Members of the teleost family Syngnathidae (seahorses, pipefishes and seadragons) (Extended Data Fig. 1), comprising approximately 300 species, display a complex array of morphological innovations and reproductive behaviours. This includes specialized morphological phenotypes such as an elongated snout with a small terminal mouth, fused jaws, absent pelvic and caudal fins, and an extended body covered with an armour of bony plates instead of scales 1 (Fig. 1a). Syngnathids are also unique among vertebrates due to their 'male pregnancy' , whereby males nourish developing embryos in a brood pouch until hatching and parturition occurs 2,3 . In addition, members of the subfamily Hippocampinae (seahorses) exhibit other derived features such as the lack of a caudal fin, a characteristic prehensile tail, and a vertical body axis 4 (Fig. 1a). To understand the genetic basis of the specialized morphology and reproductive system of seahorses, we sequenced the genome of the tiger tail seahorse, H. comes, and carried out comparative genomic analyses with the genome sequences of other ray-finned fishes (Actinopterygii). Genome assembly and annotationThe genome of a male H. comes individual was sequenced using the Illumina HiSeq 2000 platform. After filtering low-quality and duplicate reads, 132.13 Gb (approximately 190-fold coverage of the estimated 695 Mb genome) of reads from libraries with insert sizes ranging from 170 bp to 20 kb were retained for assembly. The filtered reads were assembled using SOAPdenovo (version 2.04) to yield a 501.6 Mb assembly with an N50 contig size and N50 scaffold size of 34.7 kb and 1.8 Mb, respectively. Total RNA from combined soft tissues of H. comes was sequenced using RNA-sequencing (RNA-seq) and assembled de novo. The H. comes genome assembly is of high quality, as > 99% of the de novo assembled transcripts (76,757 out of 77,040) could be mapped to the assembly; and 243 out of 248 core eukaryotic genes mapping approach (CEGMA) genes are complete in the assembly.We predicted 23,458 genes in the genome of H. comes based on homology and by mapping the RNA-seq data of H. comes and a closely related species, the lined seahorse, Hippocampus erectus, to the genome assembly (see Methods and Supplementary Information). More than 97% of the predicted genes (22,941 genes) either have homologues in public databases (Swissprot, Trembl and the Kyoto Encyclopedia of Genes and Genomes (KEGG)) or are supported by assembled RNAseq transcripts. Analysis of gene family evolution using a maximum likelihood framework identified an expansion of 25 gene families (261 genes; 1.11%) and contraction of 54 families (96 genes; 0.41%) in the H. comes lineage (Extended Data Fig. 2 and Supplementary Tables 4.1, 4.2). Transposable elements comprise around 24.8% (124.5 Mb) of the H. comes genome, with class II DNA transposons being the most abundant class (9%; 45 Mb). Only one wave of transposable element expansion was identified, with no evidence for a recent transposable element burst (Kimura divergence ≤ 5) (Extended D...

BackgroundBlunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. Right now, only limited EST resources were available for M. amblycephala. Recent advances in large-scale RNA sequencing provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes.Methodology and Principal FindingsUsing 454 pyrosequencing, a total of 1,409,706 high quality reads (total length 577 Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals. These sequences were assembled into 26,802 contigs and 73,675 singletons. After BLAST searches against the NCBI non-redundant (NR) and UniProt databases with an arbitrary expectation value of E−10, over 40,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, tetraodon, fugu, stickleback, human, mouse, and chicken, and identified a substantial number of potentially novel M. amblycephala genes. A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized. A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.ConclusionsThis study is the first comprehensive transcriptome analysis for a fish species belonging to the genus Megalobrama. These large EST resources are expected to be valuable for the development of molecular markers, construction of gene-based linkage map, and large-scale expression analysis of M. amblycephala, as well as comparative genome analysis for the genus Megalobrama fish species. The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

Aquaculture is one of the fast-growing industries in the past decades. The fast expansion of aquaculture largely relies on the introduction and use of non-native species. This forms a paradox: some species significantly contribute to the fast expansion of aquaculture, while negative effects associated with unregulated introduction and irresponsible use of non-native species are increasing in number and area affected. However, lessons from reported disasters are slowly learned, and risks raised have been highly overlooked. Here, we discuss the known and potential risks derived from the introduction and use of non-native species in China to urge the necessity of incorporating sound management into sustainable aquaculture. Sound management needs to be performed based on the characteristics of each aquaculture activity or related event. We discuss risks based on aquaculture activities or related events popularly employed in the past decades in China, including (i) transfers of non-native species; (ii) fellow travellers, accidental introductions; (iii) artificial hybridization; and (iv) mass release of non-native species for ranching. For each aquaculture activity or related event, we provide general background, status of this activity, risks raised and recommendations for management. Finally, we call for the collaboration of researchers from academia, government and aquaculture industry for proper risk assessment and sound management for sustainable development of aquaculture.

BackgroundBlunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important roles in regulation of almost all biological processes in eukaryotes. Although previous studies have identified thousands of miRNAs from many species, little information is known for miRNAs of M. amblycephala. To investigate functions of miRNAs associated with growth of M. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) of M. amblycephala using individuals with relatively high and low growth rates.ResultsIn this study, we have identified 347 conserved miRNAs (belonging to 123 families) and 22 novel miRNAs in M. amblycephala. Moreover, we observed sequence variants and seed edits of the miRNAs. Of the 5,166 single nucleotide substitutions observed in two libraries, the most abundant were G-to-U (15.9%), followed by U-to-C (12.1%), G-to-A (11.2%), and A to G (11.2%). Subsequently, we compared the expression patterns of miRNAs in the two libraries (big-size group with high growth rate versus small-size group with low growth rate). Results indicated that 27 miRNAs displayed significant differential expressions between the two libraries (p < 0.05). Of these, 16 were significantly up-regulated and 11 were significantly down-regulated in the big-size group compared to the small-size group. Furthermore, stem-loop RT-PCR was applied to validate and profile the expression of the differentially expressed miRNAs in ten tissues, and the result revealed that the conserved miRNAs expressed at higher levels than the novel miRNAs, especially in brain, liver and muscle. Also, targets prediction of differentially expressed miRNAs and KEGG pathway analysis suggested that differentially expressed miRNAs are involved in growth and metabolism, signal transduction, cell cycle, neural development and functions.ConclusionsThe present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile related to different growth performances. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes and the study of miRNA function and phenotype-associated miRNA identification in fish.

The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala, with 779.54 Mb anchored on 24 linkage groups. Integrating spatiotemporal transcriptome analyses, we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification and may be involved in muscle contractibility and coordinating cellular events. Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M. amblycephala. The composition of gut microflora, which contributes to the herbivorous adaptation of M. amblycephala, was found to be similar to that of other herbivores. As a valuable resource for the improvement of M. amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation.

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Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.