PlantRep: a database of plant repetitive elements

Key message We re-annotated repeats of 459 plant genomes and released a new database: PlantRep (http://www.plantrep.cn/). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome.

REPETITIVE ELEMENTS AND THEIR OBJECTIVES IN ANCIENT AND CONTEMPORARY MOSQUES

Mosques are the most important buildings in Islamic architectures. They represent the place of worship for Muslims. Like other architectural buildings, they consist of components and repeated elements forming their general structures. However, some of these formal elements have changed due to the mosque development and the contemporary trends. Therefore, this research was conducted to discover the repetitive use of the elements and the differences between ancient and contemporary mosques by studying ten samples of mosques. It showed the difference between these two periods in terms of element repetition and utilization. Moreover, it tried to find the related objectives of repetitive use within these two periods. It concluded that some elements from the ancient period were used repetitively in the contemporary mosques. Based on the analysis findings, the design objective is achieved by the repetitive use in both periods. Furthermore, the repetitive use of the elements as structural objective takes second place in ancient mosques. Meanwhile, the environmental objective is second to achieve in contemporary mosques.

Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and Gnetum Species

Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The “repeatome” information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their “repeatome”. We utilized a combination of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants: Pinus taeda, Pinus sylvestris, Pinus sibirica, Picea glauca, Picea abies, Abies sibirica, Larix sibirica, Juniperus communis, Taxus baccata, and Gnetum gnemon. We found that genome abundances of known and newly discovered putative repeats are specific to phylogenetically close groups of species and match biological taxa. The grouping of species based on abundances of known repeats closely matches the grouping based on abundances of newly discovered putative repeats (kChains) and matches the known taxonomic relations.

The 5′ and 3′ Untranslated Regions of the Japanese Encephalitis Virus (JEV): Molecular Genetics and Higher Order Structures

The untranslated region (UTRs) of viral genome are important for viral replication and immune modulation. Japanese encephalitis virus (JEV) is the most significant cause of epidemic encephalitis worldwide. However, little is known regarding the characterization of the JEV UTRs. Here, systematic analyses of the UTRs of JEVs isolated from a variety of hosts worldwide spanning about 80 years were made. All the important cis-acting elements and structures were compared with other mosquito-borne Flaviviruses [West Nile virus (WNV), Yellow fever virus (YFV), Zika virus (ZIKV), Dengue virus (DENV)] and annotated in detail in the UTRs of different JEV genotypes. Our findings identified the JEV-specific structure and the sequence motif with unique JEV feature. (i) The 3’ dbsHP was identified as a small hairpin located in the DB region in the 3′ UTR of JEV, with the structure highly conserved among the JEV genotypes. (ii) The spacer sequence UARs of JEV consist of four discrete spacer sequences, whereas the UARs of other mosquito-borne Flaviviruses are continuous sequences. In addition, repetitive elements have been discovered in the UTRs of mosquito-borne Flaviviruses. The lengths, locations, and numbers of the repetitive elements of JEV also differed from other Flaviviruses (WNV, YFV, ZIKV, DENV). A 300 nt-length region located at the beginning of the 3′ UTR exhibited significant genotypic specificity. This study lays the basis for future research on the relationships between the JEV specific structures and elements in the UTRs, and their important biological function.

Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in N. pectoralis. The haploid genome size estimated using a k-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in N. pectoralis consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic N. pectoralis.

Comparative Genomics of Copia and Gypsy Retroelements in Three Banana Genomes: A, B, and S Genomes

In plants, the proportion of transposable elements (TEs) is generally dominated by long terminal repeat (LTR) retroelements. Therefore, it significantly impacts on genome expansion and genetic and phenotypic variation, namely Copia and Gypsy. Despite such contribution, TEs characterisation in an important crop such as banana [Musa balbisiana (B genome), Musa acuminata (A genome), and Musa schizocarpa (S genome)] remains poorly understood. This study aimed to compare B, A, and S genomes based on repetitive element proportions and copy numbers and determine the evolutionary relationship of LTR using phylogenetic analysis of the reverse transcriptase (RT) domain. Genome assemblies were acquired from the Banana Genome Hub (banana-genome-hub.southgreen.fr). Repetitive elements were masked by RepeatMasker 4.0.9 before Perl parsing. Phylograms were constructed according to domain analysis using DANTE (Domain-based ANnotation of Transposable Elements), alignments were made using MAFFT 7 (multiple alignments using fast Fourier transform), and trees were inferred using FastTree 2. The trees were inspected using SeaView 4 and visualised with FigTree 1.4.4. We reported that B, A, and S genomes are composed of repetitive elements with 19.38%, 20.78%, and 25.96%, respectively. The elements were identified with dominant proportions in the genome are LTR, in which Copia is more abundant than Gypsy. Based on RT phylogenetic analysis, LTR elements are clustered into 13 ancient lineages in which Sire (Copia) and Reina (Gypsy) are shown to be the most abundant LTR lineages in bananas.

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans

Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. We focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed region-specific gain and loss of both histone marks, but the changes are more evident for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most statistically significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed “aging-specific repressive regions” (ASRRs). These ASRRs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Maintenance of high H3K9me2 levels in these regions have been shown to correlate with a longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear element (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals. It is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.

Digging into the lesser-known aspects of CRISPR biology

A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.