The complete mitochondrial genome of the American lobster, Homarus americanus (Crustacea, Decapoda)
ABSTRACT Although relatively a large number of the complete mitochondrial genome sequences have been determined from various decapod species (29 mtDNA sequences reported so far), the information for the infraorder Astacidea (including lobsters, crayfishes, and their relatives) is very limited and represented by only one complete sequence from the Australian freshwater crayfish species Cherax destructor. In this study, we determined the complete mitochondrial DNA sequence of Homarus americanus, the first representative of the family Nephropidae to be fully characterized. Comparison of the gene arrangement reveals that H. americanus mtDNA is identical to those of other pancrustacean species but differs from the other astacidean species (C. destructor). Based on these data, it can be assumed that an idiosyncratic gene order discovered in C. destructor mtDNA may be secondarily acquired from the ancestral lineage of the Astacidea.
Full-textDOI: · Available from: Han-Gu Choi, Mar 05, 2015
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- "The two CRs show 59.6% similarity and have an identical sequence region of 295 bp. The M. thomsoni mitogenome shows a novel gene arrangement compared with that of H. americanus mitogenome, showing the pancrustacean ground pattern (Kim et al., 2011b). However, the gene arrangement in M. thomsoni is identical to that in M. sibogae (NC_025323), except for the two additional tRNAs (trnW and trnL1) found in M. thomsoni. "
ABSTRACT: The complete mitochondrial genome (mitogenome) of the red-banded lobster, Metanephrops thomsoni (Decapoda, Astacidea, Nephropidae), is 19,835 bp in length and contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 24 transfer RNAs (including additional copies of trnW and trnL1), and 2 control regions (CR). The mitogenome of M. thomsoni has 10 long intergenic sequences (71-237 bp) with a high AT content (70.0%). The two CRs show 59.6% similarity and have an identical sequence region with a length of 295 bp. The mitogenome of M. thomsoni shows a novel gene arrangement compared with the pancrustacean ground pattern and is identical to that of M. sibogae, except for the two additional tRNAs (trnW and trnL1). Phylogenetic tree from maximum likelihood analysis using the concatenated sequences of 13 PCGs depicted M. thomsoni as one of the members of the superfamily Nephropoidea within Astacidea.Mitochondrial DNA 08/2015; · 1.21 Impact Factor
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- "Nephropoidea Homarus gammarus (Linnaeus, 1758) NC_020020.1 Shen et al. (2013) Homarus americanus H. Milne Edwards, 1837 NC_015607.1 Kim et al. (2011) Nephrops norvegicus (Linnaeus, 1758) NC_025958.1 Gan et al. (2015a) Astacoidea Procambarus clarkii (Girard, 1852) NC_016926.1 Kim et al. (2012) Procambarus fallax f. virginalis (Hagen, 1870 and Martin et al. 2010) NC_020021.1 Shen et al. (2013) Cambaroides similis (Koelbel, 1892) NC_016925.1 Kim et al. (2012) Orconectes limosus (Rafinesque, 1817) NC_026561.1 Gan et al. (2015b) Parastacoidea Engaeus sericatus Clark, 1936 NC_024441.1 Unpublished Engaeus cunicularius (Erichson, 1846) NC_023809.1 Tan et al. (2015) Engaeus quadrimanus Clark, 1936 NC_024442.1 Unpublished Engaeus lyelli (Clark, 1936) NC_023477.1 Gan et al. (2014d) Engaeus lengana Horwitz, 1990 NC_022847.1 Gan et al. (2014f) Cherax crassimanus Riek, 1967 NC_024029.1 Tan et al. (2015) Cherax quinquecarinatus (Gray, 1845) NC_023479.1 Tan et al. (2015) Cherax quadricarinatus (Von Martens, 1868) NC_022937.1 Gan et al. (2014a) Cherax preissii (Erichson, 1846) NC_023482.1 Tan et al. (2015) Cherax dispar Riek, 1951 NC_023480.1 Tan et al. (2015) Cherax robustus Riek, 1951 NC_023478.1 Tan et al. (2015) Cherax cairnsensis Riek, 1969 NC_023481.1 Tan et al. (2015) Cherax cainii Austin & Ryan, 2002 NC_022936.1 Austin et al. (2014b) Cherax monticola Holthuis, 1950 NC_022938.1 Gan et al. (2014b) Cherax glaber Riek, 1967 NC_022939.1 Austin et al. (2014a) Cherax destructor Clark, 1936 NC_011243.1 Miller et al. (2004) Gramastacus lacus McCormack, 2014 NC_024295.1 Tan et al. (2015) Euastacus yarraensis (McCoy, 1888) NC_023811.1 Gan et al. (2014e) Geocharax gracilis Clark, 1936 NC_023810.1 Gan et al. (2014c) Table 2. Primer pairs and size of PCR products providing overlapping fragments for the whole mitogenomes of Hommarus gammarus and Enoplometopus occidentalis (Shen et al. 2013 "
ABSTRACT: We sequenced the complete mitogenomes of three species of Decapoda, Astacidea, comprising Astacida (freshwater crayfish) and Homarida (marine clawed lobsters): 1. Procambarus fallax f. virginalis (Astacida, Astacoidea), 2. Homarus gammarus (Homarida, Nephropoidea) and 3. Enoplometopus occidentalis (Homarida, Enoplometopoidea). Together with the available species in GenBank, the taxon Astacidea is covered with at least one representative for each of the four main subtaxa. Astacidea show unexpectedly diverse genomic organizations. Ten different gene arrangements have been observed in the 28 investigated species. Compared with the decapod ground pattern, a huge inversion, involving more than half of the mitogenome, has been found in four freshwater crayfish species of Astacoidea and convergently in one lobster species. Surprisingly, this inversion can also be observed in the distantly related Priapulida. This multiple convergent evolution suggests a relative ease in the evolution of great similarities in mitochondrial gene order. In addition, a partial or complete loss of the protein-coding gene nad2 has been found in E. occidentalis and H. gammarus but not in Nephrops norvegicus, Homarus americanus and Enoplometopus debelius. A reversal of the strand asymmetry has been found in five astacideans which is supposed to be caused by the inversion of a replication origin in the control region.Journal of Zoological Systematics and Evolutionary Research 07/2015; DOI:10.1111/jzs.12106 · 1.68 Impact Factor
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- "The gene orders for these mitogenomes were then compared with that of other crayfish mitogenomes that have recently become available for these genera and for Geocharax and Euastacus (Gan et al., 2014a,b,e,f). These are in turn compared with the mitogenome of the lobster, Homarus americanus (Kim et al., 2011). Importantly, in view of the significant increase in the number of publicly available Decapoda mitogenomes since the study by Shen et al. (2013), we sought to provide an update of the Decapoda mitogenomic phylogeny using a total of 95 mitogenomes, 89 of which are decapods and the remaining six as outgroups, and to use these mitogenomes to demonstrate the efficiency of MitoPhAST. "
ABSTRACT: The increased rate at which complete mitogenomes are being sequenced and their increasing use for phy- logenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phy- logenetic analysis. Hence, we present MitoPhAST, an automated tool that (1) identifies annotated protein- coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to under- take an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical over- view of the mitogenomes under study at the gene level, allowing the identification of missing or dupli- cated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evo- lutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogen- ome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogen- ome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST.Molecular Phylogenetics and Evolution 02/2015; 85:180-188. · 3.92 Impact Factor