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The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. In artificial reproduction, they must be matched by one male and one female, whereas phenotype investigation indicated that there are no significant differences in appearance between males and females, which causes great difficulties in the mating during artificial reproduction. So, it is of great importance to establish artificial sex identification methods for the discus fish. The molecular mechanism of the sexual dimorphism of the discus fish was previously unknown. In this study, we constructed six cDNA libraries from three adult testes and three adult ovaries and performed RNA sequencing for identifying sex-biased candidate genes and microRNAs (miRNAs). A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries. A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries. Eight differentially expressed unigenes, seven differentially expressed miRNAs and one non-differential miRNA were validated by quantitative real-time polymerase chain reaction. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 miRNA–mRNA interaction pairs, and some of vital sex-related metabolic pathways were also identified. These results revealed these differentially expressed genes and miRNAs between ovary and testis might be involved in regulating gonadal development, sex determination, gametogenesis, and physiological function maintenance, and there are complex regulatory networks between genes and miRNAs. It can help us understand the molecular mechanism of the sexual dimorphism and obtain a high-efficiency sex identification method in the artificial reproduction process of the discus fish.

Discus fish (Symphysodon haraldi) is a well-known and economical ornamental fish. In this study, RNA-seq technology was applied to de novo assemble a gonad transcriptome of discus fish, and to discover sex-related genes. Assembly of these reads generated 115,050 transcripts, corresponding to 97,074 non-redundant unigenes, with an average length of 748 bp and N50 length of 1,531 bp. A total of 14,073 unique proteins were assigned at least one Gene Ontology (GO) category and 52,764 unigenes involved in 345 predicted KEGG metabolic pathways were identified. More importantly, about 12 candidate genes involved in sex determination were identified. Furthermore, 10,571 single nucleotide polymorphisms and 26,083 simple sequence repeats were also detected. The results of the present study can provide basic information for examining the potential roles of sex-related genes in the sex determination of discus fish.

Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multi-target sequencing technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in lymphoblastoid cell line. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.

Genome-wide association studies have identified more than 100 common single nucleotide polymorphisms (SNPs) that are associated with prostate cancer risk. However, the vast majority of these SNPs lie in noncoding regions of the genome. To test whether these risk SNPs regulate their target genes through long-range chromatin interactions, we applied capture-based 3C sequencing technology to investigate possible cis-interactions at ten prostate cancer risk loci in six cell lines. We identified significant physical interactions between risk regions and their potential target genes including CAPG at 2p11.2, C2orf43 at 2p24.1, RFX6 at 6q22.1, NFASC at 1q32.1, MYC at 8q24.1 and AGAP7P at 10q11.23. Most of the interaction peaks were co-localized to regions of active histone modification and transcription factor binding sites. Expression quantitative trait locus (eQTL) analysis showed suggestive eQTL signals at rs1446669, rs699664 and rs1078004 for CAPG (p C2orf43 (p = 2.25E-27), rs10993994 and rs4631830 for AGAP7P (p

In this study, the complete mitogenome sequence of the Symphysodon aequifasciatus has been sequenced by next-generation sequencing method. The mitogenome consists of 16 545 bp, including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of the fish is 28.8% for A, 30.1% for C, 15.0% for G, and 26.1% for T, suggesting a 99% identity to S. discus Heckel and a 98% identity to S. haraldi. It provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Symphysodon phylogeny.

In this study, the complete mitogenome sequence of Protomelas annectens Regan 1922 has been sequenced by next-generation sequencing method. The assembled mitogenome consisting of 16 583 bp, includes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and 1 control region. The overall base composition of P. annectens is 27.41% for A, 30.07% for C, 15.88% for G, 26.64% for T and shows 94% identity to threadfin cichlid, Petrochromis trewavasae. These data will provide useful molecular information for phylogenetic relationships within the family Cichlidae species.

In this study, the complete mitogenome sequence of the Symphysodon haraldi (Schultz, 1960) has been sequenced by next-generation sequencing method. The mitogenome consists of 16 543 bp, including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of the fish is 28.8% for A, 30.1% for C, 15.0% for G, and 26.1% for T, suggesting a 97% identity to S. discus Heckel. It provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Symphysodon phylogeny.

The Redhead cichlid (Vieja synspila) is an important aquarium fish and a useful phylogenetic organism of the Cichlidae family. In this study, we sequenced the mitochondrial genome of the Redhead cichlid for the first time. The mitogenome (16,543 bp) had the typical mitochondrial characteristics of other cichlid fish, including 13 protein-coding, 22 tRNA, two rRNA genes and one putative control region. This sequence will be helpful in studying the phylogenetic relationships between cichlid fish.

In this study, the mitochondrial genome of Melanotaenia praecox Weber and de Beaufort, 1922(Atheriniformes: Melanotaeniidae) was sequenced for the first time. The assembled mitogenome consisting of 16,536 bp, includes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and 1 putative control region. The overall base composition of M. praecox is 27.51% for A, 29.97% for C, 16.18% for G, 26.34% for T and shows 89% identities to Lake Kutubu Rainbowfish, Melanotaenia lacustris. These data would provide useful molecular information for phylogenetic relationships within the family Melanotaeniidae species.

In this study, the complete mitogenome sequence of the Mekong tiger fish Datnioides undecimradiatus (Perciformes: Datnioididae) has been sequenced by next-generation sequencing method. The assembled mitogenome consisting of 16,534 bp, includes 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of the Mekong tiger fish is 27.9% for A, 30.69% for C, 16.51% for G, 24.91% for T and show 77% identities to Anoplocapros lenticularis(GenBank accession no. NC011319.1). The complete mitogenome of the Mekong tiger fish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Datnioididae family.

In this study, the mitochondrial genome of Melanotaenia australis Castelnau, 1875 (Atheriniformes:Melanotaeniidae) was sequenced for the first time. The assembled mitogenome consisting of 16,530 bp, includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes and one putative control region. The overall base composition of M. australis is 27.79% for A, 29.66% for C, 15.90% for G, 26.66% for T and shows 92% identities to Lake Kutubu Rainbowfish, Melanotaenia lacustris. These data would provide useful molecular information for phylogenetic relationships within the family Melanotaeniidae species.

In this study, the complete mitogenome sequence of the big-belly seahorse, Hippocampus abdominalis (Lesson, 1827) (Syngnathiformes: Syngnathidae), has been sequenced by the next-generation sequencing method. The assembled mitogenome is 16 521 bp in length which includes 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs genes. The overall base composition of the seahorse is 31.1% for A, 23.6% for C, 16.0% for G, 29.3% for T and shows 87% identities similar to tiger tail seahorse, Hippocampus comes. The complete mitogenome of the big-belly seahorse provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for seahorse family.

In this study, the complete mitogenome sequence of the altum angelfish Pterophyllum altum (Pellegrin, 1903) has been sequenced by next-generation sequencing method. The mitogenome consists of 16 495 bp, including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of P. altum is 27.5% for A, 30.3% for C, 15.5% for G, and 26.7% for T, which shows a 92% identity to P. scalare. The complete mitogenome of the P. altum provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for the genus Pterophyllum phylogeny.

In this study, the mitochondrial genome of Melanotaenia boesemani (Allen & Cross, 1980 ) (Atheriniformes: Melanotaeniidae) was sequenced for the first time. The assembled mitogenome consisting of 16 493 bp, includes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and 1 putative control region. The overall base composition of M. boesemani is 27.88% for A, 29.92% for C, 15.74% for G, 26.47% for T and shows 96% identities to Lake Kutubu rainbowfish, Melanotaenia lacustris. These data would provide useful molecular information for phylogenetic relationships within the family Melanotaeniidae species.

In this study, the complete mitogenome sequence of the Parkinson's Rainbowfish, Melanotaenia parkinsoni (Atheriniformes: Melanotaeniidae) has been sequenced by next-generation sequencing method. The assembled mitogenome is 16 529 bp in length including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of Parkinson's Rainbowfish is 28.1% A, 29.7% C, 15.7% G, 26.5% T and shows 93% identity with Lake Kutubu Rainbowfish, M. lacustris. The complete mitogenome of the Parkinson's Rainbowfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Rainbowfish phylogeny.

The midas cichlid (Amphilophus citrinellus) is an important aquarium fish that has served as a model organism for studying sympatric speciation. In this study, we sequenced the complete mitochondrial genome of the midas cichlid. We report that the cichlid’s mitochondrial genome is a circular DNA double strand of 16,521 bp length, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall-base compositions of the H-strand are as follows: A, 28.56%; C, 30.69%; G, 15.11%; T, 25.64%. This study provides important genomic data to further the research of the genetic evolution of cichlids.