Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA.

The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.

Influence of Flagellin Polymorphisms, Gene Regulation, and Responsive Memory on the Motility of Xanthomonas Species That Cause Bacterial Spot Disease of Solanaceous Plants.

Increasingly, new evidence has demonstrated variability in the epitope regions of bacterial flagellin, including in regions harboring the microbe-associated molecular patterns flg22 and flgII-28 that are recognized by the pattern recognition receptors FLS2 and FLS3, respectively. Additionally, because bacterial motility is known to contribute to pathogen virulence and chemotaxis, reductions in or loss of motility can significantly reduce bacterial fitness. In this study, we determined that variations in flg22 and flgII-28 epitopes allow some but not all Xanthomonas spp. to evade both FLS2- and FLS3-mediated oxidative burst responses. We observed variation in the motility for many isolates, regardless of their flagellin sequence. Instead, we determined that past growth conditions may have a significant impact on the motility status of isolates, because we could minimize this variability by inducing motility using chemoattractant assays. Additionally, motility could be significantly suppressed under nutrient-limited conditions, and bacteria could "remember" its prior motility status after storage at ultracold temperatures. Finally, we observed larger bacterial populations of strains with flagellin variants predicted not to be recognized by either FLS2 or FLS3, suggesting that these bacteria can evade flagellin recognition in tomato plants. Although some flagellin variants may impart altered motility and differential recognition by the host immune system, external growth parameters and gene expression regulation appear to have more significant impacts on the motility phenotypes for these Xanthomonas spp.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genome Sequencing and Functional Characterization of Xanthomonas cucurbitae, the Causal Agent of Bacterial Spot Disease of Cucurbits.

Bacterial leaf spot disease caused by Xanthomonas cucurbitae has severely affected the pumpkin industries in the Midwestern region of United States, with the bacteria mainly infecting pumpkin leaves and fruits, and leading to significant yield losses. In this study, we utilized genomics and genetics approaches to elucidate X. cucurbitae molecular mechanisms of pathogenesis during interaction with its host. We generated the first reference-quality whole-genome sequence of the X. cucurbitae type isolate and compared with other Xanthomonas species, X. cucurbitae has a smaller genome size with fewer virulence-related genes. RNA-seq analysis of X. cucurbitae under plant-mimicking media conditions showed altered transcriptional responses, with upregulation of virulence genes and downregulation of cellular homeostasis genes. Additionally, characterization of key virulence genes using gene deletion methods revealed that both type II enzymes and type III effectors are necessary for X. cucurbitae to cause infection in the pumpkin host.

Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA.

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.