The genomic ecosystem of transposable elements in maize

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.

The fushi tarazu zebra element is not required for Drosophila viability or fertility

Expression of genes in precisely controlled spatiotemporal patterns is essential for embryonic development. Much of our understanding of mechanisms regulating gene expression comes from the study of cis-regulatory elements (CREs) that direct expression of reporter genes in transgenic organisms. This reporter-transgene approach identifies genomic regions sufficient to drive expression but fails to provide information about quantitative and qualitative contributions to endogenous expression, although such conclusions are often inferred. Here we evaluated the endogenous function of a classic Drosophila CRE, the fushi tarazu (ftz) zebra element. ftz is a pair-rule segmentation gene expressed in seven stripes during embryogenesis, necessary for formation of alternate body segments. Reporter transgenes identified the promoter-proximal zebra element as a major driver of the seven ftz stripes. We generated a precise genomic deletion of the zebra element (ftzΔZ) to assess its role in the context of native chromatin and neighboring CREs, expecting large decreases in ftz seven-stripe expression. However, significant reduction in expression was found for only one stripe, ftz stripe 4, expressed at ∼25% of wild type levels in ftzΔZ homozygotes. Defects in corresponding regions of ftzΔZ mutants suggest this level of expression borders the threshold required to promote morphological segmentation. Further, we established true-breeding lines of homozygous ftzΔZ flies, demonstrating that the body segments missing in the mutants are not required for viability or fertility. These results highlight the different types of conclusions drawn from different experimental designs and emphasize the importance of examining transcriptional regulatory mechanisms in the context of the native genomic environment.

IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context

Biopesticide-based crop protection is constantly challenged by insect resistance. Thus, expansion of available biopesticides is crucial for sustainable agriculture. Although Bacillus thuringiensis is the major agent for pesticide bioprotection, the number of bacteria species synthesizing proteins with biopesticidal potential is much higher. The Bacterial Pesticidal Protein Resource Center (BPPRC) offers a database of sequences for the control of insect pests, grouped in structural classes. Here we present IDOPS, a tool that detects novel biopesticidal sequences and analyzes them within their genetic environment. The backbone of the IDOPS detection unit is a curated collection of high-quality hidden Markov models that is in accordance with the BPPRC nomenclature. IDOPS was positively benchmarked with BtToxin_Digger and Cry_Processor. In addition, a scan of the UniProtKB database using the IDOPS models returned an abundance of new pesticidal protein candidates distributed across all of the structural groups. Gene expression depends on the genomic environment, therefore, IDOPS provides a comparative genomics module to investigate the genetic regions surrounding pesticidal genes. This feature enables the investigation of accessory elements and evolutionary traits relevant for optimal toxin expression and functional diversification. IDOPS contributes and expands our current arsenal of pesticidal proteins used for crop protection.

Molecular Epidemiology of Fosfomycin Resistant E. coli from a Pigeon Farm in China

We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli isolates that displayed high-level resistance (MIC ≥ 256 mg L−1) and carried the fosA3 gene on plasmids with sizes ranging from 80 to 370 kb. MLST analysis of these fosA3-positive E. coli isolates indicated the presence of nine sequence types (ST6856, ST8804, ST457, ST746, ST533, ST165, ST2614, ST362 and ST8805) of which ST6856 was the most prevalent (24.5%, 12/49). PFGE combined with genomic context comparative analyses indicated that the fosA3 gene was spread by horizontal transfer as well as via clonal transmission between E. coli in the pigeon farm, and IS26 played an important role in fosA3 transmission. The high prevalence of fosA3 in the pigeon farm and the high similarity of the fosA3 genomic environment between E. coli isolates from humans and pigeons indicated that the pigeon farm served as a potential reservoir for human infections. The pigeon farm was found to be an important reservoir for the fosA3 gene and this should be further monitored.

Sexual fate of murine external genitalia development: Conserved transcriptional competency for male-biased genes in both sexes

Testicular androgen is a master endocrine factor in the establishment of external genital sex differences. The degree of androgenic exposure during development is well known to determine the fate of external genitalia on a spectrum of female- to male-specific phenotypes. However, the mechanisms of androgenic regulation underlying sex differentiation are poorly defined. Here, we show that the genomic environment for the expression of male-biased genes is conserved to acquire androgen responsiveness in both sexes. Histone H3 at lysine 27 acetylation (H3K27ac) and H3K4 monomethylation (H3K4me1) are enriched at the enhancer of male-biased genes in an androgen-independent manner. Specificity protein 1 (Sp1), acting as a collaborative transcription factor of androgen receptor, regulates H3K27ac enrichment to establish conserved transcriptional competency for male-biased genes in both sexes. Genetic manipulation of MafB, a key regulator of male-specific differentiation, and Sp1 regulatory MafB enhancer elements disrupts male-type urethral differentiation. Altogether, these findings demonstrate conservation of androgen responsiveness in both sexes, providing insights into the regulatory mechanisms underlying sexual fate during external genitalia development.

Genomic architecture of 5S rDNA cluster and its variations within and between species

Ribosomal genes (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosome. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. Here, we generate ultra-long Nanopore and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform manual assembly of the cluster using the long reads that carry these units, which led to an assembly of rDNA cluster consisting of up to 167 5S rDNA units. The ordering and copy number of various rDNA units are indicative of separation time between strains. Surprisingly, we observed a drastically lower level of variation in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than C. elegans N2 strain, suggesting a unique mechanism in maintaining the rDNA cluster stability in the N2. Single-copy transgenes landed into the rDNA cluster shows the expected expression in the soma, supporting that rDNA genomic environment is transcriptionally compatible with RNA polymerase II. Delineating the structure and variation of rDNA cluster paves the way for its functional and evolutionary studies.

Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the 4th selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

Genomic structural variation in ‘Nebbiolo’ grapevines at the individual, clonal and cultivar levels

Structural Variants (SVs) are a widely unexplored source of genetic variation, both due to methodological limitations and because they are generally associated to deleterious effects. However, with the advent of long-range genomic platforms, it has become easier to directly detect SVs. In the same direction, clonally propagated crops provide a unique opportunity to study SVs, offering a suitable genomic environment for their accumulation in heterozygosis. In particular, it has been reported that SVs generate drastic levels of heterozygosity in grapevines. ‘Nebbiolo’ (Vitis vinifera L.) is a grapevine cultivar typical of north-western Italy, appreciated for its use in producing high-quality red wines. Here, we aimed to analyze the frequency of SVs in ‘Nebbiolo’, at three different organizational levels. For this purpose, we generated genomic data based on long-reads, linked-reads and optical mapping. We assembled a reference genome for this cultivar and compared two different clones, including V. vinifera reference genome (PN40024) in our comparisons. Our results indicate that SVs differentially occurring between ‘Nebbiolo’ clones might be rare, while SVs differentiating haplotypes of the same individual are as abundant as those that occur differentially between cultivars.

DeepHPV: a deep learning model to predict human papillomavirus integration sites

Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: [email protected], [email protected], [email protected]

Engineered expression of the invertebrate-specific scorpion toxin AaHIT reduces adult longevity and female fecundity in the diamondback moth Plutella xylostella

BACKGROUNDPrevious Genetic Pest Management (GPM) systems in diamondback moth (DBM) have relied on expressing lethal proteins (‘effectors’) that are ‘cell-autonomous’ i.e. do not leave the cell they are expressed in. To increase the flexibility of future GPM systems in DBM, we aimed to assess the use of a non cell-autonomous, invertebrate-specific, neurotoxic effector – the scorpion toxin AaHIT. This AaHIT effector was designed to be secreted by expressing cells, potentially leading to effects on distant cells, specifically neuromuscular junctions.RESULTSExpression of AaHIT caused a ‘shaking/quivering’ phenotype which could be repressed by provision of an antidote (tetracycline); a phenotype consistent with the AaHIT mode-of-action. This effect was more pronounced when AaHIT expression was driven by the Hr5/ie1 promoter (82.44% of males, 65.14% of females) rather than Op/ie2 (57.35% of males, 48.39% of females). Contrary to expectations, the shaking phenotype and observed fitness costs were limited to adults where they caused severe reductions in mean longevity (–81%) and median female fecundity (–93%). qPCR of AaHIT expression patterns and analysis of piggyBac-mediated transgene insertion sites suggest that restriction of observed effects to the adult stages may be due to influence of local genomic environment on the tetO-AaHIT transgene.CONCLUSIONWe have demonstrated the feasibility of using non cell-autonomous effectors within a GPM context for the first time in the Lepidoptera, one of the most economically damaging orders of insects. These findings provide a framework for extending this system to other pest Lepidoptera and to other secreted effectors.