Utility of mitochondrial DNA sequences from four gene regions for systematic studies of Australian freshwater crayfish of the Genus Cherax (Decapoda: Parastacidae)

One of the most important requirements for systematic and phylogenetic studies is the identification of gene regions with the appropriate level of variation for the question of interest. Molecular phylogenetic and systematic studies of freshwater crayfish have made use of DNA sequences mainly from ribosomal genes, especially the 16S rRNA gene region. Thus, little information is available on other potentially useful mitochondrial gene regions for systematic studies in these animals. In this study, we look at nucleotide variation and phylogenetic relations within and between four species of freshwater crayfish of the genus Cherax from the southwest of Western Australia using four fragments amplified from the 16S rRNA, 12S rRNA, Cytochrome Oxidase I (COI), and Cytochrome b (Cyt b) gene regions. Samples of Engaeus strictifrons, Euastacus bispinosus, and Geocharax falcata were also sequenced for comparative purposes. The size of the fragments varied from 358 bp to 600 bp. Across all samples, the four fragments showed significant phylogenetic signal and showed similar proportions of variable sites (28.81–37.33%). Average divergence within species for the mitochondrial gene regions varied from 1.18% to 4.91%, with the 16S rRNA being the least variable and Cyt b the most variable. Average divergence between species ranged 7.63–15.53%, with 16S rRNA being the least variable and COI the most variable. At the generic level, average divergence ranged 17.21–23.82%. Phylogenetic analyses of the 16S rRNA, 12S rRNA, and COI regions generated four clades consistent with the presence of four species previously identified on the basis of allozyme and morphological studies. The relationships among samples were largely congruent across the data set, although some relationships remained unresolved. Not all samples could be amplified using the Cyt b primers, and some of those that were showed quite anomalous relationships, suggesting that one or more Cyt b pseudogenes were being amplified.

The taxonomy and phylogeny of the Cherax destructor complex (Decapoda : Parastacidae) examined using mitochondrial 16S sequences

This study uses nucleotide sequences from the 16S rRNA mitochondrial gene to investigate the taxonomy and phylogeny of freshwater crayfish belonging to the 'Cherax destructor' complex. The sequencing of an approximately 440-bp fragment of this gene region from freshwater crayfish sampled from 14 locations identified significant haplotype diversity. Phylogenetic analysis found three distinct clades that correspond to the species C. rotundus, C. setosus and C. destructor. C. rotundus is largely confined to Victoria, and C. setosus is restricted to coastal areas north of Newcastle in New South Wales. C. destructor is widely distributed in eastern Australia and shows significant phylogeographic structure, with three well supported clades. None of these clades, however, correspond to species previously recognised as C. esculus, C. davisi or C. albidus. The failure to genetically distinguish these morphologically defined species is consistent with reproductive information and morphological plasticity relating to habitat similar to that documented for other Cherax species.

Multiple origins of the endemic Australian Macrobrachium (Descapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences

The evolutionary relationships of the freshwater prawn genus Macrobrachium are obscure. Members of this genus are widely distributed across tropical and subtropical regions. The phylogenetic relationships among the seven endemic and six non-endemic Australian Macrobrachium, along with five non-Australian species, were inferred from the mitochondrial 16S rRNA gene sequences. Methods of analysis yielded phylogenetic trees of differing topologies; however, none supported a monophyletic origin for endemic Australian Macrobrachium. Enforced monophyly of a single origin of endemic Macrobrachium was statistically tested and rejected. These results support the view that the endemic Australian Macrobrachium arose from multiple origins. Previous biogeographical hypotheses related to the radiation of Macrobrachium into Australia are re-examined in the context of these results.

The systematics of freshwater crayfish of the genus Cherax Erichson (Decapoda : Parastacidae) in eastern Australia re-examined using nucleotide sequences from 12S rRNA and 16S rRNA genes

Nucleotide sequence data were used to re-examine systematic relationships and species boundaries within the genus Cherax from eastern Australia. Partial sequences were amplified from the 12S (~365 bp) and 16S (~545 bp) rRNA mitochondrial gene regions. Levels of intra- and inter-specific divergence for Cherax species were very similar between the two gene regions and similar to that reported for other freshwater crayfish for 16S rRNA. Phylogenetic analyses using the combined data provided strong support for a monophyletic group containing 11 eastern Australian species and comprising three well-defined species-groups: the 'C. destructor' group containing three species, the 'C. cairnsensis' group containing four species and the 'C. cuspidatus' group containing two species. Cherax dispar and C. robustus are distinct from all other species and each other. In addition, two northern Australian and a New Guinean species were placed in the 'Astaconephrops' group, which is the sister-group to the eastern Australian Cherax lineage. Several relationships were clarified, including: the status of northern and southern C. cuspidatus as separate species; a close relationship between C. cairnsensis and C. depressus; the validity of C. rotundus and C. setosus as separate species and their close affinities with C. destructor; and the distinctiveness of the northern forms of Cherax. The analysis of the 12S rRNA and 16S rRNA data is highly concordant with the results of previous allozyme studies.

Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percicthyidae: Gadopsis) from south-eastern Australia

Fish of the genus Gadopsis are a distinctive component of the freshwater fish fauna of south-eastern Australia. Gadopsis marmoratus and G. bispinosus are the only two species recognised within the genus, with the former of uncertain taxonomic status, as it is thought to be composed of at least two distinct geographical forms based on morphological and allozyme data. The objective of this study was to investigate DNA sequence divergence in Gadopsis, especially in the western portion of its distribution, using an approximately 400 base pair fragment of the mitochondrial small subunit 12S rRNA gene region in order to reassess the taxonomy of the genus. Individuals from 11 locations were sequenced and confirm that G. marmoratus and G. bispinosus are genetically distinct, and further that the G. marmoratus complex consists of two divergent clades representing the previously identified northern and southern forms. The degree of divergence between the three Gadopsis clades was similar (5–6% nucleotide substitutions), suggesting that they diverged from a common ancestor at approximately the same period in geological time. These results are consistent with previous allozyme studies and highlight the usefulness of mitochondrial DNA data coupled with allozyme information for clarifying taxonomic boundaries in morphologically conservative aquatic organisms.

Using mitochondrial nucleotide sequences to investigate diversity and genealogical relationships within common carp (Cyprinus carpio L.)

Direct sequencing of mitochondrial DNA (mtDNA) D-loop (745 bp) and MTATPase6/MTATPase8 (857 bp) regions was used to investigate genetic variation within common carp and develop a global genealogy of common carp strains. The D-loop region was more variable than the MTATPase6/MTATPase8 region, but given the wide distribution of carp the overall levels of sequence divergence were low. Levels of haplotype diversity varied widely among countries with Chinese, Indonesian and Vietnamese carp showing the greatest diversity whereas Japanese Koi and European carp had undetectable nucleotide variation. A genealogical analysis supports a close relationship between Vietnamese, Koi and Chinese Color carp strains and to a lesser extent, European carp. Chinese and Indonesian carp strains were the most divergent, and their relationships do not support the evolution of independent Asian and European lineages and current taxonomic treatments.

Complete mitochondrial DNA sequences of the decapod crustaceans pseudocarcinus gigas (Menippidae) and macrobrachium rosenbergii (Palaemonidae)

The complete mitochondrial DNA sequence was determined for the Australian giant crab Pseudocarcinns gigas (Crustacea: Decapoda: Menippidae) and the giant freshwater shrimp Macrobrachium rosenbergii (Crustacea: Decapoda: Palaemonidae). The Pse gigas and Mrosenbergii mitochondrial genomes are circular molecules, 15,515 and 15,772 bp in length, respectively, and have the same gene composition as found in other metazoans. The gene arrangement of M. rosenbergii corresponds with that of the presumed ancestral arthropod gene order, represented by Limulus polyphemus, except for the position of the tRNA^Leu(UUR) gene. The Pse. gigas gene arrangement corresponds exactly with that reported for another brachyuran, Portunus trituberculatus, and differs from the M. rosenbergii gene order by only the position of the tRNA^His gene. Given the relative positions of intergenic nonoding nucleotides, the “duplication/random loss” model appears to be the most plausible mechanism for the translocation of this gene. These data represent the first caridean and only the second brachyuran complete mtDNA sequences, and a source of information that will facilitate surveys of intraspecific variation within these commercially important decapod species.

Frequency distribution of TATA box and extension sequences on human promoters

TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear yet. In this study, we conducted a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from TATA Box motif, TATAWAWN, were classified into three distribution patterns: peak, bottom-peak and bottom. Fourteen TATA extension sequences (up to two base extensions) were predicted to be the new TATA Box elements because of their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mouse, zebrafish and drosophila melanogaster verified seven of these elements. It was also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human.

Finding motifs in miRNA sequences

Recently, the emergence of non-coding miRNA has attracted biology and computer researchers. miRNA plays an important role in regulation of genes. Finding motifs in RNA is one of important topics. In our work, we attempt to find motifs in mature miRNA from combinations ranging from two to ten nucleotides. Interestingly, we have found several motifs only appear in mature miRNA but not appear in other regions of primary miRNA sequences taken from latest miRNA datasets. The findings of our investigation may help in the building model to predict all possible miRNAs in genomes

Phylogenetic relationships among nine scallop species (Bivalvia : Pectinidae) inferred from nucleotide sequences of one mitochondrial and three nuclear gene regions

Current knowledge of the evolutionary relationships among scallop species (Mollusca: Bivalvia: Pectinidae) in the Indo-Pacific region is rather scanty. To enhance the understanding of the relationships within this group, phylogenies of nine species of scallops with the majority from coastal regions of Thailand, were reconstructed by maximum parsimony, maximum likelihood, and Bayesian methods using sequences of the 16S rRNA of the mitochondrial genome, and a fragment containing the ITS1, 5.8S and ITS2 genes of the nuclear DNA. The trees that resulted from the three methods of analysis were topologically identical, however, gained different levels of support at some nodes. Nine species were clustered into two major clades, corresponding to two subfamilies (Pectininae and Chlamydinae) of the three currently recognized subfamilies within Pectinidae. Overall, the relationships reported herein are mostly in accordance with the previous molecular studies that used sequences of the mtDNA cytochrome oxidase subunit I, and the classification system based on microsculpture of shell features and morphological characteristics of juveniles. Levels of divergences were different among genes (i.e., the 5.8S gene showed the lowest levels of nucleotide divergence at all levels, whereas the 16S rRNA showed the highest level of variation within species, and ITS2 gene revealed the highest level of divergence at higher levels).