coding genes started with ATG. Within stop codons of 13 protein-coding genes, three kinds of codon were found in C. nilotica gracilipes: TAA (COXI, COXII, ATPase 8, ATPase 6, COXIII, NAD3, ND4L, NAD6, NAD2); TAG (Cytb); and incomplete stop codon T (NAD5, NAD4, NAD1). This feature is common among invertebrate mitochondrial proteincoding genes, and these incomplete stop codons were presumably completed as TAA via post-transcriptional polyadenylation (Ojala et al., 1981). The two ribosomal RNA genes, 12srR NA (797 bp) Correspondence: Ruobo Gu, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, People’s Republic of China. Tel: +86-510-85390029. Fax: +86510-85390026. E-mail: [email protected]
History Received 19 June 2014 Accepted 27 June 2014 Published online 4 August 2014
and 16SrR NA (1329 bp), were located between D-loop and tRNALeu and are separated by tRNAVal gene. As in vertebrates (Chang et al., 2014; Li et al., 2014; Zhou et al., 2014), C. nilotica gracilipes has a non-coding regions within its mitogenome: a CR (673 bp) located between 12S rRNA and tRNAIle. Table 1. Characteristics of the mitochondrial genome of C. nilotica gracilipes.
Gene/Elemen
From
To
COXI tRNALeu COXII tRNALys tRNAAsp ATPase8 ATPase6 COXIII tRNAGly NAD3 tRNAAla tRNAArg tRNAAsn tRNASer tRNAGlu tRNAPhe NAD5 tRNAHis NAD4 ND4L tRNAThr tRNAPro NAD6 Cyt b tRNASer NAD1 tRNALeu 16S rRNA tRNAVal 12S rRNA
1 1538 1604 2299 2382 2449 2601 3275 4061 4126 4482 4546 4609 4676 4743 4810 4880 6606 6672 8004 8309 8369 8443 8958 10,087 10,182 11,150 11,216 12,545 12,613
1536 1601 2284 2381 2448 2607 3275 4060 4128 4482 4547 4610 4675 4742 4811 4874 6587 6671 8010 8306 8374 8440 8958 10,094 10,164 11,123 11,215 12,544 12,612 13,409
Length Intergenic (bp) Start Stop nucleotides* Strand# 1536 64 681 83 67 159 675 786 67 357 66 65 67 67 69 65 1705 66 1339 303 66 72 515 1137 78 942 66 1329 68 797
CTG TAA ATG TAA ATC TAA ATG TAA ATG TAA ATA TAA
ATT
T
ATG T ATG TAA ATT TAA ATG TAG ATG
T
0 1 2 14 0 0 7 1 1 3 1 2 2 0 0 2 5 21 0 7 2 6 2 1 8 17 26 0 0 0
H H H H H H H H H H H H H H H L L L L L L L H H H L L L L L (continued )
2
G. Xu et al.
Mitochondrial DNA, Early Online: 1–2
References
Table 1. Continued
Gene/Elemen
From
To
D-Loop tRNAIle tRNAGln tRNAMet NAD2 tRNATrp tRNACys tRNATyr
13,410 14,083 14,152 14,237 14,304 15,306 15,375 15,509
14,082 14,154 14,231 14,303 15,308 15,376 15,442 15,550
Length Intergenic (bp) Start Stop nucleotides* Strand# 673 72 80 67 1005 71 67 42
ATT TAA
0 0 3 5 0 3 1 66
H H L H H H L H
Mitochondrial DNA Downloaded from informahealthcare.com by Universite De Sherbrooke on 04/11/15 For personal use only.
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. #H and L indicate genes transcribed on the heavy and light strand, respectively.
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 a grant from the National Key Technology R&D Program of China (2012BAD26B05) and Three New Projects of Agricultural Aquaculture Program of Jiangsu Province (DZ2012-1).
Chang CH, Jabado RW, Lin YS, Shao KT. (2014). The complete mitochondrial genome of the sand tiger shark, Carcharias taurus (Chondrichthyes, Odontaspididae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2013.845761. Kenny NJ, Sin YW, Shen X, Zhe Q, Wang W, Chan TF, Tobe SS, et al. (2014). Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Mar Drugs 12: 1419–37. Lavrov DV, Boore JL, Brown WM. (2000). The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Mol Biol Evol 17:813–24. Li Q, Xu R, Shu H, Chen Q, Huang J. (2014). The complete mitochondrial genome of the Zig-zag eel Mastacembelus armatus (Teleostei, Mastacembelidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736.2014.892102. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ. (2008). The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): A novel arrangement and incomplete tRNA suite. BMC Genomics 9:257. Zhou C, Wang X, Guan L, He S. (2014). The complete mitochondrial genome of Clarias fuscus (Teleostei, Siluriformes: Clariidae). Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.823177.
