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Long noncoding RNAs (lncRNAs) are emerging as important regulators in plant development, but few of them have been functionally characterized in fruit ripening. Here, we have identified 25,613 lncRNAs from strawberry ripening fruits based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries, most of which exhibited distinct temporal expression patterns. A novel lncRNA, FRILAIR harbours the miR397 binding site that is highly conserved in diverse strawberry species. FRILAIR overexpression promoted fruit maturation in the Falandi strawberry, which was consistent with the finding from knocking down miR397, which can guide the mRNA cleavage of both FRILAIR and LAC11a (encoding a putative laccase-11-like protein). Moreover, LAC11a mRNA levels were increased in both FRILAIR overexpressing and miR397 knockdown fruits, and accelerated fruit maturation was also found in LAC11a overexpressing fruits. Overall, our study demonstrates that FRILAIR can act as a noncanonical target mimic of miR397 to modulate the expression of LAC11a in the strawberry fruit ripening process.

Accurate annotation of genes and transposable elements (TEs) is vital for understanding genomes, but current annotation pipelines often misannotate TEs as genes. This study reveals how the general transcription factor II-I repeat domain-containing protein 2 (GTF2IRD2) erroneously annotated DNA transposons in non-mammalian species, as it contains a 3′ fused hAT transposase domain. We also demonstrate the generality of this problem by identifying misannotated TEs as genes in other vertebrate genomes. Such misannotations can lead to errors in phylogenetic analyses and wasted time for investigators. The study proposes adding a final TE-check to gene annotation pipelines to mitigate this problem.

Background Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. Results Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today’s mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms. Conclusions We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.

piRNAs are critical for transposable element (TE) repression and germ cell survival during the early phases of spermatogenesis, however, their role in adult germ cells and the relative importance of piRNA methylation is poorly defined in mammals. Using a mouse model of HEN methyltransferase 1 (HENMT1) loss-of-function, RNA-Seq and a range of RNA assays we show that HENMT1 is required for the 2' O-methylation of mammalian piRNAs. HENMT1 loss leads to piRNA instability, reduced piRNA bulk and length, and ultimately male sterility characterized by a germ cell arrest at the elongating germ cell phase of spermatogenesis. HENMT1 loss-of-function, and the concomitant loss of piRNAs, resulted in TE de-repression in adult meiotic and haploid germ cells, and the precocious, and selective, expression of many haploid-transcripts in meiotic cells. Precocious expression was associated with a more active chromatin state in meiotic cells, elevated levels of DNA damage and a catastrophic deregulation of the haploid germ cell gene expression. Collectively these results define a critical role for HENMT1 and piRNAs in the maintenance of TE repression in adult germ cells and setting the spermatogenic program.

Elephantids are the world’s most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant’s ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.

Background Retrotransposons play outsized roles in the evolution of gene regulation, genome function, and disease pathogenesis, and more recently they have sparked interest as instruments for new gene therapy approaches. R2 retrotransposons insert site-specifically into the multicopy genes encoding 28S ribosomal RNA at a target sequence conserved broadly across eukaryotic evolution. R2 retrotransposons have been detected in many animals, but previous surveys have been limited in scope and methodology. Results Here, we substantially expand the known distribution of R2 retrotransposons from previously unrepresented or underrepresented taxonomic groups, ranging from ctenophores to amphibians and reptiles. We discover diverse R2 domain architectures and motifs and identify many new avian R2 candidates for genome engineering development. Overall, phylogenetic analyses reveal two highly successful R2 lineages. We describe lineage-distinctive features of the N-terminal DNA recognition domains and reverse-transcriptase domain signatures. Within a lineage, R2 protein sequences do not necessarily preserve the unifying configuration of N-terminal domains assumed in the current clade classification scheme. We show that recombinant R2 proteins with distinctive domain architectures and distribution across major animal classes support target-primed reverse transcription with conserved site specificity. Conclusions Our analysis of the surprisingly varied domain architectures that support target-site specificity informs new R2 classification criteria and provides a greatly expanded foundation for additional structure/function insights about DNA binding selectivity. This expanded perspective on R2 evolution informs approaches for engineering therapeutic gene insertion technologies and offers an opportunity to investigate the conservation and diversification of retrotransposons.

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2)=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ(2)=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.

Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L . . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.

Background In this report we examine candidate pathways perturbed by Compound Kushen Injection (CKI), a Traditional Chinese Medicine (TCM) that we have previously shown to alter the gene expression patterns of multiple pathways and induce apoptosis in cancer cells. Methods We have measured protein levels in Hep G2 and MDA-MB-231 cells for genes in the cell cycle pathway, DNA repair pathway and DNA double strand breaks (DSBs) previously shown to have altered expression by CKI. We have also examined energy metabolism by measuring [ADP]/[ATP] ratio (cell energy charge), lactate production and glucose consumption. Our results demonstrate that CKI can suppress protein levels for cell cycle regulatory proteins and DNA repair while increasing the level of DSBs. We also show that energy metabolism is reduced based on reduced glucose consumption and reduced cellular energy charge. Results Our results validate these pathways as important targets for CKI. We also examined the effect of the major alkaloid component of CKI, oxymatrine and determined that it had no effect on DSBs, a small effect on the cell cycle and increased the cell energy charge. Conclusions Our results indicate that CKI likely acts through the effect of multiple compounds on multiple targets where the observed phenotype is the integration of these effects and synergistic interactions.