Geng Qin

The seahorse genome and the evolution of its specialized morphology

Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4, a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a ‘pelvic fin-loss’ phenotype similar to that of seahorses.

The dynamics of reproductive rate, offspring survivorship and growth in the lined seahorse, Hippocampus erectus Perry, 1810

Summary Seahorses are the vertebrate group with the embryonic development occurring within a special pouch in males. To understand the reproductive efficiency of the lined seahorse, Hippocampus erectus Perry, 1810 under controlled breeding experiments, we investigated the dynamics of reproductive rate, offspring survivorship and growth over births by the same male seahorses. The mean brood size of the 1-year old pairs in the 1st birth was 85.4±56.9 per brood, which was significantly smaller than that in the 6th birth (465.9±136.4 per brood) (P<0.001). The offspring survivorship and growth rate increased with the births. The fecundity was positively correlated with the length of brood pouches of males and trunk of females. The fecundity of 1-year old male and 2-year old female pairs was significantly higher than that from 1-year old couples (P<0.001). The brood size (552.7±150.4) of the males who mated with females that were isolated for the gamete-preparation, was larger than those (467.8±141.2) from the long-term pairs (P<0.05). Moreover, the offspring from the isolated females had higher survival and growth rates. Our results showed that the potential reproductive rate of seahorses H. erectus increased with the brood pouch development.

A novel pathogenic bacteria (Vibrio fortis) causing enteritis in cultured seahorses, Hippocampus erectus Perry, 1810

[Wang, X.; Zhang, Y.; Qin, G.; Luo, W.; Lin, Q.] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou 510301, Guangdong, Peoples R China; [Wang, X.; Qin, G.] Univ Chinese Acad Sci, Beijing, Peoples R China

The leptin system and its expression at different nutritional and pregnant stages in lined seahorse Hippocampus erectus

ABSTRACT Leptin is an essential hormone for the regulation of energy metabolism and food intake in vertebrate animals. To better understand the physiological roles of leptin in nutrient regulation in paternal ovoviviparous fish (family Syngnathidae), the present study cloned the full-length of leptin-a and leptin receptor (lepr) genes in lined seahorse (Hippocampus erectus). Results showed that there was a 576-bp intron between two exons in leptin-a gene but no leptin-b gene in seahorse. Although the primary amino acid sequence conservation of seahorse leptin-a was very low, the 3-D structure modeling of seahorse leptin-a revealed strong conservation of tertiary structure with other vertebrates. Seahorse leptin-a mRNA was highly expressed in brain, whereas lepr mRNA was mainly expressed in ovary and gill. Interestingly, both leptin-a and lepr mRNA were expressed in the brood pouch of male seahorse, suggesting the leptin system plays a role during the male pregnancy. Physiological experiments showed that the expression of hepatic leptin-a and lepr mRNA in unfed seahorses was significantly higher than that in those fed 100%, as well as 60%, of their food during the fasting stage, showing that seahorse might initiate the leptin system to regulate its energy metabolism while starving. Moreover, the expression of leptin-a in the brood pouch of pregnant seahorse was significantly upregulated compared with non-pregnant seahorse, whereas the expression of lepr was downregulated, suggesting that the leptin system might be involved in the male pregnancy. In conclusion, the leptin system plays a role in the energy metabolism and food intake, and might provide new insights into molecular regulation of male pregnancy in seahorse. Summary: This study provided insights into the function of the leptin system in energy metabolism regulation and male pregnancy in lined seahorse (Hippocampus erectus).

The complete mitochondrial genome sequence of the network pipefish (Corythoichthys flavofasciatus) and the analyses of phylogenetic relationships within the Syngnathidae species.

This study determined the mitochondrial genome sequence of the network pipefish (Corythoichthys flavofasciatus) (Gasterosteiformes: Syngnathidae). The mitogenome was a circular molecule consisting of 16,961 nucleotides, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. The nucleotide composition of the genome was biased toward A+T content at 59.3%. All tRNA genes had typical cloverleaf secondary structure except for tRNA(Ser (AGY)), in which the dihydrouridine arm was missing. The C. flavofasciatus control region of 1130 bp contained several features common to other teleost, including conserved sequence blocks. We also performed comparative analysis of the network pipefish mitogenome to the available mitogenome sequences of other Syngnathidae species, and phylogenetic relationship of the Syngnathidae species was constructed based on the data sets including all the concatenated nucleotide sequences of the mitogenomes except the third codon positions. Partitioned Bayesian inference and maximum likelihood analyses showed that all seahorse species formed a monophyletic group of Hippocampus with 100% PPs and BPs, but the pipefish species did not form a monophyletic group. Corythoichthys flavofasciatus was placed as a sister relationship to the Hippocampus clade by strong node-supporting values. The availability of mitogenome of the network pipefish will shed light on the molecular systematics, biogeography and genetic differentiation in this species.

Seasonal distribution and reproductive strategy of seahorses

Seasonal distribution and reproductive strategy of seahorses Geng Qin, Yanhong Zhang, Adeljean L. F. C. Ho, Yuan Zhang, and Qiang Lin* Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.164, Xingangxi Rd, Haizhu District, Guangzhou 510301, PR China Department of Integrated Environmental Science, Bethune-Cookman University, 640 Dr Mary McLeod Bethune Boulevard, Daytona Beach, FL 32114, USA University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing 100049, PR China *Corresponding author: tel: þ86 020 89023161; fax: þ86 020 84451672; e-mail: linqiangzsu@163.com

The evolution and functional characterization of lined seahorse (Hippocampus erectus) CCKs involved in fasting and thermal stress response

The peptide cholecystokinin (CCK) plays an important role in the regulation of vertebrate appetite and feeding behaviour. In the present study, the full-length cDNA and genomic DNA sequences of two CCK precursors were cloned and analysed in the Syngnathidae fish, the lined seahorse (Hippocampus erectus). Both CCK1 and CCK2 in the seahorse consist of four exons. The sequence of the octapeptide of seahorse CCK1 (DYMGWMDF) was the same as that of the chicken and human, while the octapeptide of seahorse CCK2 (DYEGWMDF) was unique among vertebrates. According to the phylogenetic analysis, two types of CCKs were produced by teleost-specific genome duplication (TGD). Both CCK1 and CCK2 were highly expressed in the brain, while detectable amounts of CCK1 mRNA in the brood pouch and CCK2 mRNA in the intestine were also found. Both CCK1 and CCK2 mRNA levels significantly increased during the transition from endogenous to exogenous nutrition. Additionally, fasting induced a significant increase in the CCK1 mRNA expression in the brain of juvenile seahorses but had no effect on CCK2 transcript levels. In addition, the CCK1 and CCK2 mRNA levels in the seahorse brain significantly increased after a high-temperature treatment. Thus, the mRNA expression of CCK had obvious tissue specificities and this preliminary study opens new avenues for further functional studies on the endocrine regulations of CCK in the transition from endogenous to exogenous nutrition, food intake regulation and metabolism in the seahorse.

A bacterial infection by Vibrio harveyi causing heavy reduction of cultured lined seahorse Hippocampus erectus.

[Qin, G.; Wang, X.; Lin, Q.] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou, Guangdong, Peoples R China; [Qin, G.; Wang, X.] Univ Chinese Acad Sci, Beijing, Peoples R China; [Tan, S.] Guangzhou Univ, Sch Life Sci, Guangzhou, Guangdong, Peoples R China

Draft genome of the lined seahorse, Hippocampus erectus

Abstract 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.

A new species of seahorse (Teleostei: Syngnathidae) from the South China Sea

A new species of seahorse, Hippocampus casscsio sp. nov. was collected over shallow seagrass beds in Beibu Bay, China. This species is diagnosed from all other seahorse species by morphological characters, including the lower number of tail rings (35); 15 pectoral-fin rays; 16 dorsal-fin rays; a rounded nuchal plate without a raised coronet; a snout length 30% head length; two cheek spines and a dark brown coloration. In addition, molecular analysis showed all individuals of the new species clustering together suggesting a monophyletic lineage. This combined analysis supports the distinctness of H. casscsio sp. nov. as a new species, which is described herein.