The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using ...short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and ...physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.
RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, ...the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.
Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation ...technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system.
The direct biological effects of radiofrequency electromagnetic radiation (RF-EMR) from wireless communication equipment on the testes are still unclear. Our previous study proved that long-term ...exposure to 2605 MHz RF-EMR gradually damage spermatogenesis and resulted in time-dependent reproductive toxicity by directly disrupting blood-testis barrier circulation. Although short-term exposure did not cause readily observable damage to fertility, whether it caused specific biological effects and how these effects contributed to the time-dependent reproductive toxicity of RF-EMR were currently unknown. Studies on this issue are important for elucidating the time-dependent reproductive toxicity of RF-EMR. The present study established a 2605 MHz RF-EMR (SAR=1.05 W/Kg) scrotal exposure model with rats and extracted primary Sertoli cells for exposure to investigate the direct biological effects of short-term RF-EMR exposure on the testis. The results showed that short-term RF-EMR exposure did not decrease sperm quality and spermatogenesis, but it increased the levels of testicular testosterone (T) and zinc transporter 9 (ZIP9) in Sertoli cells of rats. In vitro, 2605 MHz RF-EMR exposure did not increase the apoptosis rate of Sertoli cells, but it increased the apoptosis rate and MDA of Sertoli cells exposed to H2O2. T reversed these changes and increased ZIP9 level in Sertoli cells, whereas inhibiting ZIP9 expression significantly suppressed these T-mediated protective effects. Moreover, T increased the levels of phosphorylated inositol-requiring enzyme 1 (P-IRE1), phosphorylated protein kinase R (PKR)-like endoplasmic reticulum kinase (P-PERK), phosphorylated eukaryotic initiation factor 2a (P-eIF2a) and phosphorylated activating transcription factor 6 (P-ATF6) in Sertoli cells, and these effects were reversed by ZIP9 inhibition. With prolonged exposure time, testicular ZIP9 was gradually downregulated, and testicular MDA increased. ZIP9 level was negatively correlated with MDA level in the testes of exposed rats. Thus, although short-term exposure to 2605 MHz RF-EMR (SAR=1.05 W/kg) did not significantly disturb spermatogenesis, it suppressed the ability of Sertoli cells to resist external insults, which was rescued by enhancing the ZIP9-centered androgen pathway in the short term. Increasing the unfolded protein response might be an important downstream mechanism involved. These results promote a better understanding of the time-dependent reproductive toxicity of 2605 MHz RF-EMR.
Display omitted
•RF-EMR suppress ability of sertoli cells to resist external insults.•Testosterone reversed reduction of resistence ability of sertoli cells exposed to RF-EMR.•Testosterone exerted its compensatory effect via ZIP9 in sertoli cells.•Unfolding protein response involved in testosterone-ZIP9 mediated compensatory effects.•Testosterone-ZIP9 mediated effect might gradually weared off with exposure time prolonged.
The naked mole rat (Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal. Although it is the size of a mouse, its maximum lifespan exceeds 30 years, making ...this animal the longest-living rodent. Naked mole rats show negligible senescence, no age-related increase in mortality, and high fecundity until death. In addition to delayed ageing, they are resistant to both spontaneous cancer and experimentally induced tumorigenesis. Naked mole rats pose a challenge to the theories that link ageing, cancer and redox homeostasis. Although characterized by significant oxidative stress, the naked mole rat proteome does not show age-related susceptibility to oxidative damage or increased ubiquitination. Naked mole rats naturally reside in large colonies with a single breeding female, the 'queen', who suppresses the sexual maturity of her subordinates. They also live in full darkness, at low oxygen and high carbon dioxide concentrations, and are unable to sustain thermogenesis nor feel certain types of pain. Here we report the sequencing and analysis of the naked mole rat genome, which reveals unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness and insensitivity to low oxygen, and altered visual function, circadian rythms and taste sensing. This information provides insights into the naked mole rat's exceptional longevity and ability to live in hostile conditions, in the dark and at low oxygen. The extreme traits of the naked mole rat, together with the reported genome and transcriptome information, offer opportunities for understanding ageing and advancing other areas of biological and biomedical research.
Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now ...offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.
Here we show, using new RNA-sequencing (RNA-seq) data, that NMR cells are considerably more resistant to transcriptomic changes induced by oncogenic HRAS than mouse, blind mole-rat and human cells, ...indicating that suppressed RAS signalling is an anti-cancer mechanism in NMR cells that can be interrupted by high expression of HRAS(G12V), rendering NMR cells susceptible to oncogenic transformation. Consistently, multiple Gene Ontology (GO) terms that were significantly changed by SV40LT and HRAS(G12V) in mouse cells, such as cell cycle, cell division and mitotic nuclear division, were not altered or altered to a much lower extent in NMR cells (Extended Data Fig. 2a). In mice, partial inactivation of PI3K or AKT enhances metabolic function and extends lifespan14,15. ...the natural suppression of the PI3K-AKT pathway in NMR probably contributes not only to cancer resistance, but also to a long lifespan. Acknowledgements This study is supported by US National Institutes of Health grant AG047200 to V.G. and A.S., and Natural Science Foundation of China grant 81672818, Science Technology and Innovation Committee of Shenzhen Municipality grant JCYJ20160331190123578 and Guangzhou Science and Technology Program key project 201604020005 to X.F. Author contributions The list of authors is different from the original study, because new data were included in this Reply.
Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced ...aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.
Display omitted
•Genome of the Damaraland mole rat and improved genome assembly of the naked mole rat•Transcriptomes of subterranean rodents and comparative genome analyses•Common adaptations for subterranean life: arginase, globins, and Na(V)1.7•Unique NMR adaptations: UCP1, 28S rRNA processing, melatonin, actin, and pain systems
Subterranean rodents thrive in harsh underground environments. Many are long-lived and hold promise as animal models of successful aging and sustained good health. Here, Fang et al. sequence the genome of the Damaraland mole rat (Fukomys damarensis), improve the genome assembly of the naked mole rat (Heterocephalus glaber), and compare the transcriptomes of subterranean rodents. Comparative analyses reveal candidate molecular adaptations for subterranean life and longevity, as well as traits unique to the naked mole rat, including unusual thermogenesis and novel processing of 28S rRNA.
The primary objective of this study was to realize the large-scale discovery of conotoxin sequences from different organs (including the venom duct, venom bulb and salivary gland) of the vermivorous ...Oak cone snail,
. Using high-throughput transcriptome sequencing, we identified 133 putative conotoxins that belong to 34 known superfamilies, of which nine were previously reported while the remaining 124 were novel conotoxins, with 17 in new and unassigned conotoxin groups. A-, O₁-, M-, and I₂- superfamilies were the most abundant, and the cysteine frameworks XIII and VIII were observed for the first time in the A- and I₂-superfamilies. The transcriptome data from the venom duct, venom bulb and salivary gland showed considerable inter-organizational variations. Each organ had many exclusive conotoxins, and only seven of all the inferred mature peptides were common in the three organs. As expected, most of the identified conotoxins were synthesized in the venom duct at relatively high levels; however, a number of conotoxins were also identified in the venom bulb and the salivary gland with very low transcription levels. Therefore, various organs have different conotoxins with high diversity, suggesting greater contributions from several organs to the high-throughput discovery of new conotoxins for future drug development.
PDF
