Elsevier

Gene

Volume 394, Issues 1–2, 1 June 2007, Pages 35-44
Gene

The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae)

https://doi.org/10.1016/j.gene.2007.01.009Get rights and content

Abstract

Shrimp of the family Atyidae are important members of nearly all tropical (and most temperate) fresh and brackish water ecosystems in the world. To date, a complete mitochondrial genome from this important crustacean group has not been reported. Here, we present the complete mitochondrial DNA sequence of the Hawaiian atyid Halocaridina rubra [Holthuis, L.B., 1963. On red coloured shrimps (Decapoda, Caridea) from tropical land-locked saltwater pools. Zool. Meded.16, 261–279.] (Crustacea: Decapoda: Atyidae). The genome is a circular molecule of 16,065 bp and encodes the 37 mitochondrial genes (13 protein-coding, 22 tRNAs, and two rRNAs) typically found in the metazoa. Gene order and orientation in the H. rubra mitochondrial genome is syntenic with most malacostracans that have been examined to date. Of special note is the absence of the dihydrouridine (DHU) arm stem from tRNATyr and the use of CCG as an initiation codon for cytochrome oxidase subunit I (COI); these represent the first reported examples of such phenomena in the Malacostraca. Phylogenetic analyses utilizing complete mitochondrial sequences from other malacostracans place H. rubra as sister to Macrobrachium rosenbergii, which also belongs to the Infraorder Caridea. However, the placement of this infraorder, as well as the Infraorder Dendrobrachiata, in the phylogeny of the Decapoda varied depending on outgroup selection. Data from additional mitochondrial genomes, such as basal decapods like the Stenopodidea, should contribute to a better overall understanding of decapod phylogenetics.

Introduction

Mitochondria are organelles found in eukaryotic cells and are responsible for the majority of cellular ATP production (Dimijian, 2000, Hedges et al., 2001). Mitochondria contain their own genome composed of double-stranded circular molecules that typically code for 37 genes (i.e., 13 protein-coding, 22 tRNAs and two rRNAs) involved in the electron transport chain (reviewed by Ballard and Whitlock, 2004). Mitochondrial genes are commonly utilized as genetic markers in determining the evolutionary history and phylogenetic relationships of organisms. Biological characteristics such as a uniparental (usually maternal) mode of inheritance, lack of recombination, and an accelerated rate of mutation have made mitochondrial genes popular tools in molecular genetic studies (Brown et al., 1979, Birky, 1995, Ballard and Whitlock, 2004).

The Atyidae are a family of caridean shrimp characterized by chelae with hair-like setae (Bruce, 1992) and occur in nearly all tropical, and most temperate, fresh and brackish water systems of the world. Typically of small (i.e., < 35 mm) size, members of this family serve key ecological roles in sediment decomposition (Pringle and Blake, 1994), processing of particulate organic matter (Pringle et al., 1999) and influencing the composition of benthic communities (Pringle et al., 1993, Pringle, 1996, Pringle and Hamazaki, 1998) in these habitats.

Although numerous studies have utilized mitochondrial genes to explore the phylogeography (e.g., Hurwood and Hughes, 2001, Chenoweth and Hughes, 2003, Hurwood et al., 2003, Baker et al., 2004) and evolution (e.g., Page et al., 2005, Porter et al., 2005, Page et al., in press) of the Atyidae, a complete mitochondrial genome from this crustacean group has not been reported. Here, we present the complete mitochondrial genome sequence of the endemic Hawaiian atyid Halocaridina rubra, Holthuis 1963 (Holthuis, 1963). These small (i.e., ∼ 10 mm) microphagous grazers, which live up to 20 years in captivity, occupy the unique niche of anchialine habitats in the archipelago (Bailey-Brock and Brock, 1993). Anchialine habitats are classified as “bodies of haline waters, usually with restricted exposure to air, always with extensive subterranean connections to the sea, and showing noticeable marine and terrestrial influences” (Stock, 1986). The complete mitochondrial genome sequence of H. rubra will provide additional genetic markers for elucidating the population structure and planning conservation management strategies for the species (Santos, 2006) as well as contribute fundamental information for evolutionary studies, such as inferring the phylogenetic history of the malacostracan crustaceans.

Section snippets

Sample collection and DNA extraction

Total DNA was obtained from one H. rubra individual collected from an anchialine habitat at Cape Hanamanioa on the island of Maui in June 2005. This individual belongs to a distinct mitochondrial lineage from those reported by Santos (2006) to occur on the Island of Hawaii (unpublished data). The specimen was collected and immediately stored in 100% acetone (Fukatsu, 1999) prior to DNA extraction as described in Santos (2006).

PCR and sequence determination

As a starting point, the mitochondrial cytochrome oxidase subunit I (

Genome composition

The H. rubra mitochondrial genome is a circular molecule of 16,065 bp and encodes the 37 genes (13 protein-coding, 22 tRNAs and two rRNAs) typically found in metazoan mitochondrial genomes (Fig. 1). Overlap between genes of up to 6 bp was observed on four occasions (Table 2). Most genes (23 of 37; 62%) are encoded on the positive (+) strand while the remaining 14 genes are located on the negative (−) strand (Table 2). A total of 1255 bp of non-coding nucleotides occur over 19 intergenic regions

Acknowledgements

We would like to thank Mike N. Yamamoto and Tom Iwai (State of Hawai'i Division of Aquatic Resources — Oahu) for assistance in acquiring samples and the photograph of Halocaridina rubra used in Fig. 1 as well as two anonymous reviewers for valuable suggestions that improved this work. This is contribution #19 to the Auburn University (AU) Marine Biology Program.

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