Mitochondrial COI sequences revealed shallow but significant divergences among Amphioctopus aegina (Octopoda, Octopodidae) populations in coastal waters of China

Amphioctopus aegina is an important fishery resource in the coastal waters of China. In the present study, the genetic diversity and population genetic structure among four populations of A. aegina throughout its distributional range in China were assessed using the mitochondrial cytochrome oxidase 1 (COI) sequences. The results revealed a generally low genetic diversity (Hd: 0.2842–0.6670; Pi: 0.0007–0.0015) in A. aegina populations. The neighbor-joining (NJ) phylogenetic tree and the haplotype networks, as well as the results of the molecular variance (AMOVA) analyses, indicated a shallow phylogeographic structure among the four populations. However, pairwise ΦST statistics and genetic distance analyses revealed significant (p<0.01) genetic differentiation among Qinzhou and the rest three populations of Zhanjiang, Huizhou, and Dongshan. The demographic history analyses indicated a population expansion in A. aegina, and the role of Leizhou peninsula isolation in shaping the population differentiation. These results would largely enhance our understanding of the genetic structure and hence promote the scientific management of A. aegina fishery resources in coastal waters of China

Characterization of the complete mitochondrial genome of Cottiusculus nihonkaiensis (Scorpaeniformes, Cottidae) and phylogenetic studies of Scorpaeniformes

In this study, the complete mitochondrial genome of Cottiusculus nihonkaiensis was presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 16,612 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNAs (12S and 16S), 22 transfer RNA genes (tRNA), one non-coding control region (CR) and one origin of replication on the light-strand. Overall base composition of the complete mitochondrial DNA was 26.4% A, 17.4% G, 31.5% C, 24.7% T. The phylogenetic tree suggested that C. nihonkaiensis shared the most recent common ancestor with Gymnocanthus herzensteini, Gymnocanthus intermedius and Gymnocanthus tricuspis

Identification, Characterization, and Expression Analysis of a FMRFamide-Like Peptide Gene in the Common Chinese Cuttlefish (Sepiella japonica)

The peptide FMRFamide is one of the well-known peptides involved in multiple physiological processes in the phylum Mollusca. In this study, a FMRFamide gene (GenBank accession No. KJ933411) was identified in a cuttlefish species called Sepiella japonica and was designated as SjFMRFamide. The total length of the SjFMRFamide sequence was found to be 1880 bp while the open reading frame contained 996 bp encoding a protein of 331 amino acid residues with a predicted isoelectric point (pI) and molecular weight (MW) of 9.18 and 38.8 kDa along with a 333 bp 5′-untranslated region (UTR) and 551 bp 3′-UTR. The deduced SjFMRFamide precursor protein contains one signal peptide and expresses four kinds FMRFamide-related peptides including a single copy of FLRFamide, ALSGDAFLRFamide, and FIRFamide and multiple copies of FMRFamide. Results of phylogenetic relation analysis strongly indicated that the sequence of this gene shares high identity with the genes of known FMRFamides. Spatial expression analysis indicated the highest mRNA expression of SjFMRFamide in the brain of male and female cuttlefishes among the eight tissues analyzed. An in situ hybridization assay of the brain indicated that SjFMRFamide was transcribed in several functional lobes, which suggests that it might be related to many physiological regulatory mechanisms. This is the first study describing FMRFamide in S. japonica and the results may contribute to future studies of neuropeptide evolution or may prove useful for the development of aquaculture methods for this cuttlefish species

The complete mitochondrial genome of Nerita albicilla (Neritimorpha: Neritidae)

The complete mitochondrial genome of Nerita albicilla was determined. The mitochondrial genome is 15,314 bp in length, comprising two ribosomal RNA (12S and 16S) genes, 13 protein-coding genes, and 22 transfer RNA genes. Of these 37 genes identified, seven protein-coding genes, and eight transfer RNA genes are encoded on the heavy strand and the other genes on the light strand. This gene order is consistent with the previously published mitochondrial genomes of the other neritid species. The length of 22 tRNAs ranges from 65 bp to 73 bp and the overall base composition is 14.9% of C, 20.7% of G, 34.0% of T, and 30.5% of A. The phylogenetic tree was constructed based on 13 protein-coding genes of N. albicilla and other 13 Archaeogastropoda species, Argopecten purpuratus as outgroup using the Neighbor-joining method, the tree showed that N. albicilla is most closely related to the Nerita yoldii. We believe that this result will further supplement the genome information in mitochondria of the family Neritidae and facilitate the study on population genetic

Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby <i>Taenioides</i> sp. (Teleost: Amblyopinae)

Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts

Insulin-like Peptide Receptor (ILPR) in the Cuttlefish Sepiella japonica: Characterization, Expression, and Regulation of Reproduction

Insulin-like peptide receptor (ILPR) can effectively regulate ovarian development in invertebrates, but its effect in cuttlefish has not been reported. We isolated and characterized a ILPR gene from Sepiella japonica, referred to as SjILPR. This gene displayed significant homologies to Octopus bimaculoides ILPR, and contained all typical features of insulin receptors and tyrosine kinase domain structure. SjILPR is expressed in all detected tissues, with the highest expression in the ovary. During ovarian development stages, its expression levels in the ovary, pancreas, and liver were correlated to the female reproductive cycle. After the silencing of SjILPR in vivo, comparative transcriptome analysis identified 4314 differentially expressed genes (DEGs) in the injected group, including 2586 down-regulated genes and 1728 up-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that 832 DEGs were assigned to 222 pathways, many pathways of which were related to gonadal development. Four down-regulated genes relevant to ovarian development (Vitellogenin 1, Vitellogenin 2, Cathepsin L1-like, and Follistatin) were selected to confirm the accuracy of RNA-seq data by qRT-PCR. These results showed that SjILPR might regulate ovarian development to control reproduction by affecting the expression of the relevant genes in female S. japonica

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca)

Abstract The eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer. The scaffold N50 is 41.67 Mbp, and 23 chromosomes were assembled using Hi-C technology with a mounting rate of 99.96%. Genome annotation indicates that 53.29% of the genome is repetitive sequences, and 22,999 protein-coding genes are predicted, of which 21,855 have functional annotations. The chromosome-level genome of O. rebecca will not only provide important genomic resources for comparative genomic studies of gobies, but also expand our knowledge of the genetic origin of their unique features fascinating researchers for decades

De novo assembly and comparison of the ovarian transcriptomes of the common Chinese cuttlefish (Sepiella japonica) with different gonadal development

The common Chinese cuttlefish (Sepiella japonica) has been considered one of the most economically important marine Cephalopod species in East Asia and seed breeding technology has been established for massive aquaculture and stock enhancement. In the present study, we used Illumina HiSeq2000 to sequence, assemble and annotate the transcriptome of the ovary tissues of S. japonica for the first time. A total of 53,116,650 and 53,446,640 reads were obtained from the immature and matured ovaries, respectively (NCBI SRA database SRX1409472 and SRX1409473), and 70,039 contigs (N50 = 1443 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 47,288 contigs show differential expression profile and 793 contigs are highly expressed in the immature ovary, while 38 contigs are highly expressed in the mature ovary with FPKM >100. We hope that the ovarian transcriptome and those stage-enriched transcripts of S. japonica can provide some insight into the understanding of genome-wide transcriptome profile of cuttlefish gonad tissue and give useful information in cuttlefish gonad development. Keywords: Cuttlefish, Gonad development, Transcriptom