The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

Shen, Xin; Sun, Ming-an; Wu, Zhigang; Tian, Mei; Cheng, Hanliang; Zhao, Fangqing; Meng, Xianhong

doi:10.1016/j.gene.2009.02.014

Cited by 44 publications

(39 citation statements)

References 55 publications

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“…6% (Tables 4, 7). However, at the third position the overall AT composition is 82.5% (Table 7), which is higher than most other malacostracan mitochondrial genomes (Shen et al, 2009).…”

Section: Base Composition and Codon Usagementioning

confidence: 72%

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Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster

Shi¹,

Liu²,

Sha³

et al. 2012

Marine Genomics

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“…6% (Tables 4, 7). However, at the third position the overall AT composition is 82.5% (Table 7), which is higher than most other malacostracan mitochondrial genomes (Shen et al, 2009).…”

Section: Base Composition and Codon Usagementioning

confidence: 72%

“…1; Table 5). This transcriptional polarity is common in Malacostraca (Shen et al, 2009). The start and stop codons of the 13 PCGs in the S. hispidus mitogenome are shown in Table 3.…”

Section: Protein-coding Genesmentioning

confidence: 87%

Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster

Shi¹,

Liu²,

Sha³

et al. 2012

Marine Genomics

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“…2 Caridea phylogeny: IB topology, with posterior probability shown when [0.94. asterisk nodes only supported in BI. All other nodes have similar support both in ML and in BI (bootstrap [70 in ML and posterior probability [0.96 in BI) the mitogenomes that are available for 11 Caridean species (Miller et al 2005;Ivey and Santos 2007;Shen et al 2009;Qian et al 2011;Kim et al 2013;Yang et al 2012Yang et al , 2013. Indeed, sequencing complete mitochondrial genomes is easier and more affordable that sequencing complete genomes or transcriptomes.…”

Section: Discussionmentioning

confidence: 87%

An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods

et al. 2015

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During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection among those available for Decapoda. Here we test in the Caridea if improving the taxonomic coverage following the hierarchical scheme of the classification, as it is currently accepted, provides a better phylogenetic resolution for the inter-families relationships. The rich collections of the Muséum National d'Histoire Naturelle de Paris are used for sampling as far as possible at least two species of two different genera for each family or subfamily. All potential markers are tested over this sampling. For some coding genes the amplification success varies greatly among taxa and the phylogenetic signal is highly saturated. This result probably explains the taxon-heterogeneity among previously published studies. The analysis is thus restricted to the genes homogeneously amplified over the whole sampling. Thanks to the taxonomic sampling scheme the monophyly of most families is confirmed. However the genes commonly used in Decapoda appear non-adapted for clarifying inter-families relationships, which remain poorly resolved. Genome-wide analyses, like transcriptome-based exon capture facilitated by the new generation sequencing methods might provide a sounder approach to resolve deep and rapid radiations like the Caridea.

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“…However, we found that a translocation of the trnE gene involving inversion was present in the two Alpheus mitochondrial genomes (Figure 2). The translocation of this gene has not been reported in any of the other crustacean mitochondrial genomes studied so far; however, compared with pancrustacean ground pattern, the translocation of one tRNA gene (either trnP or trnT) has been found in the mitochondrial genome of E. carinicauda [14].…”

Section: Gene Ordermentioning

confidence: 84%

Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea

Shen

Xiao

Sha

et al. 2012

Sci. China Life Sci.

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The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers (Crustacea: Decapoda: Caridea) is presented here. A comparative analysis based on the currently available mitochondrial genomic data revealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mitochondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mitochondrial genomes of four previously studied carideans (Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra) were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rearrangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving inversion was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mitochondrial genome that has been studied so far; however, the translocation of one transfer RNA gene (trnP or trnT) was reported in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous substitutions rates (Ka/Ks) for the 13 protein coding genes from two Alpheus species (A. japonicus and A. distinguendus) and three Macrobrachium species (M. rosenbergii, M. nipponense, M. lanchesteri) were calculated, the Ka/Ks values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 (between 0.0048 and 0.2057), indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, (Palaemonidae+Alpheidae)+Atyidae, at the family level. With few exceptions, the mitochondrial DNA of Metazoa is circular, 11-20 kb in length, and encodes 37 genes: 13 protein coding genes cob, nad4L, atp6 and atp8), two ribosomal RNAs (rRNAs: srRNA and lrRNA), and 22 transfer RNAs (tRNAs) [1]. Complete mitochondrial genomes are potentially powerful tools that have been used to study the evolutionary history and phylogenetic relationships among metazoans [2]. Mitochondrial genomes also can provide important background information for molecular ecology and population genetics of related species. Caridea Dana, 1852 is one of the largest infraorders in the order Decapoda and is very common in marine and fresh waters. It contains many species of commercial interest. Alpheidae, which currently contains 46

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The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

Cited by 44 publications

References 55 publications

Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster

Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster

An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods

Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea

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