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 the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin (2014): The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA, DOI: 10.3109/19401736.2014.919460 To link to this article: http://dx.doi.org/10.3109/19401736.2014.919460
Published online: 20 May 2014.
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Date: 06 December 2015, At: 03:51
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919460
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae) Han Ming Gan1, Mun Hua Tan1, Huan You Gan1, Yin Peng Lee1, Mark B. Schultz2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia and 2Faculty of Medical and Dental Health Sciences, The University of Melbourne, Bio21 Research Institute, Parkville, Victoria, Australia
Downloaded by [University of Liverpool] at 03:51 06 December 2015
1
Abstract
Keywords
The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
Freshwater crayfish, mitogenome, Parastacidae
Australia’s freshwater crayfish fauna is distinctive with approximately 150 species classified into 10 genera (Crandall et al., 1999; Schultz et al., 2009). One of the less well studied groups are the black yabbies, placed in the genus Geocharax, which are part of Australia’s most diverse crayfish assemblage centered in the southeast of mainland Australia. The genus Geocharax was described by Clark (1936), but there has been significant disputation over the number of species making up the genus (Clark, 1936; Riek, 1969; Schultz et al., 2007). Currently the genus is thought to comprise of 4 species, 2 of which are undescribed cryptic species (Schultz et al., 2007). Mitogenomes of several representatives of the Australian crayfish genera have been sequenced (Austin et al., 2014a,b; Gan et al., 2014a,b,c,d; Miller & Austin, 2006) and they all share a highly unusual gene order first described by Miller et al. (2004). Further, differences within and between genera have been found with respect to the position of several trnRNA genes (Gan et al., 2014d). To further explore mitogenome evolution in freshwater crayfish, we have sequenced the complete mitochondrial genome of G. gracilis. Linear mitogenome comparison was performed using EasyFig (default setting) (Sullivan et al., 2011). The G. gracilis sample was collected from Yaloak Ck, Princes Hwy, E of Panmure, Victoria, Victoria, Australia (sample code: MBS006). Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into
History Received 13 April 2014 Accepted 24 April 2014 Published online 20 May 2014
small pieces. The purification of genomic DNA, partial whole genome sequencing (2 250 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014a). The partial 16S ribosomal RNA gene sequence of G. gracilis (GenBank accession number: FJ965960) was used as the initial bait for MITObim assembly. The G. gracilis mitogenome is 15,924 bp in length (GenBank accession number: HG942174) and contains 38 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 23 tRNAs) and an AT-rich non-coding region of 985 bp. The base composition is 35% A, 32% T, 11% G and 22% C and the order of genes differs slightly from the genus Engaeus and Cherax (Figure 1). The trnQ gene is duplicated in the mitogenome of G. gracilis. The first trnQ is situated immediately downstream of the control region similar to that reported in all five Cherax species that have full mitogenomes sequenced. The second trnQ gene is situated downstream of the rrnL gene which has not been previously observed in crayfish mitogenome. Additionally, the trnP gene is situated within the trnI and trnC genes instead of being in the vicinity of the rrnL gene in E. lyelli and C. quadricarinatus. Our sample of G. gracilis is identical at a 451 bp of the 16S rRNA region for 2 samples sequenced by Schultz et al. (2007) from the Curdies River and Mount Ema Creek, Victoria (GenBank accession numbers: EF493059.1 and EF493072.1).
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
Downloaded by [University of Liverpool] at 03:51 06 December 2015
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H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. The gene organization in the G. gracilis mitogenome and comparison with Cherax quadricarinatus and Engaeus lyelli (Acceesion number: NC_022947.1 and NC_023477.1 respectively). Genes are to scale, are transcribed in the direction indicated by arrows and abbreviated with the exception of tRNA genes which are assigned their corresponding amino acid letter code. Vertical blocks between the mitogenome tracks show similarity with the darker shades indicating higher degrees of similarity according to BLASTn.
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 Austin CM, Tan MH, Croft LJ, Gan HM. (2014a). The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.880897. Austin CM, Tan MH, Croft LJ, Gan HM. (2014b). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Clark E. (1936). The freshwater and land crayfishes of Australia. Mem Natl Mus Melb 10:5–58. Crandall KA, Fetzner J, James W, Lawler SH, Kinnersley M, Austin CM. (1999). Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Aust J Zool 47:199–214. Gan HM, Schultz MB, Austin CM. (2014a). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the red claw crayfish Cherax qaudricarinatus (Von Martens 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.895997.
Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014c). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.892105. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014d). The complete mitogenome of the Australian land crayfish Engaeus lyelli (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.908361. Miller AD, Austin CM. (2006). The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38:565–74. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): A novel gene order revealed. Gene 331:65–72. Riek E. (1969). The Australian freshwater crayfish (Crustacea: Decapoda: Parastacidae), with descriptions of a new species. Aust J Zool 17: 855–918. Schultz MB, Smith SA, Horwitz P, Richardson AM, Crandall KA, Austin CM. (2009). Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 50:580–98. Schultz MB, Smith SA, Richardson AMM, Horwitz P, Crandall KA, Austin CM. (2007). Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invertebr Syst 21:569–87. Sullivan MJ, Petty NK, Beatson SA. (2011). Easyfig: A genome comparison visualiser. Bioinformatics 27:1009–10.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin (2014): The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA, DOI: 10.3109/19401736.2014.919460 To link to this article: http://dx.doi.org/10.3109/19401736.2014.919460
Published online: 20 May 2014.
Submit your article to this journal
Article views: 17
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Liverpool]
Date: 06 December 2015, At: 03:51
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919460
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae) Han Ming Gan1, Mun Hua Tan1, Huan You Gan1, Yin Peng Lee1, Mark B. Schultz2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia and 2Faculty of Medical and Dental Health Sciences, The University of Melbourne, Bio21 Research Institute, Parkville, Victoria, Australia
Downloaded by [University of Liverpool] at 03:51 06 December 2015
1
Abstract
Keywords
The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
Freshwater crayfish, mitogenome, Parastacidae
Australia’s freshwater crayfish fauna is distinctive with approximately 150 species classified into 10 genera (Crandall et al., 1999; Schultz et al., 2009). One of the less well studied groups are the black yabbies, placed in the genus Geocharax, which are part of Australia’s most diverse crayfish assemblage centered in the southeast of mainland Australia. The genus Geocharax was described by Clark (1936), but there has been significant disputation over the number of species making up the genus (Clark, 1936; Riek, 1969; Schultz et al., 2007). Currently the genus is thought to comprise of 4 species, 2 of which are undescribed cryptic species (Schultz et al., 2007). Mitogenomes of several representatives of the Australian crayfish genera have been sequenced (Austin et al., 2014a,b; Gan et al., 2014a,b,c,d; Miller & Austin, 2006) and they all share a highly unusual gene order first described by Miller et al. (2004). Further, differences within and between genera have been found with respect to the position of several trnRNA genes (Gan et al., 2014d). To further explore mitogenome evolution in freshwater crayfish, we have sequenced the complete mitochondrial genome of G. gracilis. Linear mitogenome comparison was performed using EasyFig (default setting) (Sullivan et al., 2011). The G. gracilis sample was collected from Yaloak Ck, Princes Hwy, E of Panmure, Victoria, Victoria, Australia (sample code: MBS006). Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into
History Received 13 April 2014 Accepted 24 April 2014 Published online 20 May 2014
small pieces. The purification of genomic DNA, partial whole genome sequencing (2 250 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014a). The partial 16S ribosomal RNA gene sequence of G. gracilis (GenBank accession number: FJ965960) was used as the initial bait for MITObim assembly. The G. gracilis mitogenome is 15,924 bp in length (GenBank accession number: HG942174) and contains 38 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 23 tRNAs) and an AT-rich non-coding region of 985 bp. The base composition is 35% A, 32% T, 11% G and 22% C and the order of genes differs slightly from the genus Engaeus and Cherax (Figure 1). The trnQ gene is duplicated in the mitogenome of G. gracilis. The first trnQ is situated immediately downstream of the control region similar to that reported in all five Cherax species that have full mitogenomes sequenced. The second trnQ gene is situated downstream of the rrnL gene which has not been previously observed in crayfish mitogenome. Additionally, the trnP gene is situated within the trnI and trnC genes instead of being in the vicinity of the rrnL gene in E. lyelli and C. quadricarinatus. Our sample of G. gracilis is identical at a 451 bp of the 16S rRNA region for 2 samples sequenced by Schultz et al. (2007) from the Curdies River and Mount Ema Creek, Victoria (GenBank accession numbers: EF493059.1 and EF493072.1).
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
Downloaded by [University of Liverpool] at 03:51 06 December 2015
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. The gene organization in the G. gracilis mitogenome and comparison with Cherax quadricarinatus and Engaeus lyelli (Acceesion number: NC_022947.1 and NC_023477.1 respectively). Genes are to scale, are transcribed in the direction indicated by arrows and abbreviated with the exception of tRNA genes which are assigned their corresponding amino acid letter code. Vertical blocks between the mitogenome tracks show similarity with the darker shades indicating higher degrees of similarity according to BLASTn.
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 Austin CM, Tan MH, Croft LJ, Gan HM. (2014a). The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.880897. Austin CM, Tan MH, Croft LJ, Gan HM. (2014b). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Clark E. (1936). The freshwater and land crayfishes of Australia. Mem Natl Mus Melb 10:5–58. Crandall KA, Fetzner J, James W, Lawler SH, Kinnersley M, Austin CM. (1999). Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Aust J Zool 47:199–214. Gan HM, Schultz MB, Austin CM. (2014a). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the red claw crayfish Cherax qaudricarinatus (Von Martens 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.895997.
Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014c). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.892105. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014d). The complete mitogenome of the Australian land crayfish Engaeus lyelli (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.908361. Miller AD, Austin CM. (2006). The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38:565–74. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): A novel gene order revealed. Gene 331:65–72. Riek E. (1969). The Australian freshwater crayfish (Crustacea: Decapoda: Parastacidae), with descriptions of a new species. Aust J Zool 17: 855–918. Schultz MB, Smith SA, Horwitz P, Richardson AM, Crandall KA, Austin CM. (2009). Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 50:580–98. Schultz MB, Smith SA, Richardson AMM, Horwitz P, Crandall KA, Austin CM. (2007). Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invertebr Syst 21:569–87. Sullivan MJ, Petty NK, Beatson SA. (2011). Easyfig: A genome comparison visualiser. Bioinformatics 27:1009–10.
