OBITUARY Walter Munk, oceanographer extraordinaire, remembered p.176 GERMLINE EDITING NIH endorses moratorium and academies plan next steps p.175 MEDICINE Could artificial intelligence put the care back into health care? p.172 MATERIALS Beyond graphene-three steps to more 2D semiconductors p.169

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Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well as Helitron, Maverick, Kolobok, CMC, DIRS, P, I, L1, L2, and 5S (superfamily) were all positively correlated with fish genome size. Consistent with previous studies, our data suggested fish genomes to not always be dominated by DNA transposons; long interspersed nuclear elements are also prominent in many species. This study suggests CR1 distribution in fish genomes to be obviously regular, and provides new clues concerning important events in vertebrate evolution. Altogether, our results highlight the importance of TEs in the structure and evolution of fish genomes and suggest fish species diversity to parallel transposon content diversification.

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Transposable elements (TEs) are important for host gene regulation and genome evolution. Consensus sequences of TEs can assist investigators in accelerating studies on TE origins, amplification, functions and evolution, as well as comparative analyses and prediction of TEs in different species. In evolution, physiology, ecology and heredity research, fish are important models. However, to date, no comprehensive resource for TE consensus sequences exists for fish. Here, we collected genome-wide data and developed a novel database, FishTEDB, including 27 bony fishes, 1 cartilaginous fish, 1 lamprey and 1 lancelet. De novo , structure-based and homology-based approaches were combined to detect TEs. The database is open-source and user-friendly, and users can browse, search and download all data. FishTEDB also provides GetORF, BLAST and HMMER tools to analyze sequences. Database URL : http://www.fishtedb.org/

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

BackgroundThe mechanisms of kidney aging are not yet clear. Studies have shown that immunological inflammation is related to kidney aging. Toll-like receptors (TLRs) are one of the receptor types of the body's innate immune system. The function of the TLR system and the mechanisms by which it functions in renal aging remain unclear. In the present study, we, for the first time, systematically investigated the role of the TLR system and the inflammation responses activated by TLRs during kidney aging.MethodsWe used western blot and immunohistochemistry to systematically analyze the changes in the expression and activation of the endogenous TLR ligands HSP70 and HMGB1, the TLRs (TLR1–TLR11), their downstream signaling pathway molecules MyD88 and Phospho-IRF-3, and the NF-κB signaling pathway molecules Phospho-IKKβ, Phospho-IκBα (NF-κB inhibition factor α), NF-κBp65, and Phospho-NF-κBp65 (activated NF-κB p65) in the kidneys of 3 months old (youth group), 12 months old (middle age group), and 24 months old (elderly group) rats. We used RT-qPCR to detect the mRNA expression changes of the proinflammatory cytokines CCL3, CCL4, CCL5, CD80, TNF-α, and IL-12b in the rat renal tissues of the various age groups.ResultsWe found that during kidney aging, the HSP70 and HMGB1 expression levels were significantly increased, and the expression levels of TLR1, 2, 3, 4, 5, and 11 and their downstream signaling pathway molecules MyD88 and Phospho-IRF-3 were markedly elevated. Further studies have shown that in the aging kidneys, the expression levels of the NF-κB signaling pathway molecules Phospho-IKKβ, Phospho-IκBα, NF-κBp65, and Phospho-NF-κBp65 were obviously increased, and those of the proinflammatory cytokines CCL3, CCL4, CCL5, CD80, TNF-α, and IL-12b were significantly upregulated.ConclusionsThese results showed that the TLR system might play an important role during the kidney aging process maybe by activating the NF-κB signaling pathway and promoting the high expression of inflammation factors.