http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1018209
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae) Yin Peng Lee1,2, Han Ming Gan1,2, Mun Hua Tan1,2, Isabelle Lys3, Rachel Page4, Beatrice Dias Wanigasekera4, and Christopher M. Austin1,2 Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/03/15 For personal use only.
1
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia, 3School of Science, Faculty of Health Sciences, Australian Catholic University, Banyo, Queensland, Australia, and 4School of Food and Nutrition, Massey University, Wellington, New Zealand Abstract
Keywords
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
Genetic resources, mitochondrial, parastacoidea
The family Parastacidae contains the diverse southern hemisphere freshwater crayfish consisting of in excess of 170 species classified into 15 extant genera (Crandall & Buhay, 2008; Schultz et al., 2009; Toon et al., 2010). This fauna reaches its greatest diversity in Australia and New Guinea, but a small number of distinctive species also occur in New Zealand, South America and Madagascar (Toon et al., 2010). The New Zealand crayfish are of special interest because they show closer affinities to the Tasmanian genera Ombrastacoides and Spinastacoides, than these do to the other Australian Genera (Toon et al., 2010). The New Zealand crayfish are placed in the genus Paranephrops (White, 1842), with two currently recognized species (Apte et al., 2007). Complete mitogenome sequences of representatives of a number of genera of Australian crayfish genera have been determined (Austin et al., 2014, Gan et al., 2014a,c,d; Miller et al., 2004) and they all share a highly unusual protein-coding and RNA gene order as first described by Miller et al. (2004). To further explore mitogenome evolution in freshwater crayfish and to provide additional molecular resources, we have sequenced the complete mitochondrial genome of P. planifrons, the first non-Australian parastacid crayfish to have its mitogenome sequenced. The P. planifrons sample was obtained from Ormund Aquaculture Ltd, Wairau Valley, Nelson, New Zealand. Correspondence: Han Ming Gan, Monash University Malaysia, School of Science, Jalan Lagoon Selatan, Bandar Sunway, Malaysia. E-mail: [email protected]
History Received 12 January 2015 Accepted 24 January 2015 Published online 24 February 2015
Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into small pieces. Partial whole genome sequencing, mitogenome assembly and annotation were performed as previously described (Gan et al., 2014a) with a slight modification, e.g. initially assembly was performed using IDBA-UD (Peng et al., 2012) and subsequently extended using MITObim (Hahn et al., 2013) to generate the complete mitogenome. The P. planifrons mitogenome was 16,147 bp in length (GenBank accession number: LN681402), had a base composition of 35% A, 34% T, 10% G and 22% C, and contains 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and an AT-rich non-coding region of 771 bp. The five Australian freshwater crayfish genera so far sequenced share the same gene order with the exception of a small number of either duplicated or translocated tRNAs (Gan et al., 2014b,e,f). The gene order in the P. planifrons mitogenome differs considerably from the typical gene order observed in Australia crayfish (Figure 1). The nad6 gene is translocated from immediately up stream of the trnP and 16S ribosomal RNA genes to immediately downstream of the 12S ribosomal RNA and trnI genes and no less than five tRNAs (K, N, L1, R and Q) differ in their locations. Our sample of P. planifrons was 99.8% identical to a 523 bp fragment of the 16S rRNA region obtained from a P. planifrons sample (accession number: EF060247) in the study by Apte et al. (2007). It will be of interest to investigate the gene order of the remaining parastacid genera from Australia, South America and Madascar (Crandall & Buhay, 2008).
2
Y. P. Lee et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/03/15 For personal use only.
Figure 1. The gene organization of the P. planifrons mitogenome and comparison with the mitogenome of C. cainii (Accession number: NC_022936.1) representing the putative primitive arrangement for Australian mainland genera. The translocation of nad6 between two mitogenomes is indicated with a thick line, tRNAs in different positions are indicated with thin lines.
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 Apte S, Smith PJ, Wallis GP. (2007). Mitochondrial phylogeography of New Zealand freshwater crayfishes, Paranephrops sp. Mol Ecol 16: 1897–908. Austin CM, Tan MH, Croft LJ, Gan HM. (2014). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.878907. Crandall K, Buhay J. (2008). Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae—Decapoda) in freshwater. Hydrobiologia 595:295–301. 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. doi:10.1186/1471-214814-19. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.926490. Gan HM, Tan MH, Austin CM. (2014c). The complete mitogenome of the red claw crayfish Cherax quadricarinatus (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. (2014d). 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, Gan HY, Lee YP, Schultz MB, Austin CM. (2014e). The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736. 2014.919460. Gan, HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014f). 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. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—A baiting and iterative mapping approach. Nucl Acids Res 41:e129. 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. Peng Y, Leung HC, Yiu SM, Chin FY. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–8. 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. Toon A, Pe´rez-Losada M, Schweitzer CE, Feldmann RM, Carlson M, Crandall KA. (2010). Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): Evidence from fossils and molecules. J Biogeogr 37:2275–90.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons White 1842 (Crustacea: Decapoda: Parastacidae) Yin Peng Lee1,2, Han Ming Gan1,2, Mun Hua Tan1,2, Isabelle Lys3, Rachel Page4, Beatrice Dias Wanigasekera4, and Christopher M. Austin1,2 Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/03/15 For personal use only.
1
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia, 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia, 3School of Science, Faculty of Health Sciences, Australian Catholic University, Banyo, Queensland, Australia, and 4School of Food and Nutrition, Massey University, Wellington, New Zealand Abstract
Keywords
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
Genetic resources, mitochondrial, parastacoidea
The family Parastacidae contains the diverse southern hemisphere freshwater crayfish consisting of in excess of 170 species classified into 15 extant genera (Crandall & Buhay, 2008; Schultz et al., 2009; Toon et al., 2010). This fauna reaches its greatest diversity in Australia and New Guinea, but a small number of distinctive species also occur in New Zealand, South America and Madagascar (Toon et al., 2010). The New Zealand crayfish are of special interest because they show closer affinities to the Tasmanian genera Ombrastacoides and Spinastacoides, than these do to the other Australian Genera (Toon et al., 2010). The New Zealand crayfish are placed in the genus Paranephrops (White, 1842), with two currently recognized species (Apte et al., 2007). Complete mitogenome sequences of representatives of a number of genera of Australian crayfish genera have been determined (Austin et al., 2014, Gan et al., 2014a,c,d; Miller et al., 2004) and they all share a highly unusual protein-coding and RNA gene order as first described by Miller et al. (2004). To further explore mitogenome evolution in freshwater crayfish and to provide additional molecular resources, we have sequenced the complete mitochondrial genome of P. planifrons, the first non-Australian parastacid crayfish to have its mitogenome sequenced. The P. planifrons sample was obtained from Ormund Aquaculture Ltd, Wairau Valley, Nelson, New Zealand. Correspondence: Han Ming Gan, Monash University Malaysia, School of Science, Jalan Lagoon Selatan, Bandar Sunway, Malaysia. E-mail: [email protected]
History Received 12 January 2015 Accepted 24 January 2015 Published online 24 February 2015
Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into small pieces. Partial whole genome sequencing, mitogenome assembly and annotation were performed as previously described (Gan et al., 2014a) with a slight modification, e.g. initially assembly was performed using IDBA-UD (Peng et al., 2012) and subsequently extended using MITObim (Hahn et al., 2013) to generate the complete mitogenome. The P. planifrons mitogenome was 16,147 bp in length (GenBank accession number: LN681402), had a base composition of 35% A, 34% T, 10% G and 22% C, and contains 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and an AT-rich non-coding region of 771 bp. The five Australian freshwater crayfish genera so far sequenced share the same gene order with the exception of a small number of either duplicated or translocated tRNAs (Gan et al., 2014b,e,f). The gene order in the P. planifrons mitogenome differs considerably from the typical gene order observed in Australia crayfish (Figure 1). The nad6 gene is translocated from immediately up stream of the trnP and 16S ribosomal RNA genes to immediately downstream of the 12S ribosomal RNA and trnI genes and no less than five tRNAs (K, N, L1, R and Q) differ in their locations. Our sample of P. planifrons was 99.8% identical to a 523 bp fragment of the 16S rRNA region obtained from a P. planifrons sample (accession number: EF060247) in the study by Apte et al. (2007). It will be of interest to investigate the gene order of the remaining parastacid genera from Australia, South America and Madascar (Crandall & Buhay, 2008).
2
Y. P. Lee et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Emory University on 08/03/15 For personal use only.
Figure 1. The gene organization of the P. planifrons mitogenome and comparison with the mitogenome of C. cainii (Accession number: NC_022936.1) representing the putative primitive arrangement for Australian mainland genera. The translocation of nad6 between two mitogenomes is indicated with a thick line, tRNAs in different positions are indicated with thin lines.
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 Apte S, Smith PJ, Wallis GP. (2007). Mitochondrial phylogeography of New Zealand freshwater crayfishes, Paranephrops sp. Mol Ecol 16: 1897–908. Austin CM, Tan MH, Croft LJ, Gan HM. (2014). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.878907. Crandall K, Buhay J. (2008). Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae—Decapoda) in freshwater. Hydrobiologia 595:295–301. 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. doi:10.1186/1471-214814-19. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.926490. Gan HM, Tan MH, Austin CM. (2014c). The complete mitogenome of the red claw crayfish Cherax quadricarinatus (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. (2014d). 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, Gan HY, Lee YP, Schultz MB, Austin CM. (2014e). The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736. 2014.919460. Gan, HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014f). 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. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—A baiting and iterative mapping approach. Nucl Acids Res 41:e129. 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. Peng Y, Leung HC, Yiu SM, Chin FY. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–8. 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. Toon A, Pe´rez-Losada M, Schweitzer CE, Feldmann RM, Carlson M, Crandall KA. (2010). Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): Evidence from fossils and molecules. J Biogeogr 37:2275–90.
