ABSTRACT
In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.
Subject(s)
Cyclooxygenase 1/genetics , Perciformes/genetics , Animals , China , DNA Barcoding, Taxonomic/methods , DNA, Mitochondrial/genetics , Gene Flow , Genetic Drift , Genetic Variation/genetics , Genetics, Population , Genome, Mitochondrial/genetics , Haplotypes , Mitochondria/genetics , Phenotype , Philippines , Phylogeny , Phylogeography , Sequence Analysis, DNA/methodsABSTRACT
WD40 repeat (WDR) domains are protein interaction scaffolds that represent one of the largest protein families in human, and a first WDR inhibitor-an allosteric antagonist of polycomb repressive complex 2-just entered the clinic. A systematic analysis of the CORUM database of protein complexes shows that WDR is the most represented domain in transcriptional regulation and one of the most prevalent in the ubiquitin proteasome system, two pathways of high relevance to drug discovery. Parsing the literature and the vulnerability of cancer cell lines to CRISPR knockout indicates that WDR proteins are targets of interest in oncology and other disease areas. A quantitative analysis of WDR structures reveals that druggable binding pockets can be found on multiple surfaces of these multifaceted protein interaction platforms. These data support the development of chemical probes to further interrogate WDR proteins as an emerging therapeutic target class.
Subject(s)
Antineoplastic Agents/chemistry , Neoplasms/drug therapy , Polycomb Repressive Complex 2/genetics , Protein Domains/genetics , WD40 Repeats/genetics , Animals , Antineoplastic Agents/therapeutic use , Drug Discovery , Gene Expression Regulation/drug effects , Gene Knockout Techniques , Humans , Neoplasms/genetics , Polycomb Repressive Complex 2/antagonists & inhibitors , Proteasome Endopeptidase Complex/drug effects , Proteasome Endopeptidase Complex/genetics , Protein Binding/drug effects , Protein Conformation/drug effects , Protein Domains/drug effects , Ubiquitin/genetics , WD40 Repeats/drug effectsABSTRACT
In this study, morphology observation and illumina sequencing were performed on two different coloration skins of crimson snapper (Lutjanus erythropterus), the black zone and the red zone. Three types of chromatophores, melanophores, iridophores and xanthophores, were organized in the skins. The main differences between the two colorations were in the amount and distribution of the three chromatophores. After comparing the two transcriptomes, 9200 unigenes with significantly different expressions (ratio change ≥ 2 and q-value ≤ 0.05) were found, of which 5972 were up-regulated in black skin and 3228 were up-regulated in red skin. Through the function annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially transcribed genes, we excavated a number of uncharacterized candidate pigment genes as well as found the conserved genes affecting pigmentation in crimson snapper. The patterns of expression of 14 pigment genes were confirmed by the Quantitative real-time PCR analysis between the two color skins. Overall, this study shows a global survey of the morphological characters and transcriptome analysis of the different coloration skins in crimson snapper, and provides valuable cellular and genetic information to uncover the mechanism of the formation of pigment patterns in snappers.
Subject(s)
Fishes/anatomy & histology , Fishes/genetics , Genetic Association Studies , Skin Pigmentation/genetics , Transcriptome , Animals , Computational Biology/methods , Gene Expression Regulation , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation , Reproducibility of ResultsABSTRACT
We have determined 222 DNA barcode sequences of 95 fish species in 86 genera of 69 families from 15 orders. Fish were captured by trawl from two important fisheries regions in South China Sea: Spratly Islands (Nansha Islands) and Beibu Gulf. The average genetic distances between intraspecies were about 60-fold less than those of interspecies within different taxonomic levels, as Kimura two-parameter genetic distances averaged 17.260% among congeners, 20.097% among genus, and only 0.317% for intraspecific individuals. There were a few examples of deep divergence within species, suggesting the need for further taxonomic work, and a few examples of closely allied species, perhaps reflecting introgressive hybridization. The results provide further evidence for the reliability and accessibility of DNA barcodes for marine fish identification, and also highlight their effectiveness for flagging cases needing taxonomical reexamination.
Subject(s)
DNA Barcoding, Taxonomic , DNA, Mitochondrial/genetics , Fishes/genetics , Animals , Fishes/classification , Sequence Analysis, DNA , Species SpecificityABSTRACT
The (CA)n DNA sequences in Lutjanus russelli were isolated through PCR arrays, and the characteristics of the microsatellite were analyzed. DNA was extracted from a sample of Lutjanus russelli, and digested with Hae+Dra. The fragments were ligated to pUCm-T vector and transferred into DH5alpha to construct a genomic library. The positive clones were isolated with universal M13 reverse and forward primers, M13 forward primer and the simple sequence repeats (SSRs) probes (CA)15, M13 reverse primer and (CA)15. After twice isolation, 121 positive clones, whose PCR products with M13 forward primer and probes (CA)15 or M13 reverse primer and (CA)15 were smaller than those with universal M13 reverse and forward primers probably contained microsatellites, were obtained. Then, 53 (CA)n(n> or =7) microsatellites were obtained by sequencing. The repeat length mainly distributed in 7-15(80.77%). Besides (CA)n repeats, other repeat motifs, such as An, (CAC)n and (AACA)n, were also obtained. Scorable and constant amplification of DNA fragments were observed with 48 pairs of SSR primers designed from the flank sequences. This research makes a positive contribution to explorating genomes of Lutjanus russelli, offers genetic tools to examine the genetic variations and constructs genetic linkage map.
