Hongmei Song

Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae

The present study examined the genetic variation of the family Osteoglossidae from different geographical locations based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) and ATPase subunit 6 (ATPase6) genes; we then re-constructed the phylogenetic relationships using the two sequences in combination. The results showed that the partial sequences of mitochondrial ND2 and ATPase6 of the family Osteoglossidae were 813 bp and 669 bp, respectively. A total of 42 species-specific nucleotide positions of the family Osteoglossidae were found to be useful for molecular identification. The sequence variation showed greater differences (8.3%~28.1% for the combined sequences, 8.3%~26.7% for the ND2 gene, and 9.3%~28.7% for the ATPase6 gene) among the different species of Osteoglossidae, and there was a significant association between the genetic difference and geographical location. Phylogenetic analyses using neighbor-joining, Bayesian inference, and maximum parsimony (MP) methods based on the combined sequences of the two genes were able to distinguish the different species and were in agreement with the existing taxonomy based on morphological characters and in association with the geographical distribution among seven species of the family Osteoglossidae.

Characterization of the Macropodus opercularis complete mitochondrial genome and family Channidae taxonomy using Illumina-based de novo transcriptome sequencing

In this study, the complete mitochondrial genome of Macropodus opercularis was sequenced using Illumina-based de novo transcriptome technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,496bp in length and contained two ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes, and the control region. The gene composition and order were similar to suborder Anabantoidei. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Neighbor-joining and Bayesian analysis) both highly supported the close relationship of M. opercularis to M. ocellatus, consistent with previous classifications based on morphological and molecular studies. Furthermore, family Channidae and Parachanna insignis were clustered in the same clade. Our results supported the inclusion of family Channidae in suborder Channoidei. The complete mitochondrial genome of M. opercularis will provide genetic markers for better understanding species identification, population genetics and phylogeographics of freshwater fishes.

Transcriptome analysis between invasive Pomacea canaliculata and indigenous Cipangopaludina cahayensis reveals genomic divergence and diagnostic microsatellite/SSR markers

BackgroundPomacea canaliculata is an important invasive species worldwide. However, little is known about the molecular mechanisms behind species displacement, adaptational abilities, and pesticide resistance, partly because of the lack of genomic information that is available for this species. Here, the transcriptome sequences for the invasive golden apple snail P. canaliculata and the native mudsnail Cipangopaludina cahayensis were obtained by next-generation-sequencing and used to compare genomic divergence and identify molecular markers.ResultsMore than 46 million high quality sequencing reads were generated from P. canaliculata and C. cahayensis using Illumina paired-end sequencing technology. Our analysis indicated that 11,312 unigenes from P. canaliculata and C. cahayensis showed significant similarities to known proteins families, among which a total of 4,320 specific protein families were identified. KEGG pathway enrichment was analyzed for the unique unigenes with 17 pathways (p-value < 10−5) in P. canaliculata relating predominantly to lysosomes and vitamin digestion and absorption, and with 12 identified in C. cahayensis, including cancer and toxoplasmosis pathways, respectively. Our analysis also indicated that the comparatively high number of P450 genes in the P. canaliculata transcriptome may be associated with the pesticide resistance in this species. Additionally, 16,717 simple sequence repeats derived from expressed sequence tags (EST-SSRs) were identified from the 14,722 unigenes in P. canaliculata and 100 of them were examined by PCR, revealing a species-specific molecular marker that could distinguish between the morphologically similar P. canaliculata and C. cahayensis snails.ConclusionsHere, we present the genomic resources of P. canaliculata and C. cahayensis. Differentially expressed genes in the transcriptome of P. canaliculata compared with C. cahayensis corresponded to critical metabolic pathways, and genes specifically related to environmental stress response were detected. The CYP4 family of P450 cytochromes that may be important factors in pesticide metabolism in P. canaliculata was identified. Overall, these findings will provide valuable genetic data for the further characterization of the molecular mechanisms that support the invasive and adaptive abilities of P. canaliculata.

An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion

Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

Spatial variation in adult sex ratio across multiple scales in the invasive golden apple snail, Pomacea canaliculata.

Abstract Adult sex ratio (ASR) has critical effects on behavior and life history and has implications for population demography, including the invasiveness of introduced species. ASR exhibits immense variation in nature, yet the scale dependence of this variation is rarely analyzed. In this study, using the generalized multilevel models, we investigated the variation in ASR across multiple nested spatial scales and analyzed the underlying causes for an invasive species, the golden apple snail Pomacea canaliculata. We partitioned the variance in ASR to describe the variations at different scales and then included the explanatory variables at the individual and group levels to analyze the potential causes driving the variation in ASR. We firstly determined there is a significant female‐biased ASR for this species when accounting for the spatial and temporal autocorrelations of sampling. We found that, counter to nearly equal distributed variation at plot, habitat and region levels, ASR showed little variation at the town level. Temperature and precipitation at the region level were significantly positively associated with ASR, whereas the individual weight, the density characteristic, and sampling time were not significant factors influencing ASR. Our study suggests that offspring sex ratio of this species may shape the general pattern of ASR in the population level while the environmental variables at the region level translate the unbiased offspring sex ratio to the female‐biased ASR. Future research should consider the implications of climate warming on the female‐biased ASR of this invasive species and thus on invasion pattern.

Complete mitochondrial genome of the Red devil cichlid (Amphilophus citrinellus)

Abstract In this study, the complete mitochondrial genome sequence of Amphilophus citrinellus was firstly sequenced and determined. The total genome is 16,522 bp in length with an A + T content of 54.19%, and contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and two main non-coding regions. The gene composition and order is similar to that of most other vertebrates, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Cichlidae species.

Complete mitochondrial genome of the ocellate river stingray (Potamotrygon motoro)

Abstract We determined the first complete mitochondrial genome sequence of Potamotrygon motoro from South American freshwater stingrays. The total length of P. motoro mitogenome is 17,448 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, with the genome organization and gene order being identical to that of the typical vertebrate. The overall nucleotide composition is 32.3% A, 24.4% T, 30.5% C and 12.8% G. These data will provide useful molecular information for phylogenetic relationships within the family Potamotrygonidae species.

Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai)

In this study, we sequenced and assembled the mitochondrial (mt) genome of Osteoglossum ferreirai to re-assess the phylogenetic relationship of the family Osteoglossidae. We determined that the mitogenome of O. ferreirai contains the entire set of 37 mt genes, and the nucleotide composition and gene arrangement were similar to those of other bonytongues. Our phylogenetic analyses exhibited monophyly of the family Osteoglossidae with high bootstrap support, which is in agreement with the currently accepted phylogenetic viewpoint that is based on both morphological and molecular approaches. These findings provide additional informative data for the further study of phylogenetic relationships and help to elucidate a key component of the species radiation process within the family Osteoglossidae.

Complete mitochondrial genome of northern spotted barramundi, Scleropages jardinii.

Abstract We sequenced the complete mitogenome of northern spotted barramundi Scleropages jardinii, an ancestral bonytongue with economic and conservation value. The mitogenome is 16,670 bp in length with an A + T content of 52.9%, and contains 13 protein-coding genes, 2rRNAs, 22 tRNAs and a control region. The gene order and arrangement is similar to that of other Osteoglossidae species, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Osteoglossidae species.