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Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1 / zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes. [ABSTRACT FROM AUTHOR]

Using Ion Torrent next-generation sequencing (NGS) technology, we sequenced the complete mitochondrial genome (mitogenome) of black and reddish morphs of the coral troutPlectropomus leopardus. High-throughput sequencing generated a total of 958,614 sequence reads covering 164.80 Mb of two mitogenomes with a coverage of 4800X. Thirty-seven mitochondrial genes and gene order ofP. leoparduswas quite similar to that of other teleostean fishes. Most genes were either abutted or overlapped, and all the protein-coding genes began with an ATG start codon except for COX1 and ATP6. The number of stop codon was different for the black and reddishP. leopardus. Comparisons between the mitochondrial sequences of the two morphs revealed a total of 74 variable sites and one indel. Nucleotide diversity across protein-coding gene varied from 0.0006 (16s rRNA) to 0.0070 (Cytochrome b). As expected, the highest level of nucleotide diversity (0.0291) was detected in the control region. Our results demonstrate the NGS technology based on Ion torrent platform can be used to assemble the mitogenome of fish species. [ABSTRACT FROM AUTHOR]

The study determined the first complete mitochondrial genome (mitogenome) of the polychaete, Marphysa tamurai. A total of 21,346 reads were generated by Illumina HiSeq2500 platform with an average depth of 175.97×. The mitogenome of M. tamurai was 15,163 bp in size and consists of 38 typical genes, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 D-loop region. All the 38 genes were encoded on the heavy strand whose nucleotide compositions were 30.23% of A, 30.40% of T, 12.59% of G, 26.78% of C, showing a lower content of G + C (39.37%). Phylogenetic analysis showed that M. tamurai had a closer relationship with Marphysa sanguinea of Nereididae. [ABSTRACT FROM AUTHOR]

The mitochondrial genome of skipjack tuna,Katsuwonus pelamis, was obtained by using HiSeq next-generation sequencing technique. The circular mitogenome is 16,515 bp in length, with the gene number and arrangement being similar to those observed in other teleost fish. Overall base composition is A 28.49%, T 24.58%, C 30.27% and G 16.66%, respectively. Among 13 protein-coding genes, seven of which share the complete stop codon TAA while others terminate with TA or T, all these genes use ATG as start codon except forCOI. [ABSTRACT FROM AUTHOR]

The present study represents the first report on the complete mitochondrial genome (mitogenome) of the kawakawa tunaEuthynnus affinis. Illumina next-generation sequencing generated a total of 38,428 reads with an average sequencing depth of 232.83×. The mitogenome ofE. affiniswas 16,513 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a 849 bp control region, as found in other typical teleosts. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand, whose nucleotide composition is 28.11% A, 24.77% T, 17.16% G and 29.96% C. All the protein-coding genes shared the start codon ATG except for COXI gene (start with GTG), and appeared to be terminated with four types of stop codons including two complete codons (TAA and TAG) and two incomplete codons (T and TA). [ABSTRACT FROM PUBLISHER]

Recently, the next-generation sequencing (NGS) technology has become a powerful tool for sequencing the teleost mitochondrial genome (mitogenome). Here, we used this technology to determine the mitogenome of the yellowfin tuna (Thunnus albacares). A total of 41,378 reads were generated by Illumina platform with an average depth of 250×. The mitogenome (16,528 bp in length) contained 37 mitochondrial genes with the similar gene order to other typical teleosts. These mitochondrial genes were encoded on the heavy strand except for ND6 and eight tRNA genes. The result of phylogenetic analysis supported two distinct clades dividing the genusThunnus, but the tuna species of these two genetic clades were different from that of two recognized subgenus based on anatomical characters and geographical distribution. Our results might help to understand the structure, function, and evolutionary history of the yellowfin tuna mitogenome and also provide valuable new insights for phylogenetic affinity of tuna species. [ABSTRACT FROM PUBLISHER]

Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia. [ABSTRACT FROM AUTHOR]

Abstract: Due to high level of fishing, many marine fish species are in danger of becoming extinct. The large yellow croaker, Larimichthys crocea, was once an important commercial marine species in China. At present, this croaker is seldom captured in the wild. In this work, mitochondrial DNA data was obtained from five populations of the yellow croaker from the Yellow Sea and the East China Sea to investigate their genetic divergence and demographic history. Results of phylogenetic analysis suggest two genetic lineages for this croaker, although the divergence was relatively shallow. This might reflect the effects of glacial isolation on population structure. Furthermore, our Bayesian based approach showed that the effective population size for both genetic lineages experienced recent sharp decline. This study provides new insights into the genetic divergence and historical demography of this croaker. Strict measures must be taken to protect this species. [Copyright &y& Elsevier]