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...

The iconic phenotype of seadragons includes leaf-like appendages, a toothless tubular mouth, and male pregnancy involving incubation of fertilized eggs on an open “brood patch.” We de novo–sequenced male and female genomes of the common seadragon (Phyllopteryx taeniolatus) and its closely related species, the alligator pipefish (Syngnathoides biaculeatus). Transcription profiles from an evolutionary novelty, the leaf-like appendages, show that a set of genes typically involved in fin development have been co-opted as well as an enrichment of transcripts for potential tissue repair and immune defense genes. The zebrafish mutants for scpp5, which is lost in all syngnathids, were found to lack or have deformed pharyngeal teeth, supporting the hypothesis that the loss of scpp5 has contributed to the loss of teeth in syngnathids. A putative sex–determining locus encoding a male-specific amhr2y gene shared by common seadragon and alligator pipefish was identified.

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.

Background: The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. Findings: A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse (H. comes). Conclusion: We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior.

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Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

Salinity fluctuation is an important factor affecting outdoor microalgae culture. This investigation examined the effect of salinity change (Tr‐1:35–15 g/L, Tr‐2:35–25 g/L, Tr‐3:35–35 g/L, Tr‐4:35–45 g/L, and Tr‐5:35–55 g/L) on growth and the biochemical composition of Nannochloropsis oculata, a candidate for biodiesel production in indoor photo‐bioreactors. Results showed that the algae increased in absorbency and dry biomass as salinity decreased. When the salinity increased, the specific growth rate (SGR) of the algae decreased significantly. The salinity stress also affected the pigments of the algae, the chlorophyll‐a, and carotenoid contents of the algae which decreased with the increase of salinity from 45 to 55 g/L. The fatty acid methyl esters (FAME) content (% of dry biomass) increased with the increase of salinity (e.g., Tr‐4 and Tr‐5). The algae was rich in C16:0 (palmitic acid), C16:1n‐7 (palmitoleic acid), and C20:5n‐3 (eicosapentaenoic acid), and C16:0 content increased with decreasing salinity from 35 to 15 g/L, but C16:1n‐7 content was high in all the treatments ranging from 25.25 ± 1.42% in Tr‐1 to 27.05 ± 1.13% in Tr‐5.

The intelligent nanomachine usually has a control center to carry out self‐regulation. Unfortunately, most of the nanomaterials for chemodynamic therapy (CDT) do not have such a control center to sense and process the chemical or biological signals, which greatly weakens the selectivity and efficiency of CDT. To address this problem, here an intelligent nanomachine was constructed with a DNAzyme logic gate as the control center, and metal organic framework as the actuator. The well‐designed nanomachine showed an enhanced killing effect on cancer cells but posed no harm to normal cells, acquiring better selectivity than clinical chemotherapy drugs (doxorubicin and cisplatin). To the best of our knowledge, this is the first reported cell‐specific CDT by the guidance of DNAzyme logic gate. Our work highlights the great potential of DNAzymes in intelligent response networks, and extends the implementation of nanomachines in precision medicine.