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
The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. MilneEdwards, 1853 (Crustacea: Decapoda: Grapsoidea) Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin To cite this article: Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin (2014): The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. MilneEdwards, 1853 (Crustacea: Decapoda: Grapsoidea), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.989514
Published online: 26 Dec 2014.
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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: 06 November 2015, At: 00:27
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.989514
MITOGENOME ANNOUNCEMENT
The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Downloaded by [University of California, San Diego] at 00:27 06 November 2015
1
Abstract
Keywords
The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
Mitogenome, shore crab, Varunidae
Crabs placed in the superfamily Grapsoidea are common inhabitants of shoreline environments and include several adaptable species that exploit terrestrial, semi-terrestrial or freshwater environments. Grapsids are thought to play important ecological roles in the recycling of organic matter in shoreline communities (Lee, 1998). The Grapsoidea is one of the largest superfamilies within the Brachyura and is divided into seven families (De Grave et al., 2009). Cyclograpsus is a genus of varunid crabs (family Varunidae) containing approximately 20 species that are common in and above the intertidal zone, especially on rocky or sandy shores where they shelter under rocks and boulders. Species of Cyclograpsus occur in both temperate and tropical latitudes and show adaptations to a semi-terrestrial lifestyle (Little, 1990). Despite their common occurrence and interest to ecophysiologists, only five mitogenomes have been reported for the Grapsoidea and three of these are from the same genus (Eriocheir). Cyclograpsus granulosus is a conspicuous crab species occurring on rocky shorelines in southeastern Australia (Griffin, 1971). To provide additional molecular resources for the study of the taxonomy and phylogeny of grapsid crabs, the mitogenome for C. granulosus is presented as the first Southern Hemisphere species of grapsid crab to have its mitochondrial genome completely sequenced. The C. granulosus sample was caught from under rocks near Anglesea, Victoria, Australia. The purification of genomic DNA
History Received 16 November 2014 Accepted 16 November 2014 Published online 26 December 2014
from ethanol-preserved leg muscle tissue and partial whole genome sequencing (2 150 bp paired-end run) were performed as previously described (Gan et al., 2014). The complete mitogenome was recovered as the longest contig from IDBAUD de novo assembly (Peng et al., 2012). The contig was subsequently recircularized and annotated as done in Gan et al. (2014). The C. granulosus mitochondrial genome is 16,300 bp in length (GenBank accession number: LN624373) and has 37 mitochondrial genes (13 protein-coding genes, two rRNAs and 22 tRNAs) and a non-coding region of 696 bp (Table 1). The base composition is 33% A, 36% T, 11% G and 20% C and the order of the genes is identical to Eriocheir species also from the family Varunidae (Wang et al., 2014), which differ from the typical brachyuran mitogene order. Our sample of C. granulosus shows a 99% similarity to a 1181 bp fragment of the 16S ribosomal RNA gene for the New Zealand species Cyclograpsus lavauxi (GenBank accession number: AB440191) suggesting these two species may be conspecific. It will be of interest to study further the mitogene order within the Grapsoidea as each family so far studied displays a different gene order. Xenograpsus testudinatus, a hydrothermal vent crab (Xenograpsidae), has a distinct gene order (Ki et al., 2009), whereas Pachygrapsus crassipes (Grapsidae) shares the common brachyuran gene order, which is similar to the primitive pancrustacean arrangement (Yu et al., 2014).
Correspondence: Han Ming Gan, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
M. H. Tan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of the complete mitochondrial genome of C. granulosus.
Downloaded by [University of California, San Diego] at 00:27 06 November 2015
Gene cox1 trnL2(taa) cox2 atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnT(tgt) trnP(tgg) nad1 trnL1(tag) rrnL rrnS trnH(gtg) nad5 trnV(tac) Control region trnQ(ttg) trnC(gca) trnY(gta) trnK(ttt) trnD(gtc) trnE(ttc) trnF(gaa) nad4 nad4l nad6 cob trnS2(tga) trnI(gat) trnM(cat) nad2 trnW(tca)
Strand
Position
Length (bp)
Intergenic nucleotides
H H H H H H H H H H H H H L L L L L L L L – L L L H H H L L L H H H H H H H
1–1539 1535–1598 1606–2308 2370–2531 2525–3199 3199–3990 3990–4052 4053–4403 4405–4467 4470–4533 4533–4597 4600–4667 4750–4815 4816–4883 4919–5851 5886–5952 5901–7271 7326–8152 8228–8294 8331–10,061 10,181–10,254 10,255–10,950 10,951–11,019 11,038–11,100 11,102–11,166 11,196–11,264 11,263–11,328 11,352–11,420 11,431–11,494 11,523–12,860 12,854–13,156 13,253–13,765 13,765–14,899 14,900–14,967 15,046–15,113 15,134–15,205 15,206–16,216 16,215–16,283
1539 64 703 162 675 792 63 351 63 64 65 68 66 68 933 67 1371 827 67 1731 74 696 69 63 65 69 66 69 64 1338 303 513 1135 68 68 72 1011 69
17 5 7 61 7 1 1 0 1 2 1 2 82 0 35 34 52 54 75 36 119 0 0 18 1 29 2 23 10 28 7 96 1 0 78 20 0 2
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References De Grave S, Pentcheff ND, Ahyong ST, Chan TY, Crandall KA, Dworschak PC, Felder DL, et al. (2009). A classification of living and fossil genera of Decapod Crustaceans. Raffles Bull Zool 21:1–109. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Griffin DJG. (1971). The ecological distribution of grapsid and ocypodid shore crabs (Crustacea: Brachyura) in Tasmania. J Animal Ecol 40: 597–621.
Start codon
Stop codon
ATG
TAA
ATG ATG ATT ATG
T TAA TAA TAA
ATC
TAA
Anticodon UAA
UCC UGC UCG GUU UCU UGU UGG ATG
TAA UAG GUG
ATG
TAA UAC UUG GCA GUA UUU GUC UUC GAA
ATG ATG ATT ATG
TAA TAA TAA T UGA GAU CAU
ATC
TAG UCA
Ki J-S, Dahms H-U, Hwang J-S, Lee J-S. (2009). The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs. Comparative Biochem Physiol Part D 4:290–9. Lee SY. (1998). Ecological role of grapsid crabs in mangrove ecosystems: A review. Marine Freshwater Res 49:335–43. Little C. (1990). The terrestrial invasion: An ecophysiological approach to the origins of land animals. Cambridge University Press, Cambridge. Peng Y, Leung HCM, Yiu SM, Chin FYL. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–8. Wang J, Huang L, Cheng Q, Lu G, Wang C. (2014). Complete mitochondrial genomes of three mitten crabs, Eriocheir sinensis, E. hepuensis, and E. japonica. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.936425. Yu Y-Q, Ma W-M, Yang W-J, Yang J-S. (2014). The complete mitogenome of the lined shore crab Pachygrapsus crassipes Randall 1840 (Crustacea: Decapoda: Grapsidae). Mitochondrial DNA 25: 263–4.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. MilneEdwards, 1853 (Crustacea: Decapoda: Grapsoidea) Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin To cite this article: Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin (2014): The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. MilneEdwards, 1853 (Crustacea: Decapoda: Grapsoidea), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.989514
Published online: 26 Dec 2014.
Submit your article to this journal
Article views: 11
View related articles
View Crossmark data
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: 06 November 2015, At: 00:27
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.989514
MITOGENOME ANNOUNCEMENT
The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Downloaded by [University of California, San Diego] at 00:27 06 November 2015
1
Abstract
Keywords
The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
Mitogenome, shore crab, Varunidae
Crabs placed in the superfamily Grapsoidea are common inhabitants of shoreline environments and include several adaptable species that exploit terrestrial, semi-terrestrial or freshwater environments. Grapsids are thought to play important ecological roles in the recycling of organic matter in shoreline communities (Lee, 1998). The Grapsoidea is one of the largest superfamilies within the Brachyura and is divided into seven families (De Grave et al., 2009). Cyclograpsus is a genus of varunid crabs (family Varunidae) containing approximately 20 species that are common in and above the intertidal zone, especially on rocky or sandy shores where they shelter under rocks and boulders. Species of Cyclograpsus occur in both temperate and tropical latitudes and show adaptations to a semi-terrestrial lifestyle (Little, 1990). Despite their common occurrence and interest to ecophysiologists, only five mitogenomes have been reported for the Grapsoidea and three of these are from the same genus (Eriocheir). Cyclograpsus granulosus is a conspicuous crab species occurring on rocky shorelines in southeastern Australia (Griffin, 1971). To provide additional molecular resources for the study of the taxonomy and phylogeny of grapsid crabs, the mitogenome for C. granulosus is presented as the first Southern Hemisphere species of grapsid crab to have its mitochondrial genome completely sequenced. The C. granulosus sample was caught from under rocks near Anglesea, Victoria, Australia. The purification of genomic DNA
History Received 16 November 2014 Accepted 16 November 2014 Published online 26 December 2014
from ethanol-preserved leg muscle tissue and partial whole genome sequencing (2 150 bp paired-end run) were performed as previously described (Gan et al., 2014). The complete mitogenome was recovered as the longest contig from IDBAUD de novo assembly (Peng et al., 2012). The contig was subsequently recircularized and annotated as done in Gan et al. (2014). The C. granulosus mitochondrial genome is 16,300 bp in length (GenBank accession number: LN624373) and has 37 mitochondrial genes (13 protein-coding genes, two rRNAs and 22 tRNAs) and a non-coding region of 696 bp (Table 1). The base composition is 33% A, 36% T, 11% G and 20% C and the order of the genes is identical to Eriocheir species also from the family Varunidae (Wang et al., 2014), which differ from the typical brachyuran mitogene order. Our sample of C. granulosus shows a 99% similarity to a 1181 bp fragment of the 16S ribosomal RNA gene for the New Zealand species Cyclograpsus lavauxi (GenBank accession number: AB440191) suggesting these two species may be conspecific. It will be of interest to study further the mitogene order within the Grapsoidea as each family so far studied displays a different gene order. Xenograpsus testudinatus, a hydrothermal vent crab (Xenograpsidae), has a distinct gene order (Ki et al., 2009), whereas Pachygrapsus crassipes (Grapsidae) shares the common brachyuran gene order, which is similar to the primitive pancrustacean arrangement (Yu et al., 2014).
Correspondence: Han Ming Gan, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
M. H. Tan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of the complete mitochondrial genome of C. granulosus.
Downloaded by [University of California, San Diego] at 00:27 06 November 2015
Gene cox1 trnL2(taa) cox2 atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnT(tgt) trnP(tgg) nad1 trnL1(tag) rrnL rrnS trnH(gtg) nad5 trnV(tac) Control region trnQ(ttg) trnC(gca) trnY(gta) trnK(ttt) trnD(gtc) trnE(ttc) trnF(gaa) nad4 nad4l nad6 cob trnS2(tga) trnI(gat) trnM(cat) nad2 trnW(tca)
Strand
Position
Length (bp)
Intergenic nucleotides
H H H H H H H H H H H H H L L L L L L L L – L L L H H H L L L H H H H H H H
1–1539 1535–1598 1606–2308 2370–2531 2525–3199 3199–3990 3990–4052 4053–4403 4405–4467 4470–4533 4533–4597 4600–4667 4750–4815 4816–4883 4919–5851 5886–5952 5901–7271 7326–8152 8228–8294 8331–10,061 10,181–10,254 10,255–10,950 10,951–11,019 11,038–11,100 11,102–11,166 11,196–11,264 11,263–11,328 11,352–11,420 11,431–11,494 11,523–12,860 12,854–13,156 13,253–13,765 13,765–14,899 14,900–14,967 15,046–15,113 15,134–15,205 15,206–16,216 16,215–16,283
1539 64 703 162 675 792 63 351 63 64 65 68 66 68 933 67 1371 827 67 1731 74 696 69 63 65 69 66 69 64 1338 303 513 1135 68 68 72 1011 69
17 5 7 61 7 1 1 0 1 2 1 2 82 0 35 34 52 54 75 36 119 0 0 18 1 29 2 23 10 28 7 96 1 0 78 20 0 2
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References De Grave S, Pentcheff ND, Ahyong ST, Chan TY, Crandall KA, Dworschak PC, Felder DL, et al. (2009). A classification of living and fossil genera of Decapod Crustaceans. Raffles Bull Zool 21:1–109. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Griffin DJG. (1971). The ecological distribution of grapsid and ocypodid shore crabs (Crustacea: Brachyura) in Tasmania. J Animal Ecol 40: 597–621.
Start codon
Stop codon
ATG
TAA
ATG ATG ATT ATG
T TAA TAA TAA
ATC
TAA
Anticodon UAA
UCC UGC UCG GUU UCU UGU UGG ATG
TAA UAG GUG
ATG
TAA UAC UUG GCA GUA UUU GUC UUC GAA
ATG ATG ATT ATG
TAA TAA TAA T UGA GAU CAU
ATC
TAG UCA
Ki J-S, Dahms H-U, Hwang J-S, Lee J-S. (2009). The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs. Comparative Biochem Physiol Part D 4:290–9. Lee SY. (1998). Ecological role of grapsid crabs in mangrove ecosystems: A review. Marine Freshwater Res 49:335–43. Little C. (1990). The terrestrial invasion: An ecophysiological approach to the origins of land animals. Cambridge University Press, Cambridge. Peng Y, Leung HCM, Yiu SM, Chin FYL. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–8. Wang J, Huang L, Cheng Q, Lu G, Wang C. (2014). Complete mitochondrial genomes of three mitten crabs, Eriocheir sinensis, E. hepuensis, and E. japonica. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.936425. Yu Y-Q, Ma W-M, Yang W-J, Yang J-S. (2014). The complete mitogenome of the lined shore crab Pachygrapsus crassipes Randall 1840 (Crustacea: Decapoda: Grapsidae). Mitochondrial DNA 25: 263–4.
