High-quality genome assembly and transcriptome of Ancherythroculter nigrocauda, an endemic Chinese cyprinid species.

Ancherythroculter nigrocauda is a cyprinid fish endemic of the upper reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. It is also a threatened species as a result of overfishing, dam construction and water pollution. In this study, a chromosome-level genome assembly of A. nigrocauda is reported and built using PacBio sequencing and the Hi-C technology. The 1.04-Gb sequenced genome of A. nigrocauda contained 2,403 contigs, with an N50 length of 3.12 Mb. Then, 1,297 contigs, which represented 54.0% of all contigs and 97.2% of the whole content of the genome nucleotide base, were assembled into 24 chromosomes. Combined with transcriptome data from 10 tissues, 27,042 (78.5%) genes were functionally annotated out of 34,414 predicted protein-coding genes. Interestingly, high expression of many positively selected genes and expanded gene families in the brain suggested that these genes might play important roles in brain development in A. nigrocauda. Finally, we found tissue-specific expression of 10,732 genes. Functional analyses showed that they were mainly composed of genes related to (a) environmental information processing, (b) the circulatory system, and (c) development, suggesting they might be important for adaptation to different environments and for development of A. nigrocauda. The high-quality genome obtained in this study not only provides a valuable genomic resource for future studies of A. nigrocauda populations and conservation, but is also an important resource for further functional genomics studies of fishes.

Successful Invasions of Short Internally Deleted Elements (SIDEs) and Its Partner CR1 in Lepidoptera Insects.

Although DNA transposons often generated internal deleted derivatives such as miniature inverted-repeat transposable elements, short internally deleted elements (SIDEs) derived from nonlong terminal-repeat retrotransposons are rare. Here, we found a novel SIDE, named Persaeus, that originated from the chicken repeat 1 (CR1) retrotransposon Zenon and it has been found widespread in Lepidoptera insects. Our findings suggested that Persaeus and the partner Zenon have experienced a transposition burst in their host genomes and the copy number of Persaeus and Zenon in assayed genomes are significantly correlated. Accordingly, the activity though age analysis indicated that the replication wave of Persaeus coincided with that of Zenon. Phylogenetic analyses suggested that Persaeus may have evolved at least four times independently, and that it has been vertically transferred into its host genomes. Together, our results provide new insights into the evolution dynamics of SIDEs and its partner non-LTRs.

Evolutionary dynamics of transposable elements during silkworm domestication.

Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.

Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes.

BACKGROUND: Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life. RESULTS: Herein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev-Mirage-CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts' autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation. CONCLUSIONS: Our discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses' diverse mobilome.

Self-Healing of Polymer in Acidic Water toward Strength Restoration through the Synergistic Effect of Hydrophilic and Hydrophobic Interactions.

To improve reliability, durability, and reworkability of bulk polymers utilized in ubiquitous acidic water, the authors develop a novel hyperbranched polymer capable of self-healing and recycling in a low-pH aqueous environment. The hyperbranched polymer has many hydrophilic and hydrophobic terminal groups. When it is damaged in acidic water, the hydrophilic groups are protonated, forming hydrogen bonds, and closing the crack. Meanwhile, hydrophobic interactions of hydrophobic groups are gradually established across the interface because of the intimate contact of the cracked surface, further reinforcing the rebonded portion. The amphiphilic structure proves to meet both the thermodynamic and kinetic requirements for autonomous rehabilitation. As a result, the unfavored water, which used to impede adhesion between hydrophobic polymeric materials, turns into a positive aid to crack healing. The mechanism involved is carefully analyzed and verified in terms of micro- and macroscopic techniques. The proposed operating environment-oriented design of the stimulus-responsive macromolecule may help to broaden the family of underwater self-healing polymers and their application scope.

[Utilization of Copper (â ¡) Wastewater for Enhancing the Treatment of Chromium (â ¥) Wastewater in Microbial Fuel Cells].

The effect of copper (Ⅱ) wastewater addition on the treatment of chromium (Ⅵ) wastewater in dual-chamber microbial fuel cells (MFCs) was investigated for different Cr(Ⅵ)/Cu(Ⅱ) concentration ratios (2:1, 1:1, 1:2, 1:4) and external resistances (10, 500, 1000, 2000 Ω). The results demonstrated that the addition of Cu(Ⅱ) and Cr(Ⅵ) into the cathode chamber of MFCs could enhance the Cr(Ⅵ) removal efficiency. The Cr(Ⅵ) removal efficiency increased with the increase in the Cr(Ⅵ)/Cu(Ⅱ) concentration ratio. The Cu(Ⅱ) on the Cr(Ⅵ) removal efficiencies increased with the decrease of external resistance. The highest Cr(Ⅵ) removal efficiency achieved was 91.00% in MFC at the Cr(Ⅵ)/Cu(Ⅱ) concentration ratio of 1:4 and external resistance of 10 Ω, which was 132.57% higher than the MFC with Cr(Ⅵ) only (39.13%). The scanning electron microscopy with coupled energy dispersive spectroscopy (SEM-EDS) and X-ray photoelectron spectroscopy (XPS) analyses of the cathode electrode at the end of the experiments indicated that Cr(Ⅵ) reduced to non-conductive Cr(Ⅲ) deposits (Cr2O3) on the cathode electrode, resulting in cathode deactivation which blocked the electron transfer. However, the addition of Cu(Ⅱ) could improve the electrical conductivity of the cathode due to its conductive reduzates (copper and Cu2O) on the cathode which could reduce the cathode deactivation and subsequently enhance the Cr(Ⅵ) removal efficiency.

Horizontal transfer of a novel Helentron in insects.

Helentrons represent a novel subtype of Helitrons. However, the evolutionary history of Helentrons in organisms is not clearly understood. In this study, we performed structure and autonomous partner analyses, which revealed that bm_455, a TE obtained from the Bombyx mori TE database, BmTEdb, was a member of Helentrons but not a long-terminal repeat (LTR) retrotransposon. Further analyses showed that bm_455 was also present in a wide range of insects including lepidopterans, coleopterans and hymenopterans using a homology-based search strategy. Several lines of evidence (high sequence identity, discontinuous distribution and lack of intense purifying selection) suggested that these elements could have been transferred into these species in part by horizontal transfers (HTs). Because Helentrons can capture host gene fragments, HTs of Helentrons might have a huge impact on their host genome evolution.

TRT, a Vertebrate and Protozoan Tc1-Like Transposon: Current Activity and Horizontal Transfer.

We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1 The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.

A seawater triggered dynamic coordinate bond and its application for underwater self-healing and reclaiming of lipophilic polymer.

In this work, water triggered dynamic catechol-Fe3+ coordinate bonds are revealed and studied at atomic, molecular and macroscopic levels using Mössbauer spectroscopy, rheological analysis, etc. DOPA-iron complexation is found to be dynamic in the presence of water, and this dynamic manner is immobilized after removing water. Accordingly, a water saturated lipophilic polymer containing catechol-Fe3+ crosslinks, rather than the dry version, exhibits dynamic coordination-dissociation behavior. In addition, a migration of iron proves to be enabled in the catechol-Fe3+ crosslinked polymer immersed in seawater. Rearrangement of the dynamic catechol-Fe3+ coordinate bonds among different molecules is thus favored. Based on these results, we develop a bulk lipophilic polymer solid capable of repeated autonomic recovery of strength in seawater without manual intervention. When the polymer is damaged in seawater, reshuffling of the mobile hyperbranched polymer networks across the crack interface, owing to the dynamic catechol-Fe3+ crosslinkages activated by the alkaline circumstances, rebinds the damaged site. By taking advantage of the same mechanism, the polymer can be remolded with the help of seawater and this recycled polymer is still self-healable in seawater. Unlike in the case of conventional polymers where water would shield macromolecules from interacting, here, seawater is a necessary environmental assistant for the material interaction to take effect. The outcomes are beneficial for deepening the understanding of coordinate bonds, and the development of robust underwater self-healing lipophilic polymers.