Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish

The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.</p

Genetic sources and diversity of the paddy field carp in the Pearl River basin inferred from two mitochondrial loci

Paddy field carp (PF-carp) is an economically important fish cocultured with rice in traditional agricultural systems. Several distinctive strains of PF-carp have been formed through years of artificial and cross breeding. There is a concern about the status of germplasm resources among PF-carp, since little is known about the genetic sources, diversity, or differentiation. In this study we collected 17 PF-carp populations covering Daotian carp (DTL), Ru Yuan No. 1 (RY), Jinbian carp (JBL), Shaijiang carp (SJL), and Wu carp (WL) along the Pearl River basin to explore their genetic sources and diversity using concatenated sequences of the mitochondrial cytochrome b gene and the D-Loop region. According to the haplotype network analyses, 1, 9, and 57 haplotypes originated from Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus, respectively, confirming that genetic introgression has occurred in Pearl River PF-carp populations and Cyprinus carpio carpio was the most common species for genetic origin. The results showed that RY exhibited the lowest level of nucleotide diversity (π = 0.0011) due to high-intensity breeding and was significantly differentiated from the other four strains. PF-carp strains in these remote traditional systems tended to experience artificial selection and a lack of farmer connection that gradually increased genetic differentiation among strains. Notably, three populations of JBL exhibited significant high-level differentiation, since they originated from mountainous areas hindering farmers from fry exchange. In contrast, no significant differentiation was uncovered in the WL populations, since this strain is the most popular cultured strain and has undergone artificial exchange of parents and fry in many cultured regions. This study helps us to understand the status of germplasm resources among PF-carp and to trace their genetic origin before being introduced for local cultivation

Mitochondrial DNA and Microsatellite Analyses Showed Panmixia between Temporal Samples in Endangered <i>Anguilla japonica</i> in the Pearl River Basin (China)

The Japanese eel (Anguilla japonica) is a commercially important species in East Asia, the abundance of which has rapidly decreased in recent decades. The fishery resource in the Pearl River basin has mainly deteriorated due to overexploitation and habitat degradation. Knowledge on its genetic status is indispensable for resource management. In this study, we explored the temporal genetic structure of A. japonica on the basis of the concatenated sequences of two mitochondrial fragments (mtDNA) and eight microsatellite markers. A total of nine temporal samples (N = 127) were collected during 2019 and 2021 from Jiangmen City, China, which is located in the Pearl River estuary. mtDNA sequence analysis showed a high level of haplotype diversity, and yielded 124 haplotypes with ranging from 9 to 19 in temporal samples. All microsatellite loci were polymorphic among each of the nine temporal samples, with 150 alleles identified across all samples. Pairwise FST values were low and nonsignificant according to both mtDNA and microsatellite markers. STRUCTURE analysis showed that all temporal samples were not clearly differentiated from each other. The yielded outcomes supported a panmictic pattern in different temporal A. japonica samples. Therefore, our results call for the management of A. japonica as a single unit and joint conservation strategy of the species, since overexploitation in any region will decrease its global resource

Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China

Abstract Background Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as “cryptic species”. Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. Results Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61–2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. Conclusions Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai–Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A

Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition

One of the most important events in vertebrate evolutionary history is the water-to-land transition, during which some morphological and physiological changes occurred in concert with the loss of specific genes in tetrapods. However, the molecular mechanisms underlying this transition have not been well explored. To explore vertebrate adaptation to different oxygen levels during the water-to-land transition, we performed comprehensive bioinformatics and experimental analysis aiming to investigate the NAMPT family in vertebrates. NAMPT, a rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, is critical for cell survival in a hypoxic environment, and a high level of NAMPT significantly augments oxidative stress in normoxic environments. Phylogenetic analysis showed that NAMPT duplicates arose from a second round whole-genome duplication event. NAMPTA existed in all classes of vertebrates, whereas NAMPTB was only found in fishes and not tetrapods. Asymmetric evolutionary rates and purifying selection were the main evolutionary forces involved. Although functional analysis identified several functionally divergent sites during NAMPT family evolution, invitro experimental data demonstrated that NAMPTA and NAMPTB were functionally conserved for NAMPT enzymatic function in the NAD+ salvage pathway. Insitu hybridization revealed broad NAMPTA and NAMPTB expression patterns, implying regulatory functions over a wide range of developmental processes. The morpholino-mediated knockdown data demonstrated that NAMPTA was more essential than NAMPTB for vertebrate embryo development. We propose that the retention of NAMPTB in water-breathing fishes and its loss in air-breathing tetrapods resulted from vertebrate adaptation to different oxygen levels during the water-to-land transition

Proximate compositions evaluation, histology and transcriptome analysis revealed the effects of formulated diets on muscle quality in Micropterus salmoides

With the gradually upgrade of formulated feeds, the largemouth bass Micropterus salmoides has been domesticated to adapt to formulated diets to reduce the use of bait fish and cut cost. However, whether the formulated diets influence the nutritional content and muscle quality of largemouth bass and related mechanisms remains unclear. In this study, we evaluated the effects of forage fish and formulated diets on growth performance, proximate compositions, muscle histology and fiber character. Largemouth bass with initial weights of 39.37 ± 1.37g and 39.45 ± 1.40g were fed with formulated diets and forage fish for 8 months, respectively. The results showed that formulated diets group (FDG) exhibited higher levels of protein content and free amino acids compared with forage fish group (FFG). Interestingly, the diameter of muscle fiber was larger in FDG than in FFG through microsection observation. A comparative analysis of transcriptome was constructed for muscle tissues of FDG and FFG, respectively. Compared with FFG, 2186 differentially expressed genes (DEGs) were identified in FDG, including 1915 upregulated genes and 271 downregulated genes. Gene ontology (GO) analyses revealed that DEGs were significantly enriched in GO terms regarding mitochondrial metabolism, muscle growth and development. KEGG enrichment indicated that DEGs were involved in the amino acid metabolism. Our results indicated that replacing forage fish with formulated diets affected the muscle quality and fiber character of largemouth bass, which could provide a basis for the regulation of nutrition and accurate selection for meat traits in largemouth bass

The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

In this study, the complete mitochondrial (mt) genome sequence of the South China deep-sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep-sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep-sea benthic environment; based on their large size, Bathynomus is included in the "supergiant group" of isopods. The mt genome of Bathynomus sp. is 14,965bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of Bathynomus sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., cob, trnT, nad5, and trnF) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in Bathynomus sp. Two tRNAs exhibit modified secondary structures: The TC arm is absent from trnQ, and trnC lacks the DHU. Within the class Malacostraca, trnC arm loss is only found in other isopods. Phylogenetic analysis revealed that Bathynomus sp. (Cymothoida) and Sphaeroma serratum (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of Bathynomus sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate]=0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep-sea environment. Overall, our results may provide useful information for understanding the evolution of deep-sea Isopoda species

Ancient duplications and functional divergence in the interferon regulatory factors of vertebrates provide insights into the evolution of vertebrate immune systems

Interferon regulatory factors (IRFs) were first discovered as transcription factors that regulate the transcription of human interferon (IFN)-beta. Increasing evidence shows that they might be important players involved in Adaptive immune system (AIS) evolution. Although numbers of IRFs have been identified in chordates, the evolutionary history and functional diversity of this gene family during the early evolution of vertebrates have remained obscure. Using IRF HMM profile and HMMER searches, we identified 148 IRFs in 11 vertebrates and 4 protochordates. For them, we reconstructed the phylogenetic relationships, determined the synteny conservation, investigated the profile of natural selection, and analyzed the expression patterns in four &quot;living fossil&quot; vertebrates: lamprey, elephant shark, coelacanth and bichir. The results from phylogeny and synteny analysis imply that vertebrate IRFs evolved from three predecessors, instead of four as suggested in a previous study, as results from an ancient duplication followed by special expansions and lost during the vertebrate evolution. The profile of natural selection and expression reveals functional dynamics during the process. Together, they suggest that the 2nd whole-genome duplication (2WGD) provided raw materials for innovation in the IRF family, and that the birth of type-I IFN might be an important factor inducing the establishment of IRF-mediated immune networks. As a member involved in the AIS evolution, IRF provide insights into the process and mechanism involved in the complexity and novelties of vertebrate immune systems. (C) 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.</p

Additional file 2: Table S2. of Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China

Information of primer pairs used in our study. Table S3 Summary statistics for the 13 loci used in this study. bp, length of locus in bases; n, number of sequences; ps, polymorphic sites; pis, parsimony informative sites; LNR, length of the longest non-recombining regions, h, number of haplotypes. Table S4 Nucleotide substitution models used in tree reconstruction. Pinvar, proportion of invariable sites; Gamma, gamma shape parameter. Table S5 Nucleotide substitution models for Cytb and three nuDNA loci used in extend Bayesian skyline plots. Table S6 Genetic diversity statistics for each population based on Cytb. n, individual numbers; Nh, haplotype numbers; ph, private haplotype within each population; Hap, Cytb haplotype; h, haplotype diversity; π, nucleotide diversity. Table S7 Genetic distance based on Cytb among the three lineages estimated by K2P distance (%). Figure S1 The entire distribution of Hemiculter leucisculus in global scale. The map derived from http://www.discoverlife.org . (DOCX 267 kb

Germline TP53 and MSH6 mutations implicated in sporadic triple-negative breast cancer (TNBC): a preliminary study

Abstract Background Germline BRCA1/2 prevalence is relatively low in sporadic triple-negative breast cancer (TNBC). We hypothesized that non-BRCA genes may also have significant germline contribution to Chinese sporadic TNBC, and the somatic mutational landscape of TNBC may vary between ethnic groups. We therefore conducted this study to investigate germline and somatic mutations in 43 cancer susceptibility genes in Chinese sporadic TNBC. Patients and methods Sixty-six Chinese sporadic TNBC patients were enrolled in this study. Germline and tumor DNA of each patient were subjected to capture-based next-generation sequencing using a 43-gene panel. Standard bioinformatic analysis and variant classification were performed to identify deleterious/likely deleterious germline mutations and somatic mutations. Mutational analysis was conducted to identify significantly mutated genes. Results Deleterious/likely deleterious germline mutations were identified in 27 (27/66, 40.9%) patients. Among the 27 patients, 9 (9/66, 13.6%) were TP53 carriers, 5 (5/66, 7.6%) were MSH6 carriers, and 5 (5/66, 7.6%) were BRCA1 carriers. Somatic mutations were identified in 64 (64/66, 97.0%) patients. TP53 somatic mutations occurred in most of the patients (45/66, 68.2%) and with highest mean allele frequency (28.1%), while NF1 and POLE were detected to have the highest mutation counts. Conclusions Our results supported our hypotheses and suggested great potentials of TP53 and MSH6 as novel candidates for TNBC predisposition genes. The high frequency of somatic NF1 and POLE mutations in this study showed possibilities for clinical benefits from androgen-blockade therapies and immunotherapies in Chinese TNBC patients. Our study indicated necessity of multi-gene testing for TNBC prevention and treatment