Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE

<p>Abstract</p> <p>Background</p> <p>We recently characterized HAmo SINE and its partner LINE in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solution using a bead-probe <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. To reveal the distribution and evolutionary history of SINEs and LINEs in cyprinid genomes, we performed a multi-species search for HAmo SINE and its partner LINE using the bead-probe capture and internal-primer-SINE polymerase chain reaction (PCR) techniques.</p> <p>Results</p> <p>Sixty-seven full-size and 125 internal-SINE sequences (as well as 34 full-size and 9 internal sequences previously reported in bighead carp and silver carp) from 17 species of the family Cyprinidae were aligned as well as 14 new isolated HAmoL2 sequences. Four subfamilies (type I, II, III and IV), which were divided based on diagnostic nucleotides in the tRNA-unrelated region, expanded preferentially within a certain lineage or within the whole family of Cyprinidae as multiple active source genes. The copy numbers of HAmo SINEs were estimated to vary from 10⁴to 10⁶in cyprinid genomes by quantitative RT-PCR. Over one hundred type IV members were identified and characterized in the primitive cyprinid Danio rerio genome but only tens of sequences were found to be similar with type I, II and III since the type IV was the oldest subfamily and its members dispersed in almost all investigated cyprinid fishes. For determining the taxonomic distribution of HAmo SINE, inter-primer SINE PCR was conducted in other non-cyprinid fishes, the results shows that HAmo SINE- related sequences may disperse in other families of order Cypriniforms but absent in other orders of bony fishes: Siluriformes, Polypteriformes, Lepidosteiformes, Acipenseriformes and Osteoglossiforms.</p> <p>Conclusions</p> <p>Depending on HAmo LINE2, multiple source genes (subfamilies) of HAmo SINE actively expanded and underwent retroposition in a certain lineage or within the whole family of Cyprinidae. From this perspective, HAmo SINE should provide useful phylogenetic makers for future analyses of the evolutionary relationships among species in the family Cyprinidae.</p

DNA barcoding for the identification of common economic aquatic products in Central China and its application for the supervision of the market trade

Common economic aquatic products are important contributors to the human food supply. However, with the rapid globalization of the aquatic products industry, aquatic products market has become increasingly disordered. Therefore, an accurate and convenient method for identifying common economic aquatic products is important and necessary in many areas. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used in species identification. To discriminate common economic aquatic species using DNA barcoding, we collected 534 COI barcode sequences of 66 common species consisting of 39 fish, 9 crustaceans and 18 mollusks. The intraspecific genetic distances based on the Kimura 2-parameter (K2P) model were less than 1.37% for fish, 7.32% for crustaceans and 3.40% for mollusks, whereas the intragenus distances ranged from 3.91% to 13.82% for fish, 14.99%-16.17% for crustaceans and 14.82%-1636% for mollusks. The average intraspecific K2P distance was also compared with the average intragenus distance. The taxonomic resolution ratio values obtained for fish, crustaceans and mollusks were 58.50, 21.59 and 27.63 respectively, which are higher than the threshold of (10 x). A neighbor-joining (NJ) tree based on the K2P distance, and a maximum likelihood (ML) tree, based on the GTR + I + G model, were constructed, and all of the species could be identified unambiguously in the trees with several branches exhibiting high bootstrap values. Our results demonstrated high efficiency of DNA barcoding as an efficient molecular tool for the identification of common economic aquatic products, and 8 substitute species were successfully detected in 66 species. Our analyses also indicated that the common aquatic products trade industry could be effectively monitored and managed by DNA barcoding. Therefore, a simple identification database of common economic aquatic products was constructed. (C) 2015 Published by Elsevier Ltd

Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

<p>Abstract</p> <p>Background</p> <p>Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.</p> <p>Results</p> <p>Ten BAC clones of a spiny pufferfish <it>Diodon holocanthus </it>were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the <it>D. holocanthus </it>genome were identified, and 77 distinct genes were predicted. In the sequenced <it>D. holocanthus </it>genome, 364 kb is homologous with 265 kb of the <it>Takifugu rubripes </it>genome, and 223 kb is homologous with 148 kb of the <it>Tetraodon nigroviridis </it>genome. The repetitive DNA accounts for 8% of the sequenced <it>D. holocanthus </it>genome, which is higher than that in the <it>T. rubripes </it>genome (6.89%) and that in the <it>Te. nigroviridis </it>genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced <it>D. holocanthus </it>genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in <it>D. holocanthus </it>genome increased to 10.6% compared with <it>T. rubripes </it>and increased to 9.19% compared with <it>Te. nigroviridis</it>. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in <it>D. holocanthus </it>genome is significantly longer than that in the smooth pufferfish genome (435 bp).</p> <p>Conclusion</p> <p>Compared with the smooth pufferfish, <it>D. holocanthus </it>has a low gene density and repeat elements rich genome. Genome size variation between <it>D. holocanthus </it>and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between <it>D. holocanthus </it>and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between <it>D. holocanthus </it>and the smooth pufferfish.</p

Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp

MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large ‘hairpin’ precursors and function as post-transcriptional regulators of target genes. Although many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes

Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)

The actinopterygians comprise nearly one-half of all extant vertebrate species and are very important for human well-being. However, the phylogenetic relationships among certain groups within the actinopterygians are still uncertain, and debates about these relationships have continued for a long time. Along with the progress achieved in sequencing technologies, phylogenetic analyses based on multi-gene sequences, termed phylogenomic approaches, are becoming increasingly common and often result in well-resolved and highly supported phylogenetic hypotheses. Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, we obtained alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians, representing 17 out of 44 orders within the class Actinopterygii. Using these alignments and probabilistic methods, we recovered relationships between basal actinopterygians and teleosts, among teleosts within protacanthopterygians and related lineages, and also within acanthomorphs. These relationships were recovered with high confidence

The rapid generation of chimerical genes expanding protein diversity in zebrafish

AbstractBackgroundVariation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome.ResultsHere we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10-9 substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice.ConclusionThere is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome

Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish

The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.</p

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data

Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis

A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy.A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy