Genome-wide assessment of oxidatively generated DNA damage

Abstract

In the tide of science nouveau after the completion of genome projects of various species, there appeared a movement to understand an organism as a system rather than the sum of cells directed for certain functions. With the advent and spread of microarray techniques, systematic and comprehensive genome-wide approaches have become reasonably possible and more required on the investigation of DNA damage and the subsequent repair. The immunoprecipitation-based technique combined with high-density microarrays or next-generation sequencing is one of the promising methods to provide access to such novel research strategies. Oxygen is necessary for most of the life on earth for electron transport. However, reactive oxygen species are inevitably generated, giving rise to steady-state levels of DNA damage in the genome, that may cause mutations leading to cancer, ageing and degenerative diseases. Previously, we showed that there are many factors involved in the genomic distribution of oxidatively generated DNA damage including chromosome territory, and proposed this sort of research area as oxygenomics. Recently, RNA is also recognized as a target of this kind of modification.     

Structural heterozygosity in Scilla hyacinthoides L. and Scilla amoena L. (Liliaceae). Karyological analysis

Abstract

A karyological analysis carried out in Scilla hyacinthoides L. and Scilla amoena L. on material collected in the Botanical Garden of Cagliari (Sardinia), has shown the presence of heterozygous karyotypes in the two species. The chromosome number of S. hyacinthoides was found to be 2n = 20, while the chromosome number of S. amoena was 2n = 12, in accordance with the data found in the literature. Both the observed karyotypes show clear structural alterations, especially evident in one pair of clearly heteromorphic chromosomes. The analysis of the karyotypes seem to exclude a hybrid origin of the material examined and it is probable that such karyotypes may be the result of various structural re-arrangements, still evolving and aiming at a cytogenetic stabilization of the genus Scilla.     

Genomic imprinting and evolution of insect societies

Reproductive division of labor is a hallmark of social insect societies where individuals follow different developmental pathways resulting in distinct morphological castes. There has been a long controversy over the factors determining caste fate of individuals in social insects. Increasing evidence in the last two decades for heritable influences on division of labor put an end to the assumption that social insect broods are fully totipotent and environmental factors alone determine castes. Nevertheless, the genes that underlie hereditary effects on division of labor have not been identified in any social insects. Studies investigating the hereditary effects on caste determination might have overlooked non-genetic inheritance, while transmission to offspring of factors other than DNA sequences including epigenetic states can also affect offspring phenotype. Genomic imprinting is one of the most informative paradigms for understanding the consequences of interactions between the genome and the epigenome. Recent studies of genomic imprinting show that genes can be differentially marked in egg and sperm and inheritance of these epigenetic marks cause genes to be expressed in a parental-origin-specific manner in the offspring. By reviewing both the eusocial Hymenoptera and termites, I highlight the current theoretical and empirical evidence for genomic imprinting in eusocial insects and discuss how genomic imprinting acts in caste determination and social behavior and challenges for future studies. I also introduce the new idea that genomic imprinting plays an essential role in the origin of eusociality.     

Sequencing two Tyr::CreERT2 transgenic mouse lines

The Cre/loxP system is a powerful tool that has allowed the study of the effects of specific genes of interest in various biological settings. The Tyr::CreER^T2 system allows for the targeted expression and activity of the Cre enzyme in the melanocyte lineage following treatment with tamoxifen, thus providing spatial and temporal control of the expression of specific target genes. Two independent transgenic mouse models, each containing a Tyr::CreER^T2 transgene, have been generated and are widely used to study melanocyte transformation. In this study, we performed whole genome sequencing (WGS) on genomic DNA from the two Tyr::CreER^T2 mouse models and identified their sites of integration in the C57BL/6 genome. Based on these results, we designed PCR primers to accurately, and efficiently, genotype transgenic mice. Finally, we discussed some of the advantages of each transgenic mouse model.     

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae,Lepidoptera)

Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first high‐quality A. pernyi genome from a single male individual. The genome is 720.67 Mb long with 49 chromosomes and a 13.77‐Mb scaffold N50. Approximately 441.75 Mb, accounting for 60.74% of the genome, was identified as repeats. The genome comprises 21,431 protein‐coding genes, 85.22% of which were functionally annotated. Comparative genomics analysis suggested that A. pernyi diverged from its common ancestor with A. yamamai ~30.3 million years ago, and that chromosome fission contributed to the increased chromosome number. The genome assembled in this work will not only facilitate future research on A. pernyi and related species but also help to progress comparative genomics analyses in Lepidoptera.     

Chromosome‐level genome assembly of an important pine defoliator,Dendrolimus punctatus (Lepidoptera; Lasiocampidae)

Dendrolimus spp. are important destructive pests of conifer forests, and Dendrolimus punctatus Walker (Lepidoptera; Lasiocampidae) is the most widely distributed Dendrolimus species. During periodic outbreaks, this species is said to make “fire without smoke” because large areas of pine forest can be quickly and heavily damaged. Yet, little is known about the molecular mechanisms that underlie the unique ecological characteristics of this forest insect. Here, we combined Pacific Biosciences (PacBio) RSII single‐molecule long reads and high‐throughput chromosome conformation capture (Hi‐C) genomics‐linked reads to produce a high‐quality, chromosome‐level reference genome for D. punctatus. The final assembly was 614 Mb with contig and scaffold N50 values of 1.39 and 22.15 Mb, respectively, and 96.96% of the contigs anchored onto 30 chromosomes. Based on the prediction, this genome contained 17,593 protein‐coding genes and 56.16% repetitive sequences. Phylogenetic analyses indicated that D. punctatus diverged from the common ancestor of Hyphantria cunea, Spodoptera litura and Thaumetopoea pityocampa ~ 108.91 million years ago. Many gene families that were expanded in the D. punctatus genome were significantly enriched for the xenobiotic biodegradation system, especially the cytochrome P450 gene family. This high‐quality, chromosome‐level reference genome will be a valuable resource for understanding mechanisms of D. punctatus outbreak and host resistance adaption. Because this is the first Lasiocampidae insect genome to be sequenced, it also will serve as a reference for further comparative genomics.     

Molecularly imprinted polymers—A closer look at the control polymer used in determining the imprinting effect: A mini review

Molecular recognition displayed by naturally occurring receptors has continued to inspire new innovations aimed at developing systems that can mimic this natural phenomenon. Since 1930s, a technology called molecular imprinting for producing biomimetic receptors has been in place. In this technology, tailor made binding sites that selectively bind a given target analyte (also called template) are incorporated in a polymer matrix by polymerizing functional monomers and cross‐linking monomers around a target analyte followed by removal of the analyte to leave behind cavities specific to the analyte. The success of the imprinting process is defined by two main figures of merit, that is, the imprinting factor, and selectivity, which are determined by comparing the amount of target analyte or structural analogue bound by the molecularly imprinted polymer (MIP) and the nonimprinted polymer (NIP). NIP is a control synthesized alongside the MIP but in the absence of the template. However, questions arise on whether these figures of merit are reliable measures of the imprinting effect because of the significant differences between the MIP and the NIP in terms of their physical and chemical characteristics. Therefore, this review critically looks into this subject, with a view of defining the best approaches for determining the imprinting effect.