A Novel Family of Terminal-Repeat Retrotransposon in Miniature (TRIM) in the Genome of the Red Harvester Ant, <i>Pogonomyrmex barbatus</i>

<div><p>We report the first described non-plant family of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous LTR retrotransposons, from the whole-genome sequence of the red harvester ant, <i>Pogonomyrmex barbatus</i> (Hymenoptera: Myrmicinae). Members of this retrotransposon family, named PbTRIM, have typical features of plant TRIMs in length and structure, although they share no overall sequence similarity. PbTRIM elements and their solo-LTRs are abundant in the host genome and exhibit an uneven distribution pattern. Elements are preferentially inserted into TA-rich regions with ATAT as the most common pattern of target site duplication (TSD). PbTRIM is most likely mobile as indicated by the young age of many complete elements, the high degree of sequence similarity among elements at different genomic locations, the abundance of elements in the host genome, and the presence of 4-bp target site duplications (TSDs) flanking the elements and solo-LTRs. Many PbTRIM elements and their solo-LTRs are located within or near genes, suggesting their potential roles in restructuring the host genes and genome. Database search, PCR and sequencing analysis revealed the presence of homologous PbTRIM elements in other ant species. The high sequence similarity between elements from distantly related ant species, the incongruence between the phylogenies of PbTRIM and its hosts, and the patchy distribution of the retroelement within the Myrmicinae subfamily indicate possible horizontal transfer events of the retroelement.</p></div

PbTRIM elements preferentially insert into AT-rich region in the <i>P. barbatus</i> genome.

<p>TSDs along with the flanking sequences from 59 complete PbTRIM elements and 112 solo-LTRs were used to generate the sequence logo.</p

Nucleotide frequencies of TSD and its flanking sequences of complete elements (n = 59) and solo-LTRs (n = 112) of PbTRIM family.

<p>Nucleotide frequencies of TSD and its flanking sequences of complete elements (n = 59) and solo-LTRs (n = 112) of PbTRIM family.</p

Frequency distribution of the estimated age of 67 complete PbTRIM elements from the <i>P. barbatus</i> genome.

<p>Frequency distribution of the estimated age of 67 complete PbTRIM elements from the <i>P. barbatus</i> genome.</p

Ant species/lineages used for PCR amplification of PbTRIM elements.

<p>Ant species/lineages used for PCR amplification of PbTRIM elements.</p

Examples of PbTRIM elements and solo-LTRs located within or near genes.

<p>Exons of predicted genes are shown as red boxes, with the last exons denoted as pentagons to indicate the transcription orientation. The solid and the dashed lines represent gene introns and intergenic regions, respectively. The direction of the LTR sequences is indicated by the grey triangles in the open square, and the TSD sequences are shown on the either side of the element or solo-LTR. (A) A complete PbTRIM element is located within 1-kb from the transcription start sites of two genes (upstream: protein SERAC1, downstream: GTP-binding protein ypt7). (B) A complete element contributes sequence to the second exon-intron boundary of the gene encoding SET and MYND domain-containing protein 4. (C) A solo-LTR is located within the first intron of a gene encoding the focal adhesion kinase 1.</p

Phylogenetic relationship among the complete PbTRIM elements identified from the <i>P. barbatus</i> genome.

<p>The neighbor-joining tree was produced with Mega 5.0. The evolutionary distances were computed using the Tamura-Nei method. All branch lengths are drawn to scale. The 64 complete elements included in the analysis can be largely grouped into 4 subfamilies.</p

General structure of PbTRIM elements.

<p>(A) Schematic diagram of the general structure of PbTRIM elements. (B) Multiple alignment of selected PbTRIM elements from <i>P. barbatus</i> genome shows the typical structure of LTR retrotransposons. The 5′ and 3′ LTR are indicated by the leftwards dashed arrows underneath the sequence alignment. Structural features are marked on the top of the aligned sequences. Green thick arrows indicate the PCR primer biding sites. LTR: long terminal repeat; PBS: primer binding site; PPT: polypurine tract; TSD: target site duplicate; U3: unique 3′ RNA region; R: repeated RNA region; U5: unique 5′ RNA region.</p

Threshold and real-time initiation mechanism of urban flood emergency response under combined disaster scenarios

Scientific and reasonable emergency response initiation mechanisms can provide important support for decision making regarding the emergency management of urban floods. However, there is a lack of a unified paradigm on how to calculate the threshold for emergency response initiation and reasonably initiate emergency response. Therefore, this study proposes a loss-driven urban flood emergency response initiation framework from the perspective of combined disasters. A discrimination mechanism of the emergency response initiation level was established based on the optimal threshold and loss function. And the rainfall event that occurred in Zhengzhou, China, on July 20, 2021, was taken as an example to realize real-time emergency response discrimination and initiation driven by forecast data. Results showed that the initiation time of the Level I emergency response using the proposed method was 9.5 h earlier than the time of the government release, thereby significantly increasing the preparation time for flood management personnel. In addition, the results of the optimal threshold selection indicated that the Natural Breakpoint method was the optimal method for loss threshold partitioning, with the comprehensive evaluation index (CEI) being 3.56–9.53 % higher than those of the K-means, Equal Interval, and Quantile method. These results constitute a reference for urban emergency management and related research.</p

waxmothF2data

The file contains the backcross progeny phenotypes and genotypes. The cross was the hybrid male progeny of a Kansas female with a Florida male crossed to a Kansas male. Included are the phenotypic and genotypic values for all individuals